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Gene Dmel\cln3

General Information
Symbol	Dmel\cln3	Species	D. melanogaster
Name	cln3	Annotation symbol	CG5582
Feature type	protein_coding_gene	FlyBase ID	FBgn0036756
Gene Model Status	Current	Stock availability	3 publicly available
Genomic Location
Chromosome (arm)	3L	Recombination map
Cytogenetic map	75A2-75A2	Sequence location	3L:17,802,330..17,807,211 [-]
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 cln3 is referred to in FlyBase by the symbol Dmel\cln3 (CG5582, FBgn0036756). It is a protein_coding_gene from Drosophila melanogaster. Its molecular function is unknown. There is experimental evidence that it is involved in the biological process: regulation of JNK cascade; determination of adult lifespan; response to oxidative stress; regulation of Notch signaling pathway. 9 alleles are reported. The phenotypes of these alleles are annotated with: wing margin; eye; wing disc; wing blade; ommatidium; wing vein. It has one annotated transcript and one annotated polypeptide. Protein features are: Batten's disease protein Cln3; Batten's disease protein Cln3, subgroup; Major facilitator superfamily domain, general substrate transporter. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of extremely low expression. Peak expression observed within 18-24 hour embryonic stages, at stages throughout the larval period, during late pupal stages, in adult male stages. Summary of FlyAtlas Anatomical Expression Data: Expression at high levels in the following post-embryonic organs or tissues: adult midgut, adult hindgut, larval/adult Malpighian tubules. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval midgut, larval hindgut, larval/adult carcass. Comments on Affy2 ProbeSet: ProbeSet 1639653_at completely aligns to an exonic region of the only FlyBase-annotated transcript isoform of cln3. Gene sequence location is 3L:17802330..17807211.
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	Controlled Vocabulary Terms response to oxidative stress determination of adult lifespan Transgenic Constructs P{cln3.Venus} Alleles cln3[T:Avic\GFP-YFP.Venus] cln3[DeltaMB1]
FB2012_01	Sequence features BKN21865 HFA10520
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 75A2-75A2   Limits computationally determined from genome sequence between P{lacW}l(3)j11B2j11B2 and P{PZ}W05014
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Please see the GBrowse view of Dmel\cln3 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) cln3-RA FBtr0075167  NM_140754   1546   422
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 cln3-PA   FBpp0074933   47.6   422   4.92     NP_649011   AAF49301
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Batten's disease protein Cln3 (IPR003492) Batten's disease protein Cln3, subgroup (IPR018460) Major facilitator superfamily domain, general substrate transporter (IPR016196)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AE014296 AAF49301   AY089564 AAL90302   AY232192   BI164113   BI230379   BT044134   CA803739   CA804153   EC052895   GH749597   GH750868   GH754806   GH779013   GH800888   GH802035   GH802873   GH803856   GH807586   GH814721   GH820239   GH823336   GH826098   GH827785   GH857343   GH863986   GH878781   GH881576   GH882502   GH885144   GH891383   GH892287   GH899682   GH902361   GH903472   GH923240   GH927955   GH930397   GH930654   GH933797   GH933822   GH937641   GH940665
UniProtKB/Swiss-Prot
UniProtKB/TrEMBL	Q8SXL8 Q9VVL0
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
