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Gene Dmel\Rnp4F

General Information
Symbol	Dmel\Rnp4F	Species	D. melanogaster
Name	RNA-binding protein 4F	Annotation symbol	CG3312
Feature type	protein_coding_gene	FlyBase ID	FBgn0014024
Gene Model Status	Current	Stock availability	4 publicly available
Also Known As	4f-rnp, rnp-4f
Genomic Location
Chromosome (arm)	X	Recombination map
Cytogenetic map	4F5-4F5	Sequence location	X:5,212,961..5,216,759 [-]
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 RNA-binding protein 4F is referred to in FlyBase by the symbol Dmel\Rnp4F (CG3312, FBgn0014024). It is a protein_coding_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: mRNA binding. There is experimental evidence that it is involved in the biological process: central nervous system development. 6 alleles are reported. No phenotypic data is available. It has 4 annotated transcripts and 4 annotated polypeptides. Protein features are: Lsm interaction; Nucleotide-binding, alpha-beta plait; RNA recognition motif domain; RNA-processing protein, HAT helix. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 00-06 hour embryonic stages, during early pupal stages, in adult female stages. Summary of FlyAtlas Anatomical Expression Data: Nearly all larval and adult tissues/organs expressed at moderate levels. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, larval/adult central nervous system, adult crop, larval/adult midgut, larval/adult hindgut, adult Malpighian tubules, adult fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult male accessory gland, larval/adult carcass. Comments on Affy2 ProbeSet: ProbeSet 1638803_at completely aligns to an exonic region common to each of the 4 FlyBase-annotated transcript isoforms of Rnp4F. Gene sequence location is X:5212961..5216759.
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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FB2011_10	References Feiber et al., 2002, J. molec. Evol. 55(4): 401--413
FB2012_01	Sequence features BKN22527 HFA18706
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 4F5-4F5   Limits computationally determined from genome sequence between P{EP}EP425 and P{EP}CG3249EP1400
Experimentally Determined Cytological Location
Cytogenetic map Notes References 4F1-4F2   (determined by in situ hybridisation)   (Hess et al., 1996) 4F1-4F2   (determined by in situ hybridisation)   (Petschek et al., 1996) 4F1-4F2   (determined by in situ hybridisation)   (Petscheck, 1995)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\Rnp4F 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) Rnp4F-RA FBtr0070752  NM_078492   3337   941 Rnp4F-RB FBtr0070753  NM_206630   3272   941 Rnp4F-RD FBtr0112876  NM_001103414   3176   941 Rnp4F-RE FBtr0301880  NM_001103413   3391   555
Additional Transcript Data & Comments
Reported size (kB)	3.127 (longest cDNA) (Petschek et al., 1997) 3.5, 3.2 (northern blot) (Hess et al., 1996)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein Rnp4F-PA   FBpp0070720   106.7   941   4.75     NP_511047   AAF46022 Rnp4F-PB   FBpp0089396   106.7   941   4.75     NP_996353   AAS65263 Rnp4F-PD   FBpp0111789   106.7   941   4.75     NP_001096884   ABW09340 Rnp4F-PE   FBpp0291094   63.4   555   4.23     NP_001096883   ABW09339
Additional Polypeptide Data & Comments
Reported size (kDa)	943, 639, 555 (aa); 124, 84, 70 (kD predicted) (Petschek et al., 1997)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • RNA recognition motif domain (IPR000504) Lsm interaction (IPR008669) Nucleotide-binding, alpha-beta plait (IPR012677) RNA-processing protein, HAT helix (IPR003107)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA801488   AA978588   AE014298 AAF46022   AE014298 AAS65263   AE014298 ABW09339   AE014298 ABW09340   AI063348   AI107667   AW943110   AY061395 AAL28943   BF499966   BF500008   BF501090   BI234958   BI632311   BI636104   BI636591   BI636788   BI639600   BP557318   CO153409   CO182672   CO185205   CO268002   CO293932   CO294626   CO310479   CO313682   CO315659   CO340582   CO340599   DQ269485   DQ269486   DQ269487 ABB89902   DQ269488 ABB89903   DQ269489 ABB89904   DQ269490 ABB89905   DQ269491 ABB89906   DQ272384 ABB82038   EC075345   EC082452   EC089173   EC214060   EC235870   EC252093   EC257065   EC263650   EL883680   GH941235   GH947332   GH956042   GH956944   GH962454   GH965273   GH965884   GH974826   GH978988   GH979127   GH979312   GH983529   GH984732   GH985119   Y15249   Y15250   Y15251 CAA75535
