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Gene Dmel\Rh4

General Information
Symbol	Dmel\Rh4	Species	D. melanogaster
Name	Rhodopsin 4	Annotation symbol	CG9668
Feature type	protein_coding_gene	FlyBase ID	FBgn0003250
Gene Model Status	Current	Stock availability	9 publicly available
Genomic Location
Chromosome (arm)	3L	Recombination map
Cytogenetic map	73D2-73D3	Sequence location	3L:16,845,621..16,856,124 [-]
Genomic Maps Select View:Gene Models/EvidenceExpression/RegulationMegaViewGene Disruptions, Stocks and Reagents modENCODE GBrowse	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene Rhodopsin 4 is referred to in FlyBase by the symbol Dmel\Rh4 (CG9668, FBgn0003250). It is a protein_coding_gene from Drosophila melanogaster. There is experimental evidence that it has the molecular function: G-protein coupled photoreceptor activity. There is experimental evidence that it is involved in the biological process: phototransduction, UV. 9 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide. Protein features are: GPCR, rhodopsin-like superfamily; GPCR, rhodopsin-like, 7TM; Opsin; Opsin RH3/RH4. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of extremely low expression. Peak expression observed in adult male stages. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult head, adult eye. Comments on Affy2 ProbeSet: ProbeSet 1626251_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of Rh4. Gene sequence location is 3L:16845621..16856124.
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	Rh4 Encodes the opsin moiety of a rhodopsin specific to the rhabdomere of the seventh photoreceptor cell; Rh3 and Rh4 are expressed in nonoverlapping subsets of ommatidia; the distribution of the two types of R7 cells within the eye is irregular. Transcript first appears during the last 48 hr of the pupal stage and is found in newly eclosed adult heads. Also expressed in Bolwig's organ [Pollock and Benzer, 1988, Nature (London) 333: 779-82)]. RH4 is a 378 amino acid protein that is 35% homologous to the opsins found in R1-6 encoded by ninaE and in the ocelli, encoded by Rh2, but 72% homologous to the Rh3-encoded protein.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2012_01	Sequence features BKN24651 HFA11268 References Xiang et al., 2010, Nature 468(7326): 921--926 Dalton et al., 2010, BMC Genomics 11: 541 Jumbo-Lucioni et al., 2010, BMC Genomics 11: 297
FB2011_10
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 73D2-73D3   Limits computationally determined from genome sequence between P{PZ}Baldspot02281 and P{PZ}blot01658
Experimentally Determined Cytological Location
Cytogenetic map Notes References 73C-73C   (determined by in situ hybridisation)   (Weber, 2005) 73D3-73D5   (determined by in situ hybridisation)   (Montell et al., 1987)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Rh4 for information on other features To submit a correction to a gene model please use the Contact FlyBase form
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Rh4-RA FBtr0075338  NM_057353   1862   378
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Rh4-PA   FBpp0075097   42.7   378   7.81     NP_476701   AAF49400
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • GPCR, rhodopsin-like, 7TM (IPR000276) Opsin RH3/RH4 (IPR000856) Opsin (IPR001760) GPCR, rhodopsin-like superfamily (IPR017452)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA433273   AA568022   AA697303   AA697304   AA697452   AE014296 AAF49400   AC006933   AI062283   AI108822   AI108920   AI109296   AI134595   AI135057   AI135312   AI386579   AI520640   AI945371   AY113582 AAM29587   BE978785   BG632531   BI161982   BI564056   BI564708   BI570331   BI570862   BI572569   BI572679   BI574259   BI576490   BI576636   BI584373   BI585149   BI587297   BI588268   BI591006   BI605818   BI610774   BI611006   BI613732   BI614042   BI618307   BI618316   BI619726   BI620834   BI621735   BI622722   BI627250   BT044485   BX042039   CO190994   CO268488   CO280696   CO303288   CO308772   CO313769   CO318249   CO320553   CZ469509   EC067238   EC078249   EC225732   EC233885   EC237626   EC238263   EC241440   EC242995   M17719   M17730 AAA28856   X51353