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 FBgn0036756    Styles Linear Logarithmic Heatmap    Scales max expr for FBgn0036756 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 extremely low expression. Peak expression observed within 18-24 hour embryonic stages, at stages throughout the larval period, during late pupal stages, 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 FBgn0036756 expression level Developmental Stage   Expression Level embryo 00-02hr    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr    290 embryo 18-20hr    1417 embryo 20-22hr    2031 embryo 22-24hr    2096 larva L1    2043 larva L2    1808 larva L3 12hr old    1223 larva L3 puffstage 1-2    1015 larva L3 puffstage 3-6    1531 larva L3 puffstage 7-9    3170 white prepupae new    661 white prepupae 12hr    927 white prepupae 24hr    164 pupae 2d postWPP    96 pupae 3d postWPP    128 pupae 4d postWPP    2851 adult male 01day    1919 adult male 05day    2007 adult male 30day    1844 adult female 01day    1367 adult female 05day    1112 adult female 30day    983 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to Very low expression Developmental Stage   Expression Level embryo 00-02hr    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr  (290) embryo 18-20hr  (1417) embryo 20-22hr  (2031) embryo 22-24hr  (2096) larva L1  (2043) larva L2  (1808) larva L3 12hr old  (1223) larva L3 puffstage 1-2  (1015) larva L3 puffstage 3-6  (1531) larva L3 puffstage 7-9  (3170) white prepupae new  (661) white prepupae 12hr  (927) white prepupae 24hr  (164) pupae 2d postWPP    96 pupae 3d postWPP  (128) pupae 4d postWPP  (2851) adult male 01day  (1919) adult male 05day  (2007) adult male 30day  (1844) adult female 01day  (1367) adult female 05day  (1112) adult female 30day  (983) Expression Level Scale  None   Extremely low   Very low   Low  Linear, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr    290 embryo 18-20hr  1417 embryo 20-22hr  (2031) embryo 22-24hr  (2096) larva L1  (2043) larva L2  (1808) larva L3 12hr old    1223 larva L3 puffstage 1-2    1015 larva L3 puffstage 3-6  (1531) larva L3 puffstage 7-9  (3170) white prepupae new    661 white prepupae 12hr    927 white prepupae 24hr    164 pupae 2d postWPP    96 pupae 3d postWPP    128 pupae 4d postWPP  (2851) adult male 01day  (1919) adult male 05day  (2007) adult male 30day  (1844) adult female 01day    1367 adult female 05day    1112 adult female 30day    983 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  Linear, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr    290 embryo 18-20hr    1417 embryo 20-22hr    2031 embryo 22-24hr    2096 larva L1    2043 larva L2    1808 larva L3 12hr old    1223 larva L3 puffstage 1-2    1015 larva L3 puffstage 3-6    1531 larva L3 puffstage 7-9    3170 white prepupae new    661 white prepupae 12hr    927 white prepupae 24hr    164 pupae 2d postWPP    96 pupae 3d postWPP    128 pupae 4d postWPP    2851 adult male 01day    1919 adult male 05day    2007 adult male 30day    1844 adult female 01day    1367 adult female 05day    1112 adult female 30day    983 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    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr    290 embryo 18-20hr    1417 embryo 20-22hr    2031 embryo 22-24hr    2096 larva L1    2043 larva L2    1808 larva L3 12hr old    1223 larva L3 puffstage 1-2    1015 larva L3 puffstage 3-6    1531 larva L3 puffstage 7-9    3170 white prepupae new    661 white prepupae 12hr    927 white prepupae 24hr    164 pupae 2d postWPP    96 pupae 3d postWPP    128 pupae 4d postWPP    2851 adult male 01day    1919 adult male 05day    2007 adult male 30day    1844 adult female 01day    1367 adult female 05day    1112 adult female 30day    983 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high   High   Very high   Extremely high  log, scaled to maximum FBgn0036756 expression level Developmental Stage   Expression Level embryo 00-02hr    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr    290 embryo 18-20hr    1417 embryo 20-22hr    2031 embryo 22-24hr    2096 larva L1    2043 larva L2    1808 larva L3 12hr old    1223 larva L3 puffstage 1-2    1015 larva L3 puffstage 3-6    1531 larva L3 puffstage 7-9    3170 white prepupae new    661 white prepupae 12hr    927 white prepupae 24hr    164 pupae 2d postWPP    96 pupae 3d postWPP    128 pupae 4d postWPP    