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q9W4D2 A8JUY0 A8JUY2
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
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
in situ Stage Tissue/Position (including subcellular localization) Reference embryonic stage 4   pole cell   (Hess et al., 1996) embryonic stage 4 -- 16     (Hess et al., 1996) embryonic stage 10   stomodeum   (Hess et al., 1996) proctodeum   (Hess et al., 1996) embryonic stage 13   presumptive embryonic/larval central nervous system   (Hess et al., 1996) embryonic stage 14   ventral nerve cord | dorsal & segmentally repeated   (Hess et al., 1996) embryonic stage 14 -- 16   embryonic/larval foregut   (Hess et al., 1996) ventral nerve cord commissure   (Hess et al., 1996) embryonic/larval hindgut   (Hess et al., 1996) epidermis   (Hess et al., 1996) longitudinal connective   (Hess et al., 1996) muscle system | restricted   (Hess et al., 1996) oogenesis stage S6 -- S14     (Hess et al., 1996) nurse cell   (Hess et al., 1996) oogenesis stage S10A -- S14   oocyte   (Hess et al., 1996) microinjection Stage Tissue/Position (including subcellular localization) Reference embryonic stage     (Petschek et al., 1997) pupal stage     (Petschek et al., 1997) adult stage   adult head   (Petschek et al., 1997) northern blot Stage Tissue/Position (including subcellular localization) Reference embryonic stage & larval stage & adult stage     (Hess et al., 1996)
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Notes
Polypeptide Expression
Additional Descriptive Data
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 FBgn0014024    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0014024 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 moderately high expression to a trough of low expression. Peak expression observed within 00-06 hour embryonic stages, during early pupal stages, in adult female 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 FBgn0014024 expression level Developmental Stage   Expression Level embryo 00-02hr    3729 embryo 02-04hr    586 embryo 04-06hr    1445 embryo 06-08hr    1308 embryo 08-10hr    1024 embryo 10-12hr    728 embryo 12-14hr    650 embryo 14-16hr    694 embryo 16-18hr    517 embryo 18-20hr    359 embryo 20-22hr    386 embryo 22-24hr    325 larva L1    1272 larva L2    1260 larva L3 12hr old    872 larva L3 puffstage 1-2    687 larva L3 puffstage 3-6    1010 larva L3 puffstage 7-9    1113 white prepupae new    1141 white prepupae 12hr    1394 white prepupae 24hr    1673 pupae 2d postWPP    1027 pupae 3d postWPP    670 pupae 4d postWPP    737 adult male 01day    766 adult male 05day    909 adult male 30day    942 adult female 01day    2050 adult female 05day    2673 adult female 30day    2810 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High  Linear, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr  (3729) embryo 02-04hr  (586) embryo 04-06hr  (1445) embryo 06-08hr  (1308) embryo 08-10hr  (1024) embryo 10-12hr  (728) embryo 12-14hr  (650) embryo 14-16hr  (694) embryo 16-18hr  (517) embryo 18-20hr  (359) embryo 20-22hr  (386) embryo 22-24hr  (325) larva L1  (1272) larva L2  (1260) larva L3 12hr old  (872) larva L3 puffstage 1-2  (687) larva L3 puffstage 3-6  (1010) larva L3 puffstage 7-9  (1113) white prepupae new  (1141) white prepupae 12hr  (1394) white prepupae 24hr  (1673) pupae 2d postWPP  (1027) pupae 3d postWPP  (670) pupae 4d postWPP  (737) adult male 01day  (766) adult male 05day  (909) adult male 30day  (942) adult female 01day  (2050) adult female 05day  (2673) adult female 30day  (2810) Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (3729) embryo 02-04hr    586 embryo 04-06hr  1445 embryo 06-08hr    1308 embryo 08-10hr    1024 embryo 10-12hr    728 embryo 12-14hr    650 embryo 14-16hr    694 embryo 16-18hr    517 embryo 18-20hr    359 embryo 20-22hr    386 embryo 22-24hr    325 larva L1    1272 