UniProtKB/Swiss-Prot	P08255
UniProtKB/TrEMBL	Q8MYV5
Mapped Features
Mapped Features have been reorganized, please see this article for details. Additional mapped features and mutations can be found on GBrowse or related reports. Type Symbol & Location Additional Notes References regulatory region FBsf0000161198 3L:16,855,730..16,855,744 comment=RUS4A element evidence=experimental regulatory region FBsf0000161197 3L:16,855,710..16,855,720 comment=RCS I element evidence=experimental regulatory region FBsf0000161196 3L:16,855,704..16,855,709 comment=RCS II element evidence=experimental
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
expression microarray Stage Tissue/Position (including subcellular localization) Reference adult stage   eye   (Xu et al., 2004) northern blot Stage Tissue/Position (including subcellular localization) Reference pupal stage | late     (FlyBase, 1992-) adult stage   adult head   (FlyBase, 1992-) photoreceptor cell R7   (FlyBase, 1992-) radioisotope in situ Stage Tissue/Position (including subcellular localization) Reference larval stage   Bolwig organ   (Pollock and Benzer, 1988) adult stage   eye   (Pollock and Benzer, 1988)
Additional Descriptive Data
	Eye-enriched transcripts determined by ratio of expression level in wild-type heads. versus expression level in so heads. (Xu et al., 2004) Rh3 and Rh4 transcripts are expressed in non-overlapping R7 ommatidia. (FlyBase, 1992-)
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
No Assay Recorded Stage Tissue/Position (including subcellular localization) Reference adult stage   photoreceptor cell R1 -- photoreceptor cell R6   (Feiler et al., 1992) immunolocalization Stage Tissue/Position (including subcellular localization) Reference adult stage   photoreceptor cell R7 | presumptive   (Feiler et al., 1992)
Additional Descriptive Data
	Wild type Rh4 protein is ectopically expressed in photoreceptors R1-R6 in the Rh1+4 allele. (Feiler et al., 1992) Rh4 is expressed inabout 70% of the R7 photoreceptors. No overlap in expression pattern isseen for Rh4 and Rh3. (Feiler et al., 1992)
Marker for
Subcellular Localization
CV Term
Notes
High-Throughput Expression Data
or
See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes. modENCODE Temporal Expression Data for FBgn0003250    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0003250 Very low expression bin max Moderate expression bin max High expression bin max Extremely high expression bin max Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of extremely low expression. Peak expression observed in adult male stages. [download data (TSV)] Guide to modENCODE expression level colors   No expression (0 - 0)   Extremely low expression (1 - 10)   Very low expression (11 - 100)   Low expression (101 - 400)   Moderate expression (401 - 1400)   Moderately high expression (1401 - 4000)   High expression (4001 - 10000)   Very high expression (10001 - 100000)   Extremely high expression (100001 - 2000000) Linear, scaled to maximum FBgn0003250 expression level Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP    1467 pupae 4d postWPP    4026 adult male 01day    5305 adult male 05day    6071 adult male 30day    11048 adult female 01day    2799 adult female 05day    1145 adult female 30day    1694 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP  (1467) pupae 4d postWPP  (4026) adult male 01day  (5305) adult male 05day  (6071) adult male 30day  (11048) adult female 01day  (2799) adult female 05day  (1145) adult female 30day  (1694) Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP  1467 pupae 4d postWPP  (4026) adult male 01day  (5305) adult male 05day  (6071) adult male 30day  (11048) adult female 01day  (2799) adult female 05day    1145 adult female 30day  (1694) Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP    1467 pupae 4d postWPP    4026 adult male 01day    