2851 adult male 01day    1919 adult male 05day    2007 adult male 30day    1844 adult female 01day    1367 adult female 05day    1112 adult female 30day    983 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    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr  (290) embryo 18-20hr  (1417) embryo 20-22hr  (2031) embryo 22-24hr  (2096) larva L1  (2043) larva L2  (1808) larva L3 12hr old  (1223) larva L3 puffstage 1-2  (1015) larva L3 puffstage 3-6  (1531) larva L3 puffstage 7-9  (3170) white prepupae new  (661) white prepupae 12hr  (927) white prepupae 24hr  (164) pupae 2d postWPP    96 pupae 3d postWPP  128 pupae 4d postWPP  (2851) adult male 01day  (1919) adult male 05day  (2007) adult male 30day  (1844) adult female 01day  (1367) adult female 05day  (1112) adult female 30day  (983) Expression Level Scale  None   Extremely low   Very low   Low  log, scaled to Moderate expression Developmental Stage   Expression Level embryo 00-02hr    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr    290 embryo 18-20hr  1417 embryo 20-22hr  2031 embryo 22-24hr  2096 larva L1  2043 larva L2  1808 larva L3 12hr old    1223 larva L3 puffstage 1-2    1015 larva L3 puffstage 3-6  1531 larva L3 puffstage 7-9  (3170) white prepupae new    661 white prepupae 12hr    927 white prepupae 24hr    164 pupae 2d postWPP    96 pupae 3d postWPP    128 pupae 4d postWPP  (2851) adult male 01day  1919 adult male 05day  2007 adult male 30day  1844 adult female 01day    1367 adult female 05day    1112 adult female 30day    983 Expression Level Scale  None   Extremely low   Very low   Low   Moderate   Moderately high  log, scaled to High expression Developmental Stage   Expression Level embryo 00-02hr    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr    290 embryo 18-20hr    1417 embryo 20-22hr    2031 embryo 22-24hr    2096 larva L1    2043 larva L2    1808 larva L3 12hr old    1223 larva L3 puffstage 1-2    1015 larva L3 puffstage 3-6    1531 larva L3 puffstage 7-9    3170 white prepupae new    661 white prepupae 12hr    927 white prepupae 24hr    164 pupae 2d postWPP    96 pupae 3d postWPP    128 pupae 4d postWPP    2851 adult male 01day    1919 adult male 05day    2007 adult male 30day    1844 adult female 01day    1367 adult female 05day    1112 adult female 30day    983 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    6 embryo 02-04hr    4 embryo 04-06hr    11 embryo 06-08hr    2 embryo 08-10hr    6 embryo 10-12hr    9 embryo 12-14hr    15 embryo 14-16hr    51 embryo 16-18hr    290 embryo 18-20hr    1417 embryo 20-22hr    2031 embryo 22-24hr    2096 larva L1    2043 larva L2    1808 larva L3 12hr old    1223 larva L3 puffstage 1-2    1015 larva L3 puffstage 3-6    1531 larva L3 puffstage 7-9    3170 white prepupae new    661 white prepupae 12hr    927 white prepupae 24hr    164 pupae 2d postWPP    96 pupae 3d postWPP    128 pupae 4d postWPP    2851 adult male 01day    1919 adult male 05day    2007 adult male 30day    1844 adult female 01day    1367 adult female 05day    1112 adult female 30day    983 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 FBgn0036756    Styles Linear Logarithmic Heatmap Back-to-back    Scales max expr for FBgn0036756 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 midgut, adult hindgut, larval/adult Malpighian tubules. Expression at moderate levels in the following post-embryonic organs or tissues: adult head, adult eye, larval midgut, larval hindgut, 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 FBgn0036756 expression level Tissue   Expression Level Larval Central Nervous System    45.175 Larval Midgut    275 Larval Hindgut    124.8 Larval Malpighian Tubules    2121.9 Larval Fat Body    3.8 Larval Salivary Gland    86.2 Larval Trachea    24.925 Larval Carcass    124.6 Adult Head    141.5 Adult Eye    308.425 Adult Brain    25.5 Adult Thoracic-Abdominal Ganglion    18.1 Adult Crop no informative data Adult Midgut    889 Adult Hindgut    812.4 