larva L2    1260 larva L3 12hr old    872 larva L3 puffstage 1-2    687 larva L3 puffstage 3-6    1010 larva L3 puffstage 7-9    1113 white prepupae new    1141 white prepupae 12hr    1394 white prepupae 24hr  (1673) pupae 2d postWPP    1027 pupae 3d postWPP    670 pupae 4d postWPP    737 adult male 01day    766 adult male 05day    909 adult male 30day    942 adult female 01day  (2050) adult female 05day  (2673) adult female 30day  (2810) Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    3729 embryo 02-04hr    586 embryo 04-06hr    1445 embryo 06-08hr    1308 embryo 08-10hr    1024 embryo 10-12hr    728 embryo 12-14hr    650 embryo 14-16hr    694 embryo 16-18hr    517 embryo 18-20hr    359 embryo 20-22hr    386 embryo 22-24hr    325 larva L1    1272 larva L2    1260 larva L3 12hr old    872 larva L3 puffstage 1-2    687 larva L3 puffstage 3-6    1010 larva L3 puffstage 7-9    1113 white prepupae new    1141 white prepupae 12hr    1394 white prepupae 24hr    1673 pupae 2d postWPP    1027 pupae 3d postWPP    670 pupae 4d postWPP    737 adult male 01day    766 adult male 05day    909 adult male 30day    942 adult female 01day    2050 adult female 05day    2673 adult female 30day    2810 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    3729 embryo 02-04hr    586 embryo 04-06hr    1445 embryo 06-08hr    1308 embryo 08-10hr    1024 embryo 10-12hr    728 embryo 12-14hr    650 embryo 14-16hr    694 embryo 16-18hr    517 embryo 18-20hr    359 embryo 20-22hr    386 embryo 22-24hr    325 larva L1    1272 larva L2    1260 larva L3 12hr old    872 larva L3 puffstage 1-2    687 larva L3 puffstage 3-6    1010 larva L3 puffstage 7-9    1113 white prepupae new    1141 white prepupae 12hr    1394 white prepupae 24hr    1673 pupae 2d postWPP    1027 pupae 3d postWPP    670 pupae 4d postWPP    737 adult male 01day    766 adult male 05day    909 adult male 30day    942 adult female 01day    2050 adult female 05day    2673 adult female 30day    2810 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0014024 expression level Developmental Stage   Expression Level embryo 00-02hr    3729 embryo 02-04hr    586 embryo 04-06hr    1445 embryo 06-08hr    1308 embryo 08-10hr    1024 embryo 10-12hr    728 embryo 12-14hr    650 embryo 14-16hr    694 embryo 16-18hr    517 embryo 18-20hr    359 embryo 20-22hr    386 embryo 22-24hr    325 larva L1    1272 larva L2    1260 larva L3 12hr old    872 larva L3 puffstage 1-2    687 larva L3 puffstage 3-6    1010 larva L3 puffstage 7-9    1113 white prepupae new    1141 white prepupae 12hr    1394 white prepupae 24hr    1673 pupae 2d postWPP    1027 pupae 3d postWPP    670 pupae 4d postWPP    737 adult male 01day    766 adult male 05day    909 adult male 30day    942 adult female 01day    2050 adult female 05day    2673 adult female 30day    2810 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High  log, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr  (3729) embryo 02-04hr  (586) embryo 04-06hr  (1445) embryo 06-08hr  (1308) embryo 08-10hr  (1024) embryo 10-12hr  (728) embryo 12-14hr  (650) embryo 14-16hr  (694) embryo 16-18hr  (517) embryo 18-20hr  (359) embryo 20-22hr  (386) embryo 22-24hr  (325) larva L1  (1272) larva L2  (1260) larva L3 12hr old  (872) larva L3 puffstage 1-2  (687) larva L3 puffstage 3-6  (1010) larva L3 puffstage 7-9  (1113) white prepupae new  (1141) white prepupae 12hr  (1394) white prepupae 24hr  (1673) pupae 2d postWPP  (1027) pupae 3d postWPP  (670) pupae 4d postWPP  (737) adult male 01day  (766) adult male 05day  (909) adult male 30day  (942) adult female 01day  (2050) adult female 05day  (2673) adult female 30day  (2810) Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr  (3729) embryo 02-04hr    586 embryo 04-06hr  1445 embryo 06-08hr    1308 embryo 08-10hr    1024 embryo 10-12hr    728 embryo 12-14hr    650 embryo 14-16hr    694 embryo 16-18hr    517 embryo 18-20hr    359 embryo 20-22hr    386 embryo 22-24hr    325 larva L1    1272 larva L2    1260 larva L3 12hr old    872 larva L3 puffstage 1-2    687 larva L3 puffstage 3-6    1010 larva L3 puffstage 7-9    1113 white prepupae new    1141 white prepupae 12hr    1394 white prepupae 24hr  1673 pupae 2d