5305 adult male 05day    6071 adult male 30day  (11048) adult female 01day    2799 adult female 05day    1145 adult female 30day    1694 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  Linear, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP    1467 pupae 4d postWPP    4026 adult male 01day    5305 adult male 05day    6071 adult male 30day    11048 adult female 01day    2799 adult female 05day    1145 adult female 30day    1694 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0003250 expression level Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP    1467 pupae 4d postWPP    4026 adult male 01day    5305 adult male 05day    6071 adult male 30day    11048 adult female 01day    2799 adult female 05day    1145 adult female 30day    1694 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP  (1467) pupae 4d postWPP  (4026) adult male 01day  (5305) adult male 05day  (6071) adult male 30day  (11048) adult female 01day  (2799) adult female 05day  (1145) adult female 30day  (1694) Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP  1467 pupae 4d postWPP  (4026) adult male 01day  (5305) adult male 05day  (6071) adult male 30day  (11048) adult female 01day  (2799) adult female 05day    1145 adult female 30day  1694 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP    1467 pupae 4d postWPP    4026 adult male 01day    5305 adult male 05day    6071 adult male 30day  11048 adult female 01day    2799 adult female 05day    1145 adult female 30day    1694 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high  log, scaled to Extremely high expression Developmental Stage   Expression Level embryo 00-02hr    3 embryo 02-04hr    34 embryo 04-06hr    94 embryo 06-08hr    50 embryo 08-10hr    48 embryo 10-12hr    35 embryo 12-14hr    13 embryo 14-16hr    6 embryo 16-18hr    3 embryo 18-20hr    8 embryo 20-22hr    3 embryo 22-24hr    5 larva L1    3 larva L2    6 larva L3 12hr old    3 larva L3 puffstage 1-2    11 larva L3 puffstage 3-6    6 larva L3 puffstage 7-9    9 white prepupae new    38 white prepupae 12hr    30 white prepupae 24hr    28 pupae 2d postWPP    56 pupae 3d postWPP    1467 pupae 4d postWPP    4026 adult male 01day    5305 adult male 05day    6071 adult male 30day    11048 adult female 01day    2799 adult female 05day    1145 adult female 30day    1694 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  Heatmap Developmental Stage   Expression Level embryo 00-02hr     embryo 02-04hr     embryo 04-06hr     embryo 06-08hr     embryo 08-10hr     embryo 10-12hr     embryo 12-14hr     embryo 14-16hr     embryo 16-18hr     embryo 18-20hr     embryo 20-22hr     embryo 22-24hr     larva L1     larva L2     larva L3 12hr old     larva L3 puffstage 1-2     larva L3 puffstage 3-6     larva L3 puffstage 7-9     white prepupae new     white prepupae 12hr     white prepupae 24hr     pupae 2d postWPP     pupae 3d postWPP     pupae 4d postWPP     adult male 01day     adult male 05day     adult male 30day     adult female 01day     adult female 05day     adult female 30day     FlyAtlas Anatomical Expression Data for FBgn0003250    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0003250 Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult head, adult eye. [download data (TSV)] Guide to FlyAtlas expression level colors   No expression (0 - 9.999)   Low expression (10 - 99.999)   Moderate expression (100 - 499.999)   High level expression (500 - 999.999)   Very high expression (1000 - 25000) Linear, scaled to maximum FBgn0003250 expression level Tissue   Expression Level Larval Central Nervous System    5.575 Larval Midgut no informative data Larval Hindgut    7.4 Larval Malpighian Tubules    6.1 Larval Fat Body no informative data Larval Salivary Gland no informative data Larval Trachea no informative data Larval Carcass    7.325 Adult Head    2290.1 Adult Eye    7208 Adult Brain    34.