Adult Malpighian Tubules    1766.3 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    6.25 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    28.7 Adult Ovary    41.5 Adult Testis    70.4 Adult Male Accessory Gland    6.1 Adult Carcass    191.6 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    45.175 Larval Midgut    275 Larval Hindgut    124.8 Larval Malpighian Tubules  (2121.9) Larval Fat Body    3.8 Larval Salivary Gland    86.2 Larval Trachea    24.925 Larval Carcass    124.6 Adult Head    141.5 Adult Eye    308.425 Adult Brain    25.5 Adult Thoracic-Abdominal Ganglion    18.1 Adult Crop no informative data Adult Midgut  (889) Adult Hindgut  (812.4) Adult Malpighian Tubules  (1766.3) Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    6.25 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    28.7 Adult Ovary    41.5 Adult Testis    70.4 Adult Male Accessory Gland    6.1 Adult Carcass    191.6 Expression Level Scale  None   Low   Moderate   High  Linear, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    45.175 Larval Midgut    275 Larval Hindgut    124.8 Larval Malpighian Tubules  (2121.9) Larval Fat Body    3.8 Larval Salivary Gland    86.2 Larval Trachea    24.925 Larval Carcass    124.6 Adult Head    141.5 Adult Eye    308.425 Adult Brain    25.5 Adult Thoracic-Abdominal Ganglion    18.1 Adult Crop no informative data Adult Midgut    889 Adult Hindgut    812.4 Adult Malpighian Tubules  (1766.3) Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    6.25 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    28.7 Adult Ovary    41.5 Adult Testis    70.4 Adult Male Accessory Gland    6.1 Adult Carcass    191.6 Expression Level Scale  None   Low   Moderate   High   Very high  Linear, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    45.175 Larval Midgut    275 Larval Hindgut    124.8 Larval Malpighian Tubules    2121.9 Larval Fat Body    3.8 Larval Salivary Gland    86.2 Larval Trachea    24.925 Larval Carcass    124.6 Adult Head    141.5 Adult Eye    308.425 Adult Brain    25.5 Adult Thoracic-Abdominal Ganglion    18.1 Adult Crop no informative data Adult Midgut    889 Adult Hindgut    812.4 Adult Malpighian Tubules    1766.3 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    6.25 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    28.7 Adult Ovary    41.5 Adult Testis    70.4 Adult Male Accessory Gland    6.1 Adult Carcass    191.6 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to maximum FBgn0036756 expression level Tissue   Expression Level Larval Central Nervous System    45.175 Larval Midgut    275 Larval Hindgut    124.8 Larval Malpighian Tubules    2121.9 Larval Fat Body    3.8 Larval Salivary Gland    86.2 Larval Trachea    24.925 Larval Carcass    124.6 Adult Head    141.5 Adult Eye    308.425 Adult Brain    25.5 Adult Thoracic-Abdominal Ganglion    18.1 Adult Crop no informative data Adult Midgut    889 Adult Hindgut    812.4 Adult Malpighian Tubules    1766.3 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    6.25 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    28.7 Adult Ovary    41.5 Adult Testis    70.4 Adult Male Accessory Gland    6.1 Adult Carcass    191.6 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Moderate expression Tissue   Expression Level Larval Central Nervous System    45.175 Larval Midgut    275 Larval Hindgut    124.8 Larval Malpighian Tubules  (2121.9) Larval Fat Body    3.8 Larval Salivary Gland    86.2 Larval Trachea    24.925 Larval Carcass    124.6 Adult Head    141.5 Adult Eye    308.425 Adult Brain    25.5 Adult Thoracic-Abdominal Ganglion    18.1 Adult Crop no informative data Adult Midgut  (889) Adult Hindgut  812.4 Adult Malpighian Tubules  (1766.3) Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    6.25 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    28.7 Adult Ovary    41.5 Adult Testis    70.4 Adult Male Accessory Gland    6.1 Adult Carcass    191.6 Expression