postWPP    1027 pupae 3d postWPP    670 pupae 4d postWPP    737 adult male 01day    766 adult male 05day    909 adult male 30day    942 adult female 01day  2050 adult female 05day  (2673) adult female 30day  (2810) Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    3729 embryo 02-04hr    586 embryo 04-06hr    1445 embryo 06-08hr    1308 embryo 08-10hr    1024 embryo 10-12hr    728 embryo 12-14hr    650 embryo 14-16hr    694 embryo 16-18hr    517 embryo 18-20hr    359 embryo 20-22hr    386 embryo 22-24hr    325 larva L1    1272 larva L2    1260 larva L3 12hr old    872 larva L3 puffstage 1-2    687 larva L3 puffstage 3-6    1010 larva L3 puffstage 7-9    1113 white prepupae new    1141 white prepupae 12hr    1394 white prepupae 24hr    1673 pupae 2d postWPP    1027 pupae 3d postWPP    670 pupae 4d postWPP    737 adult male 01day    766 adult male 05day    909 adult male 30day    942 adult female 01day    2050 adult female 05day    2673 adult female 30day    2810 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    3729 embryo 02-04hr    586 embryo 04-06hr    1445 embryo 06-08hr    1308 embryo 08-10hr    1024 embryo 10-12hr    728 embryo 12-14hr    650 embryo 14-16hr    694 embryo 16-18hr    517 embryo 18-20hr    359 embryo 20-22hr    386 embryo 22-24hr    325 larva L1    1272 larva L2    1260 larva L3 12hr old    872 larva L3 puffstage 1-2    687 larva L3 puffstage 3-6    1010 larva L3 puffstage 7-9    1113 white prepupae new    1141 white prepupae 12hr    1394 white prepupae 24hr    1673 pupae 2d postWPP    1027 pupae 3d postWPP    670 pupae 4d postWPP    737 adult male 01day    766 adult male 05day    909 adult male 30day    942 adult female 01day    2050 adult female 05day    2673 adult female 30day    2810 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 FBgn0014024    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0014024 Moderate expression bin max High level expression bin max Very high expression bin max Summary of FlyAtlas Anatomical Expression Data: Nearly all larval and adult tissues/organs expressed at moderate levels. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, larval/adult central nervous system, adult crop, larval/adult midgut, larval/adult hindgut, adult Malpighian tubules, adult fat body, larval/adult salivary gland, larval trachea, adult female reproductive system, adult male accessory gland, larval/adult carcass. [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 FBgn0014024 expression level Tissue   Expression Level Larval Central Nervous System    305.8 Larval Midgut    126 Larval Hindgut    125.7 Larval Malpighian Tubules    98.1 Larval Fat Body    80 Larval Salivary Gland    134.8 Larval Trachea    104.25 Larval Carcass    110.775 Adult Head    103.8 Adult Eye    93.025 Adult Brain    177.1 Adult Thoracic-Abdominal Ganglion    154.8 Adult Crop    144.1 Adult Midgut    121 Adult Hindgut    114 Adult Malpighian Tubules    123.7 Adult Fat Body    118.3 Adult Salivary Gland    111.6 Adult Heart    68.275 Adult VirginFemale Spermatheca    185.1 Adult InseminatedFemale Spermatheca    204.5 Adult Ovary    324.9 Adult Testis    55 Adult Male Accessory Gland    108.8 Adult Carcass    102.4 Expression Level Scale  None   Low   Moderate  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    305.8 Larval Midgut    126 Larval Hindgut    125.7 Larval Malpighian Tubules    98.1 Larval Fat Body    80 Larval Salivary Gland    134.8 Larval Trachea    104.25 Larval Carcass    110.775 Adult Head    103.8 Adult Eye    93.025 Adult Brain    177.1 Adult Thoracic-Abdominal Ganglion    154.8 Adult Crop    144.1 Adult Midgut    121 Adult Hindgut    114 Adult Malpighian Tubules    123.7 Adult Fat Body    118.3 Adult Salivary Gland    111.6 Adult Heart    68.275 Adult VirginFemale Spermatheca    185.1 Adult InseminatedFemale Spermatheca    204.5 Adult Ovary    324.9 Adult Testis    55 Adult Male Accessory Gland    108.8 Adult Carcass    102.4 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    305.8 Larval Midgut    126 Larval Hindgut    125.7 Larval Malpighian Tubules    98.1 Larval Fat Body    80 Larval Salivary Gland    134.8 Larval Trachea    104.25 Larval Carcass    110.775 Adult Head    