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    9.1 Adult Midgut    6.3 Adult Hindgut    3.2 Adult Malpighian Tubules    7.2 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart no informative data Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    7 Adult Ovary    2.8 Adult Testis    63.8 Adult Male Accessory Gland    9.8 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    5.575 Larval Midgut no informative data Larval Hindgut    7.4 Larval Malpighian Tubules    6.1 Larval Fat Body no informative data Larval Salivary Gland no informative data Larval Trachea no informative data Larval Carcass    7.325 Adult Head  (2290.1) Adult Eye  (7208) Adult Brain    34.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    9.1 Adult Midgut    6.3 Adult Hindgut    3.2 Adult Malpighian Tubules    7.2 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart no informative data Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    7 Adult Ovary    2.8 Adult Testis    63.8 Adult Male Accessory Gland    9.8 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    5.575 Larval Midgut no informative data Larval Hindgut    7.4 Larval Malpighian Tubules    6.1 Larval Fat Body no informative data Larval Salivary Gland no informative data Larval Trachea no informative data Larval Carcass    7.325 Adult Head  (2290.1) Adult Eye  (7208) Adult Brain    34.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    9.1 Adult Midgut    6.3 Adult Hindgut    3.2 Adult Malpighian Tubules    7.2 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart no informative data Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    7 Adult Ovary    2.8 Adult Testis    63.8 Adult Male Accessory Gland    9.8 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    5.575 Larval Midgut no informative data Larval Hindgut    7.4 Larval Malpighian Tubules    6.1 Larval Fat Body no informative data Larval Salivary Gland no informative data Larval Trachea no informative data Larval Carcass    7.325 Adult Head    2290.1 Adult Eye    7208 Adult Brain    34.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    9.1 Adult Midgut    6.3 Adult Hindgut    3.2 Adult Malpighian Tubules    7.2 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart no informative data Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    7 Adult Ovary    2.8 Adult Testis    63.8 Adult Male Accessory Gland    9.8 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0003250 expression level Tissue   Expression Level Larval Central Nervous System    5.575 Larval Midgut no informative data Larval Hindgut    7.4 Larval Malpighian Tubules    6.1 Larval Fat Body no informative data Larval Salivary Gland no informative data Larval Trachea no informative data Larval Carcass    7.325 Adult Head    2290.1 Adult Eye    7208 Adult Brain    34.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    9.1 Adult Midgut    6.3 Adult Hindgut    3.2 Adult Malpighian Tubules    7.2 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart no informative data Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    7 Adult Ovary    2.8 Adult Testis    63.8 Adult Male Accessory Gland    9.8 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    5.575 Larval Midgut no informative data Larval Hindgut    7.4 Larval Malpighian Tubules    6.1 Larval Fat Body no informative data Larval Salivary Gland no informative data Larval Trachea no informative data Larval Carcass    7.325 Adult Head  (2290.1) Adult Eye  (7208) Adult Brain    34.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    9.1 Adult Midgut    6.3 Adult Hindgut    3.2 Adult Malpighian Tubules    7.2 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart no informative data Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    7 Adult Ovary    2.8 Adult Testis    63.8 Adult Male Accessory Gland    9.8 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    5.575 Larval Midgut no informative data Larval Hindgut    7.4 Larval Malpighian Tubules    6.1 Larval Fat Body no informative data Larval Salivary Gland no informative data Larval Trachea no informative data Larval Carcass    7.325 Adult Head  (2290.1) Adult Eye  (7208) Adult Brain    34.