Level Scale  None   Low   Moderate   High  log, scaled to High level expression Tissue   Expression Level Larval Central Nervous System    45.175 Larval Midgut    275 Larval Hindgut    124.8 Larval Malpighian Tubules  (2121.9) Larval Fat Body    3.8 Larval Salivary Gland    86.2 Larval Trachea    24.925 Larval Carcass    124.6 Adult Head    141.5 Adult Eye    308.425 Adult Brain    25.5 Adult Thoracic-Abdominal Ganglion    18.1 Adult Crop no informative data Adult Midgut    889 Adult Hindgut    812.4 Adult Malpighian Tubules  (1766.3) Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    6.25 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    28.7 Adult Ovary    41.5 Adult Testis    70.4 Adult Male Accessory Gland    6.1 Adult Carcass    191.6 Expression Level Scale  None   Low   Moderate   High   Very high  log, scaled to Very high expression Tissue   Expression Level Larval Central Nervous System    45.175 Larval Midgut    275 Larval Hindgut    124.8 Larval Malpighian Tubules    2121.9 Larval Fat Body    3.8 Larval Salivary Gland    86.2 Larval Trachea    24.925 Larval Carcass    124.6 Adult Head    141.5 Adult Eye    308.425 Adult Brain    25.5 Adult Thoracic-Abdominal Ganglion    18.1 Adult Crop no informative data Adult Midgut    889 Adult Hindgut    812.4 Adult Malpighian Tubules    1766.3 Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart    6.25 Adult VirginFemale Spermatheca no informative data Adult InseminatedFemale Spermatheca    28.7 Adult Ovary    41.5 Adult Testis    70.4 Adult Male Accessory Gland    6.1 Adult Carcass    191.6 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 no informative data Adult Midgut     Adult Hindgut     Adult Malpighian Tubules     Adult Fat Body no informative data Adult Salivary Gland no informative data Adult Heart     Adult VirginFemale Spermatheca no informative data 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    141.5   NA  Eye    308.425   NA  Brain    25.5   45.175  Central Nervous System    NA   NA  Thoracic-Abdominal Ganglion    18.1   NA  Crop    no informative data   275  Midgut    889   124.8  Hindgut    812.4   2121.9  Malpighian Tubules    1766.3   3.8  Fat Body    no informative data   86.2  Salivary Gland    no informative data   NA  Heart    6.25   24.925  Trachea    NA   NA  VirginFemale Spermatheca    no informative data   NA  InseminatedFemale Spermatheca    28.7   NA  Ovary    41.5   NA  Testis    70.4   NA  Male Accessory Gland    6.1   124.6  Carcass    191.6 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_10
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0036756 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG5582-RA
Alleles & Phenotypes
Summary of Allele Phenotypes
Lethality Allele viable cln3ΔMB1 viable, with Scer\GAL4pnr-MD237 cln3GD2699 Sterility Allele fertile cln3ΔMB1 Other Phenotypes Allele increased cell death, with Scer\GAL4en-e16E cln3Scer\UAS.cTa long lived, with Scer\GAL4Ilp2.215-3 cln3Scer\UAS.cTa oxidative stress response defective, with Scer\GAL4Ilp2.215-3 cln3Scer\UAS.cTa oxidative stress response defective | recessive cln3ΔMB1 short lived | recessive cln3ΔMB1 starvation stress response defective | female limited | recessive cln3ΔMB1 visible, with Scer\GAL4en-e16E cln3Scer\UAS.cTa visible, with Scer\GAL4GMR.PF cln3Scer\UAS.cTa Phenotype manifest in Allele embryo | dorsal closure stage, with Scer\GAL4pnr-MD237 cln3Scer\UAS.cTa eye, with Scer\GAL4GMR.PF cln3Scer\UAS.cTa cln3Scer\UAS.T:Avic\GFP-YFP.Venus ommatidium, with Scer\GAL4GMR.PF cln3Scer\UAS.T:Avic\GFP-YFP.Venus wing blade, with Scer\GAL4en-e16E cln3Scer\UAS.cTa wing disc, with Scer\GAL4en-e16E cln3Scer\UAS.cTa wing margin, with Scer\GAL4en-e16E cln3Scer\UAS.cTa wing vein, with Scer\GAL4en-e16E cln3Scer\UAS.cTa
Classical Alleles ( 2 )
For All Classical Alleles Show
Allele of cln3 Class Mutagen Stocks Known lesion cln3MB06009 1 -- cln3ΔMB1 amorphic allele - molecular evidence transposable element activity 0 Yes