103.8 Adult Eye    93.025 Adult Brain    177.1 Adult Thoracic-Abdominal Ganglion    154.8 Adult Crop    144.1 Adult Midgut    121 Adult Hindgut    114 Adult Malpighian Tubules    123.7 Adult Fat Body    118.3 Adult Salivary Gland    111.6 Adult Heart    68.275 Adult VirginFemale Spermatheca    185.1 Adult InseminatedFemale Spermatheca    204.5 Adult Ovary    324.9 Adult Testis    55 Adult Male Accessory Gland    108.8 Adult Carcass    102.4 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    305.8 Larval Midgut    126 Larval Hindgut    125.7 Larval Malpighian Tubules    98.1 Larval Fat Body    80 Larval Salivary Gland    134.8 Larval Trachea    104.25 Larval Carcass    110.775 Adult Head    103.8 Adult Eye    93.025 Adult Brain    177.1 Adult Thoracic-Abdominal Ganglion    154.8 Adult Crop    144.1 Adult Midgut    121 Adult Hindgut    114 Adult Malpighian Tubules    123.7 Adult Fat Body    118.3 Adult Salivary Gland    111.6 Adult Heart    68.275 Adult VirginFemale Spermatheca    185.1 Adult InseminatedFemale Spermatheca    204.5 Adult Ovary    324.9 Adult Testis    55 Adult Male Accessory Gland    108.8 Adult Carcass    102.4 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0014024 expression level Tissue   Expression Level Larval Central Nervous System    305.8 Larval Midgut    126 Larval Hindgut    125.7 Larval Malpighian Tubules    98.1 Larval Fat Body    80 Larval Salivary Gland    134.8 Larval Trachea    104.25 Larval Carcass    110.775 Adult Head    103.8 Adult Eye    93.025 Adult Brain    177.1 Adult Thoracic-Abdominal Ganglion    154.8 Adult Crop    144.1 Adult Midgut    121 Adult Hindgut    114 Adult Malpighian Tubules    123.7 Adult Fat Body    118.3 Adult Salivary Gland    111.6 Adult Heart    68.275 Adult VirginFemale Spermatheca    185.1 Adult InseminatedFemale Spermatheca    204.5 Adult Ovary    324.9 Adult Testis    55 Adult Male Accessory Gland    108.8 Adult Carcass    102.4 Expression Level Scale  None   Low   Moderate   High  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    305.8 Larval Midgut    126 Larval Hindgut    125.7 Larval Malpighian Tubules    98.1 Larval Fat Body    80 Larval Salivary Gland    134.8 Larval Trachea    104.25 Larval Carcass    110.775 Adult Head    103.8 Adult Eye    93.025 Adult Brain    177.1 Adult Thoracic-Abdominal Ganglion    154.8 Adult Crop    144.1 Adult Midgut    121 Adult Hindgut    114 Adult Malpighian Tubules    123.7 Adult Fat Body    118.3 Adult Salivary Gland    111.6 Adult Heart    68.275 Adult VirginFemale Spermatheca    185.1 Adult InseminatedFemale Spermatheca    204.5 Adult Ovary    324.9 Adult Testis    55 Adult Male Accessory Gland    108.8 Adult Carcass    102.4 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    305.8 Larval Midgut    126 Larval Hindgut    125.7 Larval Malpighian Tubules    98.1 Larval Fat Body    80 Larval Salivary Gland    134.8 Larval Trachea    104.25 Larval Carcass    110.775 Adult Head    103.8 Adult Eye    93.025 Adult Brain    177.1 Adult Thoracic-Abdominal Ganglion    154.8 Adult Crop    144.1 Adult Midgut    121 Adult Hindgut    114 Adult Malpighian Tubules    123.7 Adult Fat Body    118.3 Adult Salivary Gland    111.6 Adult Heart    68.275 Adult VirginFemale Spermatheca    185.1 Adult InseminatedFemale Spermatheca    204.5 Adult Ovary    324.9 Adult Testis    55 Adult Male Accessory Gland    108.8 Adult Carcass    102.4 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    305.8 Larval Midgut    126 Larval Hindgut    125.7 Larval Malpighian Tubules    98.1 Larval Fat Body    80 Larval Salivary Gland    134.8 Larval Trachea    104.25 Larval Carcass    110.775 Adult Head    103.8 Adult Eye    93.025 Adult Brain    177.1 Adult Thoracic-Abdominal Ganglion    154.8 Adult Crop    144.1 Adult Midgut    121 Adult Hindgut    114 Adult Malpighian Tubules    123.7 Adult Fat Body    118.3 Adult Salivary Gland    111.6 Adult Heart    68.275 Adult VirginFemale Spermatheca    185.1 Adult InseminatedFemale Spermatheca    204.5 Adult Ovary    324.9 Adult Testis    55 Adult Male Accessory Gland    108.8 Adult Carcass    102.4 Expression Level Scale  None   Low   Moderate   High   Very high  Heatmap Tissue   Expression