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    9.1 Adult Midgut    6.3 Adult Hindgut    3.2 Adult Malpighian Tubules    7.2 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart no informative data Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    7 Adult Ovary    2.8 Adult Testis    63.8 Adult Male Accessory Gland    9.8 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    5.575 Larval Midgut no informative data Larval Hindgut    7.4 Larval Malpighian Tubules    6.1 Larval Fat Body no informative data Larval Salivary Gland no informative data Larval Trachea no informative data Larval Carcass    7.325 Adult Head    2290.1 Adult Eye    7208 Adult Brain    34.6 Adult Thoracic-Abdominal Ganglion no informative data Adult Crop    9.1 Adult Midgut    6.3 Adult Hindgut    3.2 Adult Malpighian Tubules    7.2 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart no informative data Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    7 Adult Ovary    2.8 Adult Testis    63.8 Adult Male Accessory Gland    9.8 Adult Carcass no informative data Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut no informative data Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body no informative data Larval Salivary Gland no informative data Larval Trachea no informative data Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion no informative data Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart no informative data Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass no informative data FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    2290.1   NA  Eye    7208   NA  Brain    34.6   5.575  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    no informative data   NA  Crop    9.1   no informative data  Midgut    6.3   7.4  Hindgut    3.2   6.1  Malpighian Tubules    7.2   no informative data  Fat Body    no informative data   no informative data  Salivary Gland    no informative data   NA  Heart    no informative data   no informative data  Trachea    NA   NA  VirginFemale Spermatheca    no informative data   NA  InseminatedFemale Spermatheca    7   NA  Ovary    2.8   NA  Testis    63.8   NA  Male Accessory Gland    9.8   7.325  Carcass    no informative data modENCODE Temporal Expression Data (Graveley et al., 2011) FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)
Expression Clusters
	A cluster of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010) mE2_34_mRNA_expression_cluster_00
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003250 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG9668-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable Rh4e04456 Rh4W25 viable, with Scer\GAL4pnr-MD237 Rh4GD17228 Sterility Allele fertile Rh4e04456 Phenotype manifest in Allele
Classical Alleles ( 5 )
For All Classical Alleles Show
Allele of Rh4 Class Mutagen Stocks Known lesion Rh4BG02648 P-element activity 2 Yes Rh4e04456 piggyBac transposase 2 -- Rh4c04779 piggyBac transposase 1 -- Rh4MI02104 1 -- Rh4W25 P-element activity 0 Yes
Alleles Carried on Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Rh4 Class Mutagen Stocks Known lesion Rh4GD17228 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Rh4KK105515 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Rh4ninaE.P in vitro construct - regulatory fusion 0 Yes Rh4Scer\UAS.T:Avic\GFP-EGFP in vitro construct - coding region fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3L)Exel9003 (Ryder, 2004.4.26) Df(3L)Exel9004 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data reporter construct P{Rh4.63,CAT} No P{Rh4.87,CAT} No P{Rh4.123,CAT} No P{Rh4.159,CAT} No P{Rh4.276,CAT} No P{Rh4.373,CAT} No P{Rh4.472,CAT} No P{Rh4.472ex,CAT} No P{Rh4.472m1,CAT} No P{Rh4.472m2,CAT} No P{Rh4.472m3,CAT} No P{Rh4.472m4,CAT} No P{Rh4.472m5,CAT} No P{Rh4.1900,CAT} No P{Rh4.1900lacZ} No P{Rh4-lacZ.PD} No UAS construct P{GD17228} NA P{KK105515} NA P{UAS-Rh4-EGFP} NA characterization construct P{Rh1+4} NA P{Rh4-GAL4} NA P{Rh4-mCD8-GFP} NA P{Rh4-taulacZ.N} NA