Alleles Carried on Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Allele of cln3 Class Mutagen Stocks Known lesion cln3GD2699 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cln3HMS01476 in vitro construct - RNAi in vitro construct - regulatory fusion 1 Yes cln3dsRNA.cLa in vitro construct - RNAi 0 Yes cln3Scer\UAS.cTa in vitro construct - regulatory fusion 0 Yes cln3Scer\UAS.T:Avic\GFP-YFP.Venus in vitro construct - regulatory fusion in vitro construct - coding region fusion 0 Yes cln3T:Avic\GFP-YFP.Venus in vitro construct - coding region fusion in vitro construct - genomic fragment 0 Yes cln3ΔC.Scer\UAS in vitro construct - regulatory fusion 0 Yes
Aneuploid Aberrations
Disrupted in	Df(3L)Exel9005 (Ryder, 2004.4.26)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD2699} NA P{TRiP.HMS01476} NA P{UAS-cln3.T} NA P{UAS-cln3.Venus} NA P{UAS-cln3.ΔC</up>} NA characterization construct P{cln3.Venus} NA
Insertions
	Type of insertions Name Expression data insertion of enhancer trap binary system Mi{ET1}cln3MB06009 No
Gene Ontology: Function, Process & Cellular Component ( 8 unique terms )
Terms Based on Experimental Evidence ( 7 terms )
Molecular Function ( 0 terms)
Biological Process
CV term Evidence References
determination of adult lifespan inferred from mutant phenotype (Tuxworth et al., 2011) regulation of JNK cascade inferred from mutant phenotype (Tuxworth et al., 2009) regulation of Notch signaling pathway inferred from mutant phenotype (Tuxworth et al., 2009) response to oxidative stress inferred from mutant phenotype (Tuxworth et al., 2011)
Cellular Component
CV term Evidence References
late endosome inferred from direct assay (Tuxworth et al., 2009) lysosome inferred from direct assay (Tuxworth et al., 2009) vesicle inferred from direct assay (Tuxworth et al., 2009)
Terms Based on Predictions or Assertions ( 1 term )
Molecular Function ( 0 terms)
Biological Process ( 0 terms)
Cellular Component
CV term Evidence References
membrane inferred from electronic annotation with InterPro:IPR003492, InterPro:IPR018460 (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 cln3 allele Gene References
External Data
Linkouts	BioGRID - A database of protein and genetic interactions • 65266 DroID - A comprehensive database of gene and protein interactions. • FBgn0036756 InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 39981
Orthologs
Genome-wide drosophilid orthologs	Dana\GF25236 Dere\GG15779 Dgri\GH14467 Dmoj\GI13613 Dper\GL22749 Dpse\GA18985 Dsec\GM24305 Dsim\GD12373 Dvir\GJ13948 Dwil\GK10451 Dyak\GE22116
Curated drosophilid orthologs	Dpse\GA18985   Dyak\GE22116
Linkouts	InParanoid A subset of ortholog calls from InParanoid. • AAEL009909-PB Aedes aegypti (mosquito) AGAP003934-PA Anopheles gambiae (mosquito) XP_394336.3 Apis mellifera (honey bee) 216655 Branchiostoma floridae (lancelet) ENSBTAP00000023952 Bos taurus (bovine) CAL0004850 Candida albicans (a form of yeast) CN04180 Caenorhabditis brenneri (small nematode) CN06267 Caenorhabditis brenneri (small nematode) CBP05583 Caenorhabditis briggsae (nematode) CE07802 Caenorhabditis elegans (worm) ENSCAFP00000025242 Canis familiaris (dog) CAGL0J05104g Candida glabrata (haploid yeast) JA17520 Caenorhabditis japonica (nematode) cn06429 Cryptococcus neoformans (yeast-like fungus) CPIJ001705 Culex pipens (mosquito) ENSCPOP00000002236 Cavia porcellus (guinea pig) RP16713 Caenorhabditis remanei (nematode) 128152 Capitella spl (polychaete worm) DDB0233983 Dictyostelium discoideum (amoeba) DEHA2A04796g Debaryomyces Hansenii (yeast) 108607 Daphnia pulex (daphnia) ENSDARP00000055169 Danio rerio (zebra fish) ENSECAP00000015483 Equus caballus (horse) XP_656090 Entamoeba histolytica (anaerobic protozoan) ENSGACP00000007204 Gymnopilus aculeatus (mushroom) 194029 Hypsipyla robusta (cedar shoot borer) ENSP00000353073 Homo sapiens (human) KLLA0F01551g Kluyveromyces lactis (yeast) 113507 Lottia gigantea (owl limpet) LmjF06.1300 Leishmania major (virus) LmjF22.0010 Leishmania major (virus) 17162 Monocosta brevicollis (choanoflagellate) ENSMODP00000019468 Monodelphis domestica (gray opossum) ENSMMUP00000000945 Macaca mulatta (rhesus monkey) ENSMUSP00000081636 Mus musculus (house mouse) 195662 Nematostella vectensis (starlet anemone) XP_001602297.1 Nasonia vitripennis (wasp) ENSOANP00000018083 Ornithorynchus anatinus (platypus) ENSORLP00000021527 Oryzias latipes (japanese killifish) PHUM003587-PA Pediculus humanus (human body louse) PP23115 Pristionchus pacificus (nematode) ENSPPYP00000008173 Pongo pygmaeus (orangutan) 82085 Phytophthora ramorum (sudden oak death pathogen) 138338 Phytophthora sojae (root rot pathogen) ENSPTRP00000039223 Pan troglodytes (chimpanzee) ENSRNOP00000025898 Rattus norvegicus (norway rat) YJL059W Saccharomyces cerevisiae (budding yeast) Smp_159270 Schistosoma mansoni (trematode parasite) SPAC607.09c Schizosaccharomyces pombe (fission yeast) XP_971061.1 Tribolium castaneum (red flour beetle) ENSTNIP00000017003 Tetraodon nigroviridis (green spotted pufferfish) 262515 Thalassiosira pseudonana (marine diatom) 85299.m00079 Trichomonas vaginalis (parasitic flagellated protozoan) ENSXETP00000018274 Xenopus tropicalis (frog) YALI0F30415g Yarrowia lipolytica (nonconventional yeast) OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • PB11771 NV15531 LH11353 ISCW004703 FBgn0068289 FBgn0212466 FBgn0201166 FBgn0179169 JGI_V11_108607 FBgn0078984 FBgn0160340 FBgn0136368 FBgn0121943 FBgn0108019 FBgn0102228 CPIJ001705 GB12798 AGAP003934 AAEL009909 PHUM352170 GLEAN_01613
Stocks & Reagents
Stocks Listed in FlyBase ( 3 )
Bloomington	27741 w1118; Mi{ET1}cln3MB06009 35734 y1 sc* v1; P{TRiP.HMS01476}attP2
VDRC	v5322 w1118; P{GD2699}v5322/CyO
Genomic Clones ( 2 )
	BACR17C17 BACR44L18 Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
cDNA Clones ( 40 )
	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	RE03692
Other clones	FI03215 yak-ad_CG5582
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RE10177
Other clones	EC052895 ESG0110b.E21_E06 ESG0112b.B21_D06 RP003011170 RP003043390 RP003046193 RP003052470 RP003070177 RP003089097 RP003093490 RP003154088 RP003180677 RP003198941 RP003225057 RP003249178 RP003252280 RP003269530 RP003298839 RP003321128 RP003337382 RP003394957 RP003407157 RP003439627 RP003453442 RP003454476 RP003460430 RP003496969 RP003507999 RP003518182 RP003568619 RP003585966 RP003600743 RP003641671 RP003660948 RP003669468 RP003680806
RNAi & Array Information
Linkouts	DRSC - Results from RNAi screens. • FBgn0036756 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 39981
Antibody Information
	polyclonal (Tuxworth et al., 2009)
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of	Source for identity of: cln3 CG5582 (Korey, 2005.3.2)
Source for database merge of
Additional comments
Other Comments
	dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology. (Kiger et al., 2003)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_140754 RefSeq (Proteins) • NP_649011 DDBJ / EMBL / GenBank • AAF49301 AAL90302 AY089564 BI164113 Entrez Gene - A searchable database of RefSeq genes. • 39981 UniProtKB/TrEMBL • Q8SXL8 Q9VVL0
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Batten's disease protein Cln3 (IPR003492) Batten's disease protein Cln3, subgroup (IPR018460) Major facilitator superfamily domain, general substrate transporter (IPR016196)
Linkouts