Level Larval Central Nervous System     Larval Midgut     Larval Hindgut     Larval Malpighian Tubules     Larval Fat Body     Larval Salivary Gland     Larval Trachea     Larval Carcass     Adult Head     Adult Eye     Adult Brain     Adult Thoracic-Abdominal Ganglion     Adult Crop     Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body     Adult Salivary Gland     Adult Heart     Adult VirginFemale Spermatheca     Adult InseminatedFemale Spermatheca     Adult Ovary     Adult Testis     Adult Male Accessory Gland     Adult Carcass     FlyAtlas Organ/Tissue Expression, larval vs. adult Larval Expression Level Tissue Adult Expression Level   NA  Head    103.8   NA  Eye    93.025   NA  Brain    177.1   305.8  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    154.8   NA  Crop    144.1   126  Midgut    121   125.7  Hindgut    114   98.1  Malpighian Tubules    123.7   80  Fat Body    118.3   134.8  Salivary Gland    111.6   NA  Heart    68.275   104.25  Trachea    NA   NA  VirginFemale Spermatheca    185.1   NA  InseminatedFemale Spermatheca    204.5   NA  Ovary    324.9   NA  Testis    55   NA  Male Accessory Gland    108.8   110.775  Carcass    102.4 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_06
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0014024 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG3312-RA FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for Rnp4F Stages(s) 1-3 Stages(s) 7-8 Stages(s) 9-10 Stages(s) 11-12 Stages(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele lethal | recessive Rnp4F532 viable, with Scer\GAL4pnr-MD237 Rnp4FGD10932 Other Phenotypes Allele wild-type Rnp4Fhs.PP Phenotype manifest in Allele
Classical Alleles ( 1 )
For All Classical Alleles Show
Allele of Rnp4F Class Mutagen Stocks Known lesion Rnp4F532 0 --
Alleles Carried on Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Rnp4F Class Mutagen Stocks Known lesion Rnp4FGD10932 in vitro construct - RNAi in vitro construct - regulatory fusion 2 Yes Rnp4FGL00383 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Rnp4FKK102446 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes Rnp4Fhs.PP in vitro construct - regulatory fusion 0 Yes Rnp4FXba:Bam in vitro construct - genomic fragment 0 Yes
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data heat-shock construct P{hs-Rnp4F.H8.3} NA UAS construct P{GD10932} NA P{KK102446} NA P{TRiP.GL00383} NA characterization construct P{Xba/Bam} NA
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 6 unique terms )
Terms Based on Experimental Evidence ( 1 term )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
central nervous system development inferred from mutant phenotype (Chen et al., 2007)
Cellular Component ( 0 terms)
Terms Based on Predictions or Assertions ( 5 terms )
Molecular Function
CV term Evidence References
mRNA binding inferred from sequence or structural similarity (Lasko, 2000) nucleic acid binding inferred from electronic annotation with InterPro:IPR000504 (FlyBase Curators et al., 2004-) nucleotide binding inferred from electronic annotation with InterPro:IPR012677 (FlyBase Curators et al., 2004-)
Biological Process
CV term Evidence References
RNA processing inferred from electronic annotation with InterPro:IPR003107 (FlyBase Curators et al., 2004-)
Cellular Component
CV term Evidence References
intracellular inferred from electronic annotation with InterPro:IPR003107 (FlyBase Curators et al., 2004-)
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 Rnp4F allele Gene References
External Data
Linkouts	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0014024 DroID - A comprehensive database of gene and protein interactions. • FBgn0014024 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 31448
Orthologs
Genome-wide drosophilid orthologs	Dana\GF20948 Dere\GG18501 Dgri\GH23233 Dmoj\GI11056 Dper\GL14328 Dpse\GA17297 Dsec\GM12648 Dvir\GJ16573 Dwil\GK16926 Dyak\GE16818
Curated drosophilid orthologs	Dana\Rnp4F (Fetherson et al., 2006) Dere\Rnp4F (Fetherson et al., 2006) Dper\Rnp4F (Fetherson et al., 2006) Dpse\GA17297 (Fetherson et al., 2006) Dsec\Rnp4F (Fetherson et al., 2006) Dsim\Rnp4F (Fetherson et al., 2006) Dyak\Rnp4F (Fetherson et al., 2006)
