FlyBase Gene Report: Dmel\Ctr1C

General Information

Symbol

Dmel\Ctr1C

Species

D. melanogaster

Name

Copper transporter 1C

Annotation Symbol

CG15551

Feature Type

protein_coding_gene

FlyBase ID

FBgn0062411

Gene Model Status

Current

Stock Availability

2 publicly available

Gene Summary

Copper transporter 1C (Ctr1C) is expressed in the male gonad. The autosomal gene seems to have originated as a retrogene copy of the X-linked Ctr1A, thus maintaining copper delivery during male spermatogenesis when the X chromosome is inactive. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

100B1-100B1

Sequence location

3R:30,963,290..30,964,320 [-]

Recombination map

3-102

RefSeq locus

NT_033777 REGION:30963290..30964320

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 (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables copper ion transmembrane transporter activity

inferred from direct assay

(Steiger et al., 2010)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables copper ion transmembrane transporter activity

inferred from electronic annotation with InterPro:IPR007274

(InterPro Project Members, 2004-)

Biological Process (4 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

involved_in copper ion import

inferred from mutant phenotype

(Steiger et al., 2010)

involved_in copper ion transport

inferred from mutant phenotype

(Steiger et al., 2010)

involved_in spermatogenesis

inferred from mutant phenotype

(Steiger et al., 2010)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in copper ion transmembrane transport

inferred from electronic annotation with InterPro:IPR007274

(InterPro Project Members, 2004-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in plasma membrane

inferred from direct assay

(Steiger et al., 2010)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in membrane

inferred from electronic annotation with InterPro:IPR007274

(InterPro Project Members, 2004-)

Gene Group (FlyBase)

SLC31 FAMILY OF COPPER TRANSPORTERS

Protein Family (UniProt)

Protein Signatures (InterPro)

Ctr copper transporter

Catalytic Activity (EC/Rhea)

copper ion transmembrane transporter activity
RHEA 28703:

Summaries

Gene Snapshot

Gene Group (FlyBase)

SLC31 FAMILY OF COPPER TRANSPORTERS -: Solute carrier family 31 (SLC31) members are high-affinity copper ion transmembrane transporters. (Adapted from FBrf0167752).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Ctr1C 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 Q9VA22)

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

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

retrogene

(dos Santos, 2014, Steiger et al., 2010, Pan and Zhang, 2009)

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Ctr1C-RA

FBtr0085749

NM_143580

1031

270

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

Ctr1C-PA

FBpp0085111

30.8

270

8.29

Q9VA22

NP_651837

AAF57103

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

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

Ctr copper transporter

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Ctr1C using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Ctr1C_1

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).

4.71

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in plasma membrane

inferred from direct assay

(Steiger et al., 2010)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Ctr1C in JBrowse

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

View exonic expression by developmental stage for Dmel\Ctr1C

View exonic expression by tissue for Dmel\Ctr1C

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

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

43668/tissue=All

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

FBgn0062411

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0062411

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

FBgn0062411

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

CG15551

Flygut - An atlas of the Drosophila adult midgut

FBgn0062411

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 12 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Ctr1C

Transgenic constructs containing regulatory region of Ctr1C

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3R)Exel6260

(Ryder, 2004.4.26)

Inferred from location ( 0 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

lethal, with Scer\GAL4^Act5C.PU

lethal - all die during larval stage | heat sensitive, with Scer\GAL4^elav.PU

Ctr1C^UAS.cLa

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Ctr1C^GD3136

viable, with Scer\GAL4^Mef2.PR

Ctr1C^GD3136

viable, with Scer\GAL4^pnr-MD237

Ctr1C^GD3136

viable, with Scer\GAL4^tin.CΔ4

Ctr1C^GD3136

viable | nutrition conditional, with Scer\GAL4^Act5C.PU

Ctr1C^UAS.cSa

Other Phenotypes

Allele

some die during second instar larval stage, with Scer\GAL4^elav.PU

Ctr1C^UAS.cLa

some die during third instar larval stage, with Scer\GAL4^elav.PU

Ctr1C^UAS.cLa

visible, with Scer\GAL4^elav.PU

Ctr1C^UAS.cLa

Phenotype manifest in

Allele

eye, with Scer\GAL4^elav.PU

Ctr1C^UAS.cLa

eye, with Scer\GAL4^GMR.PF

ommatidium, with Scer\GAL4^GMR.PF

wing, with Scer\GAL4^elav.PU

Ctr1C^UAS.cLa

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) (2)

Hsap\SLC31A1

7 of 14

Yes

Hsap\SLC31A2

6 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (2)

Rnor\Slc31a2

8 of 14

Yes

Rnor\Slc31a1

7 of 14

Mus musculus (laboratory mouse) (2)

Mmus\Slc31a2

8 of 14

Yes

Mmus\Slc31a1

6 of 14

Xenopus tropicalis (Western clawed frog) (3)

Xtro\slc31a1

4 of 13

Yes

Xtro\slc31a2

3 of 13

Yes

Xtro\lrrcc1

1 of 13

Yes

Danio rerio (Zebrafish) (2)

Drer\slc31a1

8 of 14

Yes

Drer\slc31a2

5 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (10)

