FlyBase Gene Report: Dmel\CG31904

General Information

Symbol

Dmel\CG31904

Species

D. melanogaster

Name

Annotation Symbol

CG31904

Feature Type

protein_coding_gene

FlyBase ID

FBgn0260479

Gene Model Status

Uncertain

Stock Availability

4 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

28C2-28C2

Sequence location

2L:7,734,415..7,738,809 [-]

Recombination map

2-28

RefSeq locus

NT_033779 REGION:7734415..7738809

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (7 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables glycine:sodium symporter activity

inferred from biological aspect of ancestor with PANTHER:PTN008325630

(GO Reference Genome Project, 2011-)

enables neurotransmitter transmembrane transporter activity

inferred from sequence or structural similarity with FLYBASE:DAT; FB:FBgn0034136

(Romero-Calderon et al., 2007)

Biological Process (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

involved_in amino acid transport

inferred from biological aspect of ancestor with PANTHER:PTN000907004

(GO Reference Genome Project, 2011-)

involved_in neurotransmitter transport

inferred from sequence or structural similarity with FLYBASE:DAT; FB:FBgn0034136

(Romero-Calderon et al., 2007)

involved_in sodium ion transmembrane transport

inferred from biological aspect of ancestor with PANTHER:PTN000177662

(GO Reference Genome Project, 2011-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

located_in membrane

inferred from electronic annotation with InterPro:IPR000175

(InterPro Project Members, 2004-)

is_active_in plasma membrane

inferred from biological aspect of ancestor with PANTHER:PTN000177662

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

SLC6 FAMILY OF SODIUM/CHLORIDE-DEPENDENT NEUROTRANSMITTER TRANSPORTERS

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

glycine:sodium symporter activity
RHEA 68228:

Summaries

Gene Group (FlyBase)

SLC6 FAMILY OF SODIUM/CHLORIDE-DEPENDENT NEUROTRANSMITTER TRANSPORTERS -: Solute carrier family 6 (SLC6) members are Na⁺/Cl^--dependent transporters of extracellular neurotransmitters, amino acids and osmolytes across the plasma membrane into the cytosol. (Adapted from FBrf0193583).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\CG31904 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q95TF4)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.47

Chimeric gene (of Acp1 and CG13796).

Gene model uncertain: chimeric gene created during local tandem duplication of 6.14kb.

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.52

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

CG31904-RB

FBtr0079501

NM_164768

3572

403

CG31904-RD

FBtr0079502

NM_164769

1943

403

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

CG31904-PB

FBpp0079124

43.2

403

8.76

FBpp0079125

43.2

403

8.76

Q95TF4

NP_723311

AAN10644

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

403 aa isoforms: CG31904-PB, CG31904-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q95TF4

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\CG31904 using the Feature Mapper tool.

External Data

Crossreferences

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.31

Transcript Expression

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

(Romero-Calderon et al., 2007)

adult thorax | faint

Comment: Thorax and abdomen assayed together.

(Romero-Calderon et al., 2007)

adult abdomen | faint

Comment: Thorax and abdomen assayed together.

(Romero-Calderon et al., 2007)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\CG31904 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\CG31904

View exonic expression by tissue for Dmel\CG31904

Bulk Downloads

RNA-Seq RPKM values for all genes

Reference

See Gelbart and Emmert, 2013 for analysis details and data files for all genes.

Developmental Proteome: Life Cycle

Developmental Proteome: Embryogenesis

External Data and Images

Linkouts

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0260479

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

319016/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0260479

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0260479

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG31904

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of CG31904

Transgenic constructs containing regulatory region of CG31904

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 11 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (19)

Hsap\SLC6A1

3 of 14

Yes

Hsap\SLC6A6

3 of 14

Yes

Hsap\SLC6A8

3 of 14

Yes

Hsap\SLC6A11

3 of 14

Yes

Hsap\SLC6A12

3 of 14

Yes

Hsap\SLC6A13

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (18)

Rnor\Slc6a1

2 of 14

Yes

Rnor\Slc6a2

2 of 14

Yes

Rnor\Slc6a5

2 of 14

Yes

Rnor\Slc6a6

2 of 14

Yes

Rnor\Slc6a7

2 of 14

Yes

Rnor\Slc6a9

2 of 14

Yes

Rnor\Slc6a11

2 of 14

Yes

Rnor\Slc6a12

2 of 14

Yes

Rnor\Slc6a13

2 of 14

Yes

Rnor\Slc6a14

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (20)

Mmus\Slc6a1

2 of 14

Yes

Mmus\Slc6a4

2 of 14

Yes

Mmus\Slc6a6

2 of 14

Yes

Mmus\Slc6a7

2 of 14

Yes

Mmus\Slc6a8

2 of 14

Yes

Mmus\Slc6a9

2 of 14

Yes

Mmus\Slc6a11

2 of 14

Yes

Mmus\Slc6a12

2 of 14

Yes

Mmus\Slc6a13

2 of 14

Yes

Mmus\Slc6a14

2 of 14

Yes

Mmus\Slc6a20b

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (16)