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • AAEL011961-PA Aedes aegypti (mosquito) AGAP002959-PA Anopheles gambiae (mosquito) XP_394225.3 Apis mellifera (honey bee) XP_001946245.1 Acyrthosiphon pisum (pea aphid) At4g24270.2 Arabidopsis thaliana (wall cress) 289574 Branchiostoma floridae (lancelet) BGIBMGA012967-PA Bombyx mori (silk worm) CPIJ015478 Culex pipens (mosquito) 173284 Chlamidomonas reinhardtii (green alga) 222846 Capitella spl (polychaete worm) 302363 Daphnia pulex (daphnia) ENSDARP00000004923 Danio rerio (zebra fish) ENSECAP00000000465 Equus caballus (horse) ENSGACP00000011605 Gymnopilus aculeatus (mushroom) 177713 Hypsipyla robusta (cedar shoot borer) ENSP00000228284 Homo sapiens (human) 188648 Lottia gigantea (owl limpet) ENSMODP00000003471 Monodelphis domestica (gray opossum) ENSMMUP00000022530 Macaca mulatta (rhesus monkey) ENSMUSP00000019118 Mus musculus (house mouse) XP_001602582.1 Nasonia vitripennis (wasp) ENSOANP00000014014 Ornithorynchus anatinus (platypus) ENSORLP00000008662 Oryzias latipes (japanese killifish) LOC_Os08g02130.1 Oryza sativa (asian rice) PHUM005508-PA Pediculus humanus (human body louse) ENSPPYP00000005611 Pongo pygmaeus (orangutan) 74244 Phytophthora ramorum (sudden oak death pathogen) 131159 Phytophthora sojae (root rot pathogen) 596792 Populus trichocarpa (black cottonwood) ENSRNOP00000000891 Rattus norvegicus (norway rat) 5048774 Sorghum bicolor (sorghum) SPBC1861.04c Schizosaccharomyces pombe (fission yeast) 62320 Trichoplax adhaerens (metazoa) XP_972538.1 Tribolium castaneum (red flour beetle) OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • FBgn0234310 FBgn0218925 FBgn0203757 FBgn0167584 FBgn0077310 FBgn0151933 FBgn0133819 FBgn0131819 FBgn0110714 FBgn0097953 AAEL011961
Stocks & Reagents
Stocks Listed in FlyBase ( 4 )
Bloomington	35457 y1 sc* v1; P{TRiP.GL00383}attP2
VDRC	v107063 P{KK102446}VIE-260B v24742 w1118; P{GD10932}v24742 v24743 w1118; P{GD10932}v24743
Genomic Clones ( 1 )
	BACR01M22 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 49 )
	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	LD32008
Other clones	DPiM_LD32008
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	AT14752 AT14796 AT16310 GH03096 GH05475 HL02607 RE30737 SD17673 SD18328 SD18612 SD22231 SD26057
Other clones	75377 75480 107856 156804 214225.42 214509.44 522374 CK01.118B.E11 EC23627 EC29927 EK089920 EK205164 EK207320 EK221807 EK233727 EK262125 EN01918 EP10935 EP10957 FGM308F06 IP13334 RP004068680 RP004085634 RP004198924 RP004208140 RP004210287 RP004211663 RP004252404 RP004253412 RP004255259 RP004269196 RP004355973 RP004486434 RP004494351 RP004524936
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0014024 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 31448
Antibody Information
	polyclonal (Chen et al., 2007)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: Rnp4F CG3312 (Zhong, 1999.11)
Source for database merge of
Additional comments
Other Comments
	RNAi knockdown shows that the long Rnp4F isoform is required for normal central nervous system (CNS) development and acts upstream of other genes that are important for CNS development. (Chen et al., 2007) Isolated Rnp4F cDNAs represent three structurally different transcripts arising from alternative splicing and editing of Rnp4F via A-to-G conversions. (Petschek et al., 1997) RNA editing occurs in an alternatively spliced adult head transcript arising from the single-copy nuclear Rnp4F gene via numerous A to G conversions (as shown by comparison of genomic and cDNA nucleotide sequences). (Petschek et al., 1996)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_078492 NM_206630 NM_001103413 NM_001103414 RefSeq (Proteins) • NP_511047 NP_996353 NP_001096883 NP_001096884 DDBJ / EMBL / GenBank • AA978588 AAF46022 AAL28943 AAS65263 ABB82038 ABB89902 ABB89903 ABB89904 ABB89905 ABB89906 ABW09339 ABW09340 AW943110 AY061395 CAA75533 CAA75535 DQ269485 DQ269486 DQ269487 DQ269488 DQ269489 DQ269490 DQ269491 DQ272384 Y15249 Y15250 Y15251 Entrez Gene - A searchable database of RefSeq genes. • 31448 UniProtKB/TrEMBL • A8JUY0 A8JUY2 Q9W4D2