Insertions
	Type of insertions Name Expression data miscellaneous insertions Mi{MIC}Rh4MI02104 NA P{GT1}sinaBG02648 NA PBac{PB}Rh4c04779 NA PBac{RB}Rh4e04456 NA insertion of enhancer trap P{lacW}Rh4W25 No insertion of mobile activating element P{GSV1}C427C427 NA
Gene Ontology: Function, Process & Cellular Component ( 8 unique terms )
Terms Based on Experimental Evidence ( 2 terms )
Molecular Function
CV term Evidence References
G-protein coupled photoreceptor activity inferred from direct assay (Feiler et al., 1992)
Biological Process
CV term Evidence References
phototransduction, UV inferred from direct assay (Feiler et al., 1992)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 8 terms )
Molecular Function
CV term Evidence References
G-protein coupled photoreceptor activity inferred from sequence or structural similarity (Brody and Cravchik, 2000) non-traceable author statement (Pichaud et al., 1999) traceable author statement (Britt et al., 1993) G-protein coupled receptor activity non-traceable author statement (Swiss-Prot Project Members, 1988.8.1)
Biological Process
CV term Evidence References
detection of UV traceable author statement (Montell, 1999) G-protein coupled receptor signaling pathway inferred from electronic annotation with InterPro:IPR000276, InterPro:IPR000856, InterPro:IPR001760 (FlyBase Curators et al., 2004-) inferred from sequence or structural similarity (Brody and Cravchik, 2000) phototransduction non-traceable author statement (Montell, 1999) phototransduction, UV non-traceable author statement (Pichaud et al., 1999, Swiss-Prot Project Members, 1988.8.1) traceable author statement (Britt et al., 1993) visual perception inferred from electronic annotation with InterPro:IPR000856, InterPro:IPR001760 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
integral to membrane inferred from electronic annotation with InterPro:IPR000276, InterPro:IPR000856, InterPro:IPR001760 (FlyBase Curators et al., 2004-) inferred from sequence or structural similarity (Brody and Cravchik, 2000) non-traceable author statement (Swiss-Prot Project Members, 1988.8.1)
Sequence Ontology: Class of Gene
	nuclear_gene   protein_coding_gene
Interactions & Pathways
Summary of Physical Interactions
Protein-protein
Interacting group Assay References
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Rh4 allele Gene References unspecified ninaE (Feiler et al., 1992)
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 65186 DroID - A comprehensive database of gene and protein interactions. • FBgn0003250 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 39887
Orthologs
Genome-wide drosophilid orthologs	Dana\GF10499 Dere\Rh4 Dgri\GH17066 Dmoj\GI11660 Dper\GL20699 Dpse\Rh4 Dsec\GM24362 Dsim\GD12438 Dvir\Rh4 Dwil\Rh4 Dyak\GE22185
Curated drosophilid orthologs	Dame\Rh4 (Maside et al., 2004) Damx\Rh4 (Maside and Charlesworth, 2007) Dere\Rh4   Dezo\Rh4 (Maside and Charlesworth, 2007) Dlit\Rh4   Dmon\Rh4 (Maside and Charlesworth, 2007) Dnov\Rh4   Dpse\Rh4   Drep\Rh4   Dvir\Rh4   Dwil\Rh4
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • XP_001951588.1 Acyrthosiphon pisum (pea aphid) XP_001951613.1 Acyrthosiphon pisum (pea aphid) ENSOANP00000016554 Ornithorynchus anatinus (platypus) OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • NV10460 LH19353 FBgn0242175 FBgn0239413 FBgn0067110 FBgn0064273 FBgn0210883 FBgn0013092 FBgn0013091 FBgn0184170 FBgn0179226 FBgn0172602 JGI_V11_214454 JGI_V11_303450 JGI_V11_69119 FBgn0012709 FBgn0012710 FBgn0158294 FBgn0150121 FBgn0134419 FBgn0132817 FBgn0003249 FBgn0131376 FBgn0124537 FBgn0064613 FBgn0064612 FBgn0094353 FBgn0087540 CPIJ009246 ACYPI004442 ACYPI002544 GB18171 GPROP8 PB22394 PHUM009850 GLEAN_00118
Stocks & Reagents
Stocks Listed in FlyBase ( 9 )
Bloomington	18260 w1118; PBac{RB}Rh4e04456 34465 y1 w*; Mi{MIC}Rh4MI02104 12818 w1118; P{GT1}sinaBG02648 Rh4BG02648/TM3, Sb1 Ser1
Harvard	- PBac{PB}Rh4c04779 - PBac{RB}Rh4e04456
Kyoto	111495 yd2 w1118 P{ey-FLP.N}2 P{GMR-lacZ.C(38.1)}TPN1; P{GT1}sinaBG02648 P{neoFRT}80B/TM6B, P{Car20y}TPN1, Tb1