	BioGRID - A database of protein and genetic interactions • 65266 DroID - A comprehensive database of gene and protein interactions. • FBgn0036756 DRSC - Results from RNAi screens. • FBgn0036756 FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0036756 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • CG5582-RA FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans • FBgn0036756 GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents • 39981 InParanoid A subset of ortholog calls from InParanoid. • AAEL009909-PB Aedes aegypti (mosquito) AGAP003934-PA Anopheles gambiae (mosquito) XP_394336.3 Apis mellifera (honey bee) 216655 Branchiostoma floridae (lancelet) ENSBTAP00000023952 Bos taurus (bovine) CAL0004850 Candida albicans (a form of yeast) CN04180 Caenorhabditis brenneri (small nematode) CN06267 Caenorhabditis brenneri (small nematode) CBP05583 Caenorhabditis briggsae (nematode) CE07802 Caenorhabditis elegans (worm) ENSCAFP00000025242 Canis familiaris (dog) CAGL0J05104g Candida glabrata (haploid yeast) JA17520 Caenorhabditis japonica (nematode) cn06429 Cryptococcus neoformans (yeast-like fungus) CPIJ001705 Culex pipens (mosquito) ENSCPOP00000002236 Cavia porcellus (guinea pig) RP16713 Caenorhabditis remanei (nematode) 128152 Capitella spl (polychaete worm) DDB0233983 Dictyostelium discoideum (amoeba) DEHA2A04796g Debaryomyces Hansenii (yeast) 108607 Daphnia pulex (daphnia) ENSDARP00000055169 Danio rerio (zebra fish) ENSECAP00000015483 Equus caballus (horse) XP_656090 Entamoeba histolytica (anaerobic protozoan) ENSGACP00000007204 Gymnopilus aculeatus (mushroom) 194029 Hypsipyla robusta (cedar shoot borer) ENSP00000353073 Homo sapiens (human) KLLA0F01551g Kluyveromyces lactis (yeast) 113507 Lottia gigantea (owl limpet) LmjF06.1300 Leishmania major (virus) LmjF22.0010 Leishmania major (virus) 17162 Monocosta brevicollis (choanoflagellate) ENSMODP00000019468 Monodelphis domestica (gray opossum) ENSMMUP00000000945 Macaca mulatta (rhesus monkey) ENSMUSP00000081636 Mus musculus (house mouse) 195662 Nematostella vectensis (starlet anemone) XP_001602297.1 Nasonia vitripennis (wasp) ENSOANP00000018083 Ornithorynchus anatinus (platypus) ENSORLP00000021527 Oryzias latipes (japanese killifish) PHUM003587-PA Pediculus humanus (human body louse) PP23115 Pristionchus pacificus (nematode) ENSPPYP00000008173 Pongo pygmaeus (orangutan) 82085 Phytophthora ramorum (sudden oak death pathogen) 138338 Phytophthora sojae (root rot pathogen) ENSPTRP00000039223 Pan troglodytes (chimpanzee) ENSRNOP00000025898 Rattus norvegicus (norway rat) YJL059W Saccharomyces cerevisiae (budding yeast) Smp_159270 Schistosoma mansoni (trematode parasite) SPAC607.09c Schizosaccharomyces pombe (fission yeast) XP_971061.1 Tribolium castaneum (red flour beetle) ENSTNIP00000017003 Tetraodon nigroviridis (green spotted pufferfish) 262515 Thalassiosira pseudonana (marine diatom) 85299.m00079 Trichomonas vaginalis (parasitic flagellated protozoan) ENSXETP00000018274 Xenopus tropicalis (frog) YALI0F30415g Yarrowia lipolytica (nonconventional yeast) InterologFinder Protein-protein interactions (PPI) from both known and predicted PPI data sets. • 39981 modMine - Data generated by the modENCODE project. • FBgn0036756 OrthoDB (Arthropod subset) The hierarchical catalog of eukaryotic orthologs. • PB11771 NV15531 LH11353 ISCW004703 FBgn0068289 FBgn0212466 FBgn0201166 FBgn0179169 JGI_V11_108607 FBgn0078984 FBgn0160340 FBgn0136368 FBgn0121943 FBgn0108019 FBgn0102228 CPIJ001705 GB12798 AGAP003934 AAEL009909 PHUM352170 GLEAN_01613
Synonyms & Secondary IDs ( 3 )
Reported As
Symbol Synonym	CG5582 (Metaxakis et al., 2005, Liu et al., 2003, Inlow and Restifo, 2004, Driscoll and Gerstbrein, 2003, Tuxworth et al., 2009, Ni et al., 2011.7.19) cln3 (Korey, 2007, Pauli et al., 2010, Tuxworth et al., 2011) CLN3 (Tuxworth et al., 2009)
Name Synonym	cln3
Secondary FlyBase IDs
References ( 23 )
Generate a list of	All references relating to this gene ( 23 )
List References by type	Research paper  ( 6 ) Supplementary material  ( 5 ) Personal communication to FlyBase  ( 6 ) Abstract  ( 1 ) FlyBase analysis  ( 1 ) Conference report  ( 1 ) Computer file  ( 1 ) Automatic genome annotation  ( 1 )
Recent research papers ( 2 )
	Tuxworth et al., 2011, Hum. Mol. Genet. 20(10): 2037--2047 The Batten disease gene CLN3 is required for the response to oxidative stress. [FBrf0213533] Pauli et al., 2010, Curr. Biol. 20(20): 1787--1798 A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands. [FBrf0212124] Show all research papers ...