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • RNA recognition motif domain (IPR000504) Lsm interaction (IPR008669) Nucleotide-binding, alpha-beta plait (IPR012677) RNA-processing protein, HAT helix (IPR003107)
Linkouts
	DPiM - DPiM, Drosophila Protein interaction Map • FBgn0014024 DroID - A comprehensive database of gene and protein interactions. • FBgn0014024 DRSC - Results from RNAi screens. • FBgn0014024 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0014024 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG3312-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0014024 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 31448 InParanoid A subset of ortholog calls from InParanoid. • AAEL011961-PA Aedes aegypti (mosquito) AGAP002959-PA Anopheles gambiae (mosquito) XP_394225.3 Apis mellifera (honey bee) XP_001946245.1 Acyrthosiphon pisum (pea aphid) At4g24270.2 Arabidopsis thaliana (wall cress) 289574 Branchiostoma floridae (lancelet) BGIBMGA012967-PA Bombyx mori (silk worm) CPIJ015478 Culex pipens (mosquito) 173284 Chlamidomonas reinhardtii (green alga) 222846 Capitella spl (polychaete worm) 302363 Daphnia pulex (daphnia) ENSDARP00000004923 Danio rerio (zebra fish) ENSECAP00000000465 Equus caballus (horse) ENSGACP00000011605 Gymnopilus aculeatus (mushroom) 177713 Hypsipyla robusta (cedar shoot borer) ENSP00000228284 Homo sapiens (human) 188648 Lottia gigantea (owl limpet) ENSMODP00000003471 Monodelphis domestica (gray opossum) ENSMMUP00000022530 Macaca mulatta (rhesus monkey) ENSMUSP00000019118 Mus musculus (house mouse) XP_001602582.1 Nasonia vitripennis (wasp) ENSOANP00000014014 Ornithorynchus anatinus (platypus) ENSORLP00000008662 Oryzias latipes (japanese killifish) LOC_Os08g02130.1 Oryza sativa (asian rice) PHUM005508-PA Pediculus humanus (human body louse) ENSPPYP00000005611 Pongo pygmaeus (orangutan) 74244 Phytophthora ramorum (sudden oak death pathogen) 131159 Phytophthora sojae (root rot pathogen) 596792 Populus trichocarpa (black cottonwood) ENSRNOP00000000891 Rattus norvegicus (norway rat) 5048774 Sorghum bicolor (sorghum) SPBC1861.04c Schizosaccharomyces pombe (fission yeast) 62320 Trichoplax adhaerens (metazoa) XP_972538.1 Tribolium castaneum (red flour beetle) InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 31448 modMine - Data generated by the modENCODE project. • FBgn0014024 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • FBgn0234310 FBgn0218925 FBgn0203757 FBgn0167584 FBgn0077310 FBgn0151933 FBgn0133819 FBgn0131819 FBgn0110714 FBgn0097953 AAEL011961
Synonyms & Secondary IDs ( 8 )
Reported As
Symbol Synonym	4f-rnp (Gerber and Keller, 2001, Lavorgna et al., 2004, Rangarajan et al., 2003, Peters et al., 2003, Vaughn et al., 2001, Feiber and Vaughn, 2001, Rohrbach and Vaughn, 2001, Vaughn et al., 2000, Rohrbach et al., 2000, Petschek and Smith, 2000, Petschek, 1997.10.24, Petschek, 1997.10.24, Petschek, 1997.10.24, Petschek et al., 1998, Herbert and Rich, 1999, Petschek et al., 1998, Petschek et al., 1997, Petschek et al., 1997, Petschek et al., 1997, Petschek et al., 1996, Petschek et al., 1995, Petschek et al., 1996, Feiber et al., 2002, Peters et al., 2003) 4F-rnp (Feiber et al., 2000, Hess et al., 1996, ) CG3312 (Keleman et al., 2009.8.5, Ni et al., 2011.7.19) rnp-4f (Rangarajan et al., 2004, Fetherson and Vaughn, 2004, Petschek and Concel, 2003, Petschek and Concel, 2002, Rajeshwaran et al., 2006, Fetherson et al., 2006, Chen et al., 2007, Fetherson et al., 2006, Chen et al., 2007) RNP-4F (Petschek and Concel, 2003, Chen et al., 2007) Rnp4F
Name Synonym	RNA-binding protein 4F (Petschek et al., 1995) splicing assembly factor rnp-4f (Chen et al., 2007)
Secondary FlyBase IDs
References ( 52 )
Generate a list of	All references relating to this gene ( 52 )
List References by type	Research paper  ( 8 ) Supplementary material  ( 2 ) Review  ( 3 ) Personal communication to FlyBase  ( 5 ) Abstract  ( 25 ) FlyBase analysis  ( 1 ) DNA/RNA sequence record  ( 3 ) Curated genome annotation  ( 2 ) Computer file  ( 1 ) Automatic genome annotation  ( 1 )
Recent research papers (0)
	All research papers listed in FlyBase were published before 2010 Show research papers ...
Recent reviews (0)
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