VDRC	v101708 P{KK105515}VIE-260B v46920 w1118 P{GD17228}v46920 v46919 w1118; P{GD17228}v46919
Genomic Clones ( 1 )
	BACR48E21 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 60 )
	Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones	RH33063
Other clones	FI02185
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	GH01432 GH07401 GH08115 GH08439 GH10105 GH12106 GH12992 GH16710 HL02165 HL02220 HL02222 HL02504 RH02638 RH04707 RH05713 RH08123 RH08280 RH16548 RH17074 RH23019 RH23556 RH24621 RH27835 RH29419 RH33237 RH35735 RH42954 RH43325 RH48927 RH48937 RH50821 RH52076 RH53134 RH54635 RH62206 RH68512 RH71796
Other clones	41770 108002 120912 156463 166405 181036 AA433273 bs12b06 bs82h02 CK01.62C.G7 CK01.120A.B4 EK050428 EK091638 EK154638 EK234029 EK240760 EK259315 EK271150 EK286058 GH12673 RE01426
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0003250 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 39887
Antibody Information
	polyclonal (Feiler et al., 1992)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	Confocal microscopy suggests that rhodopsin 4 is located in the pale fluorescent R7 cells. (Lee et al., 1996) Promoter fusions generated to express Rh4 under control of ninaE promoter, in a ninaE background. (Feiler et al., 1992) In contrast to D.melanogaster, where the sina gene is located within an intron of Rh4, Dvir\sina and Dvir\Rh4 are widely separated in D.virilis. This different structural arrangement may have been caused by the translocation of the Dvir\Rh4 gene to a different chromosomal location by a retrotransposition event in D.virilis. (Neufeld et al., 1991) Ecol\CAT reporter gene analysis has been used to identify the minimal R7 opsin regulatory regions of the Rh4 promoter region. The promoter region is a simple bipartite structure, the proximal region constitutes a functionally equivalent promoter core and the distal region determines cell-type specificity. (Fortini and Rubin, 1990) Identified as a cDNA clone that is expressed exclusively or predominantly in the adult visual system. (Hyde et al., 1990, Palazzolo et al., 1989) Encodes the opsin moiety of a rhodopsin specific to the rhabdomere of the seventh photoreceptor cell; Rh3 and Rh4 are expressed in nonoverlapping subsets of ommatidia; the distribution of the two types of R7 cells within the eye is irregular. Transcript first appears during the last 48 hr of the pupal stage and is found in newly eclosed adult heads. Also expressed in Bolwig's organ (FBrf0048777). Rh4 encodes a 378 amino acid protein that is 35% homologous to the opsins found in R1-6 encoded by ninaE and in the ocelli, encoded by Rh2, but 72% homologous to the Rh3-encoded protein.
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_057353 RefSeq (Proteins) • NP_476701 DDBJ / EMBL / GenBank • AAA28856 AAF49400 AAM29587 AC006933 AY113582 BI576490 CZ469509 M17719 M17730 X51353 Entrez Gene - A searchable database of RefSeq genes. • 39887 UniProtKB/Swiss-Prot • P08255 UniProtKB/TrEMBL • Q8MYV5
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • GPCR, rhodopsin-like, 7TM (IPR000276) Opsin RH3/RH4 (IPR000856) Opsin (IPR001760) GPCR, rhodopsin-like superfamily (IPR017452)
Linkouts
	BioGRID - A database of protein and genetic interactions • 65186 DroID - A comprehensive database of gene and protein interactions. • FBgn0003250 DRSC - Results from RNAi screens. • FBgn0003250 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0003250 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG9668-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0003250 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 39887 InParanoid A subset of ortholog calls from InParanoid. • XP_001951588.1 Acyrthosiphon pisum (pea aphid) XP_001951613.1 Acyrthosiphon pisum (pea aphid) ENSOANP00000016554 Ornithorynchus anatinus (platypus) InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 39887 modMine - Data generated by the modENCODE project. • FBgn0003250 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • NV10460 LH19353 FBgn0242175 FBgn0239413 FBgn0067110 FBgn0064273 FBgn0210883 FBgn0013092 FBgn0013091 FBgn0184170 FBgn0179226 FBgn0172602 JGI_V11_214454 JGI_V11_303450 JGI_V11_69119 FBgn0012709 FBgn0012710 FBgn0158294 FBgn0150121 FBgn0134419 FBgn0132817 FBgn0003249 FBgn0131376 FBgn0124537 FBgn0064613 FBgn0064612 FBgn0094353 FBgn0087540 CPIJ009246 ACYPI004442 ACYPI002544 GB18171 GPROP8 PB22394 PHUM009850 GLEAN_00118