Cele\F27C1.2

10 of 14

Yes

Cele\F58G6.3

7 of 14

Yes

Cele\K12C11.6

7 of 14

Yes

Cele\F31E8.4

6 of 14

Cele\Y58A7A.1

5 of 14

Cele\F58G6.9

4 of 14

Yes

Cele\K12C11.3

4 of 14

Yes

Cele\F01G12.1

3 of 14

Yes

Cele\F58G6.7

3 of 14

Yes

Cele\K12C11.7

3 of 14

Anopheles gambiae (African malaria mosquito) (3)

Agam\AgaP_AGAP002109

7 of 12

Yes

Agam\AgaP_AGAP000100

4 of 12

Yes

Agam\AgaP_AGAP010937

4 of 12

Yes

Arabidopsis thaliana (thale-cress) (8)

Atha\COPT5

6 of 13

Yes

Atha\COPT1

5 of 13

Yes

Atha\COPT2

5 of 13

Yes

Atha\COPT3

5 of 13

Yes

Atha\COPT6

5 of 13

Yes

Atha\COPT4

4 of 13

Yes

Atha\AT5G20670

1 of 13

Yes

Atha\emb1513

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\CTR2

8 of 13

Yes

Scer\CTR3

3 of 13

Scer\CTR1

2 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\ctr6

6 of 12

Yes

Spom\ctr4

4 of 12

Spom\ctr5

4 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Ctr1C. 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) (2)

Ctr1A

11 of 13

Ctr1B

10 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 ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 1 )

Allele

Disease

Interaction

References

Ctr1C^RNAi.UAS.cLa

ameliorates Alzheimer's disease

modeled by Hsap\APP^{Aβ42.UAS.Tag:SS(rPENK)}

(Lang et al., 2013)

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?

SLC31A1; solute carrier family 31 member 1

7 of 14

603085

NEURODEGENERATION AND SEIZURES DUE TO COPPER TRANSPORT DEFECT; NSCT

SLC31A2; solute carrier family 31 member 2

6 of 14

603088

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

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

esyN Network Key:

Suppression

Enhancement

Other Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Ctr1A

suppressible

Ctr1C

(Steiger et al., 2010)

Ctr1B

suppressible

Ctr1C

(Steiger et al., 2010)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0062411

MIST (genetic) - An integrated Molecular Interaction Database

43668

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-102

Cytogenetic map

100B1-100B1

Sequence location

3R:30,963,290..30,964,320 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

100B1-100B1

Limits computationally determined from genome sequence between P{lacW}l(3)s2500^s2500 and P{PZ}Aph-4⁰⁷⁰²⁸&P{PZ}dco^rK215

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-102

(FlyBase, 2016)

3-98.8

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (2)

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

VDRC

v102136

P{KK110883}VIE-260B

v10263

w¹¹¹⁸; P{GD3136}v10263

Genomic Clones (10)

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

cDNA Clones (1)

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

AT31946

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.

FBgn0062411

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0062411

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Steiger et al., 2010)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Ctr1C is a copper transporter present in the male germline and mutations in Ctr1C can affect male fertility.

(Steiger et al., 2010)

Ctr1C can functionally replace Ctr1A.

(Steiger et al., 2010)

Relationship to Other Genes

Source for database merge of

Source for merge of: Ctr1C CG15551

(Zhou et al., 2003)

Source for merge of: CG15551 BcDNA:AT31946

(FlyBase, 1996-)

Additional comments

The Ctr1C gene may have been derived from the Ctr1A gene by retroposition.

(Steiger et al., 2010, Pan and Zhang, 2009)

Source for merge of CG15551 BcDNA:AT31946 was a shared cDNA ( date:030728 ).

(FlyBase, 1996-)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (5)

Reported As

Symbol Synonym

BcDNA:AT31946

CG15551

(Keleman et al., 2009.8.5, Pan and Zhang, 2009, Pan and Zhang, 2009, Zhou et al., 2003)

Ctr1C

(Slobodian et al., 2021, Yu et al., 2021, Jeon et al., 2020, Calap-Quintana et al., 2017, Bouleau and Tricoire, 2015, Bischof and FlyORF project members, 2014.6.20, dos Santos, 2014, Armstrong et al., 2013, Lang et al., 2013, Japanese National Institute of Genetics, 2012.5.21, Hua et al., 2010, Steiger et al., 2010, Norgate et al., 2007, Yepiskoposyan et al., 2006)

FBgn0039813

Name Synonyms

Copper transporter 1C

(Zhou et al., 2002)

Secondary FlyBase IDs

FBgn0039813
FBgn0061424

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 29 )

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.

43668

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.

Q9VA22

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

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.

Q9VA22

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

43668/tissue=All

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

FBgn0062411

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

FBgn0062411

FlyMine - An integrated database for Drosophila genomics

FBgn0062411

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

Ctr copper transporter

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

dme:Dmel_CG15551

MARRVEL_MODEL - MARRVEL (model organism gene)

43668

Linkouts

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

FBgn0062411

DroID - A comprehensive database of gene and protein interactions.

FBgn0062411

DRSC - Results frm RNAi screens

FBgn0062411

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

Ctr1C_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0062411

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0062411

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

CG15551

Flygut - An atlas of the Drosophila adult midgut

FBgn0062411

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

TC004460

MIST (genetic) - An integrated Molecular Interaction Database

43668

References (39)

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

4.71

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