Xtro\lyl1

2 of 13

Yes

Xtro\slc6a6

2 of 13

Yes

Xtro\slc6a8l

2 of 13

Yes

Xtro\slc6a8

2 of 13

Yes

Xtro\cdc37

1 of 13

Xtro\cflar

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (29)

Drer\slc6a1l

3 of 14

Yes

Drer\slc6a8

3 of 14

Yes

Drer\si:ch211-117c9.5

2 of 14

Drer\si:ch211-132b12.1

2 of 14

Drer\si:ch211-132b12.2

2 of 14

Drer\si:ch211-132b12.3

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Drer\si:ch211-132b12.4

1 of 14

Yes

Drer\si:ch211-132b12.6

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (16)

Cele\snf-3

3 of 14

Yes

Cele\snf-11

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

Yes

Cele\snf-5

1 of 14

Cele\snf-8

1 of 14

Yes

Cele\snf-10

1 of 14

Cele\Y43D4A.1

1 of 14

Anopheles gambiae (African malaria mosquito) (27)

Agam\AgaP_AGAP009768

3 of 12

Yes

Agam\AgaP_AGAP010621

3 of 12

Yes

Agam\AgaP_AGAP010858

3 of 12

Yes

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:CG31904. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (24)

5 of 13

5 of 13

5 of 13

5 of 13

5 of 13

4 of 13

4 of 13

4 of 13

4 of 13

DAT

4 of 13

Gat

4 of 13

ine

4 of 13

List

4 of 13

NAAT1

4 of 13

Ntl

4 of 13

4 of 13

3 of 13

3 of 13

3 of 13

3 of 13

bdg

2 of 13

blot

2 of 13

CG7203

2 of 13

CG7214

2 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 2 )

Human Ortholog

Disease

Evidence

References

SLC6A8; solute carrier family 6 member 8

model of cerebral creatine deficiency syndrome 1

IEA

(FlyBase, 2019-)

SLC6A1; solute carrier family 6 member 1

model of myoclonic-atonic epilepsy

IEA

(FlyBase, 2019-)

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

SLC6A1; solute carrier family 6 member 1

3 of 14

137165

MYOCLONIC-ATONIC EPILEPSY; MAE

myoclonic-atonic epilepsy

SLC6A6; solute carrier family 6 member 6

3 of 14

186854

HYPOTAURINEMIC RETINAL DEGENERATION AND CARDIOMYOPATHY; HTRDC

SLC6A8; solute carrier family 6 member 8

3 of 14

300036

CEREBRAL CREATINE DEFICIENCY SYNDROME 1; CCDS1

cerebral creatine deficiency syndrome 1

SLC6A11; solute carrier family 6 member 11

3 of 14

607952

SLC6A12; solute carrier family 6 member 12

3 of 14

603080

SLC6A13; solute carrier family 6 member 13

3 of 14

615097

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

esyN Network Diagram

Other Interaction Browsers

Summary of Genetic Interactions

esyN Network Diagram

Other Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0260479

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-28

Cytogenetic map

28C2-28C2

Sequence location

2L:7,734,415..7,738,809 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

28C2-28C2

Limits computationally determined from genome sequence between P{EP}EP2419^EP2419&P{EP}EP575 and P{PZ}l(2)rL220^rL220

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-28

(FlyBase, 2016)

2-25.0

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (4)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

34677

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01155}attP2

67286

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06389}attP40

NIG-Fly

31904R-3

P{NIG.31904R}3

HMS01155

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01155}attP2

Genomic Clones (18)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (55)

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

GH01326

Other clones

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

FBgn0260479

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0260479

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

New annotation (CG31904) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: CG31904 anon-WO0149848.5

(FlyBase, 1996-)

Additional comments

CG31904 appears to be a chimeric gene, with the 5' part of the gene derived from CG13796 and the 3' part of the gene derived from Acp1.

(Rogers and Hartl, 2012)

"CG31904" is a putative chimeric gene derived from the "CG13796" and "Acp1" genes (where coding sequences of the two parental genes contribute to the coding sequence of the chimeric gene).

(Rogers et al., 2009)

Source for merge of CG31904 anon-WO0149848.5 was sequence comparison ( date:051113 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (3)

Reported As

Symbol Synonym

CG31904

(Denecke et al., 2020, Yurkevych et al., 2020, Daneshvar et al., 2013, Chen et al., 2012, Japanese National Institute of Genetics, 2012.5.21, Rogers and Hartl, 2012, Ni et al., 2010.12.1, Zhang et al., 2010, Perkins et al., 2009, Miller et al., 2008, Romero-Calderon et al., 2007)

CG31904-PD

(Rogers et al., 2009)

anon-WO0149848.5

Name Synonyms

Secondary FlyBase IDs

FBgn0045953
FBgn0051904

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 35 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

319016

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q95TF4

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Q95TF4

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q95TF4

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0260479

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

319016/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0260479

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0260479

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG31904

MARRVEL_MODEL - MARRVEL (model organism gene)

319016

Linkouts

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0260479

DroID - A comprehensive database of gene and protein interactions.

FBgn0260479

DRSC - Results frm RNAi screens

FBgn0260479

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0260479

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG31904

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0260479

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC013671

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

References (25)

The following external sites may use different assemblies or annotations than FlyBase.

-0.31

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