Synonyms & Secondary IDs ( 13 )
Reported As
Symbol Synonym	CG9668 (Arbeitman et al., 2004, Molnar et al., 2006, Goldman and Arbeitman, 2007, Keleman et al., 2009.8.5, Bhutkar et al., 2007) DMELRH4 (Papatsenko et al., 2001) Dm Rh4 (Townson et al., 1998) FBgn0003250 (Raychaudhuri et al., 2003) Rh (Fanning and Anderson, 1999) Rh4 (Yang et al., 2005, Sarfare et al., 2005, Mikeladze-Dvali et al., 2005, Earl and Britt, 2006, Bazigou et al., 2007, Wang and Montell, 2005, Wang, 2007, Pistillo et al., 2007, Ahmad et al., 2006, Langille and Clark, 2007, Nelson et al., 2005, Hummel and Klaembt, 2006, Hsiao et al., 2008, Molnar et al., 2006, Cooper, 2007, Zelhof et al., 2003, Landry et al., 2007, Xie et al., 2007, Miller et al., 2008, Ranade et al., 2008, Birkholz et al., 2009, Wernet et al., 2006, Morey et al., 2008, Lai et al., 2007, Birkholz et al., 2009, Bell et al., 2007, Aoyagi and Wassarman, 2001, Root et al., 2008, Bhutkar et al., 2007, Wang et al., 2010, Mishra et al., 2010, Seong et al., 2011, Charlton-Perkins et al., 2011, Xiang et al., 2010, Jumbo-Lucioni et al., 2010) rh4 (Tahayato et al., 2003, Cook et al., 2003, Pistillo et al., 2004, Cook, 2003, Wernet et al., 2002, Mazzoni et al., 2002, Pichaud et al., 2002, Beaufils et al., 1998, Beaufils et al., 1997, Mikeladze-Dvali et al., 2005, Sprecher et al., 2007, Jukam and Claude, 2008, Mazzoni et al., 2008, Shen et al., 2011) RH4 (Sun et al., 1997, Lee et al., 1996) unnamed (Palazzolo et al., 1989)
Name Synonym	rhodopsin (Wernet and Desplan, 2004, Harteneck, 2003, Suel et al., 2002, Dan et al., 2001, Suel and Ranganathan, 1999, Xu et al., 1998) Rhodopsin (Voets and Nilius, 2003, Montell, 2000, Satoh et al., 2002, Hardie and Raghu, 2001) Rhodopsin 4 (Earl and Britt, 2006, Cooper, 2007, Goldman and Arbeitman, 2007, Zhang et al., 2004) rhodopsin 4 (Dalton et al., 2010)
Secondary FlyBase IDs
References ( 155 )
Generate a list of	All references relating to this gene ( 155 )
List References by type	Research paper  ( 86 ) Supplementary material  ( 3 ) Review  ( 22 ) Personal communication to FlyBase  ( 6 ) Abstract  ( 29 ) FlyBase analysis  ( 2 ) Protein sequence record  ( 1 ) Computer file  ( 3 ) Curated genome annotation  ( 1 ) Automatic genome annotation  ( 1 ) Book  ( 1 )
Recent research papers ( 8 )
	Charlton-Perkins et al., 2011, Neural Dev. 6: 20 Prospero and Pax2 combinatorially control neural cell fate decisions by modulating Ras- and Notch-dependent signaling. [FBrf0213993] Seong et al., 2011, Biogerontology 12(2): 93--107 Genome-wide analysis of low-dose irradiated male Drosophila melanogaster with extended longevity. [FBrf0213307] Shen et al., 2011, Science 331(6022): 1333--1336 Function of rhodopsin in temperature discrimination in Drosophila. [FBrf0213227] Dalton et al., 2010, BMC Genomics 11: 541 Dynamic, mating-induced gene expression changes in female head and brain tissues of Drosophila melanogaster. [FBrf0212122] Jumbo-Lucioni et al., 2010, BMC Genomics 11: 297 Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster. [FBrf0210956] Mishra et al., 2010, Development 137(17): 2895--2904 Pph13 and Orthodenticle define a dual regulatory pathway for photoreceptor cell morphogenesis and function. [FBrf0211519] Wang et al., 2010, Curr. Biol. 20(2): 93--102 Requirement for an Enzymatic Visual Cycle in Drosophila. [FBrf0209891] Xiang et al., 2010, Nature 468(7326): 921--926 Light-avoidance-mediating photoreceptors tile the Drosophila larval body wall. [FBrf0212615] Show all research papers ...
Recent reviews (0)
	All reviews listed in FlyBase were published before 2010 Show reviews ...