FB2022_03, released June 9, 2022

Gene: Dmel\Ctr1C

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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
Key Links
Genomic Location
Cytogenetic map
100B1-100B1
Sequence location
Recombination map
3-102
RefSeq locus
NT_033777 REGION:30963290..30964320
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (8 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 biological aspect of ancestor with PANTHER:PTN000280760
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (5 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 (2 terms)
CV Term
Evidence
References
involved_in cellular copper ion homeostasis
inferred from biological aspect of ancestor with PANTHER:PTN000280760
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in copper ion transmembrane transport
inferred from electronic annotation with InterPro:IPR007274
(assigned by InterPro )
(FlyBase Curators et al., 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 (2 terms)
CV Term
Evidence
References
located_in integral component of membrane
inferred from electronic annotation with InterPro:IPR007274
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
is_active_in plasma membrane
inferred from biological aspect of ancestor with PANTHER:PTN000280760
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
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]
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
1
Number of Unique Polypeptides
1

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 New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VA22)

If you don't see the viewer to the right, 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.

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
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.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
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

GBrowse - Visual display of RNA-Seq signals

View Dmel\Ctr1C in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
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 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\SLC31A1
9 of 15
Yes
No
1  
Hsap\SLC31A2
7 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Slc31a1
8 of 15
Yes
No
Mmus\Slc31a2
8 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Slc31a1
7 of 13
Yes
No
Rnor\Slc31a2
6 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\slc31a2
6 of 12
Yes
Yes
Xtro\slc31a1
4 of 12
No
No
Danio rerio (Zebrafish) (2)
Drer\slc31a1
8 of 15
Yes
No
Drer\slc31a2
6 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (10)
Cele\F27C1.2
11 of 15
Yes
No
Cele\F01G12.1
9 of 15
No
Yes
Cele\Y58A7A.1
7 of 15
No
Yes
Cele\F31E8.4
6 of 15
No
Yes
Cele\F58G6.3
6 of 15
No
No
Cele\F58G6.9
5 of 15
No
No
Cele\K12C11.3
5 of 15
No
Yes
Cele\K12C11.6
5 of 15
No
No
Cele\K12C11.7
4 of 15
No
No
Cele\F58G6.7
3 of 15
No
No
Arabidopsis thaliana (thale-cress) (6)
Atha\COPT3
6 of 9
Yes
Yes
Atha\COPT1
5 of 9
No
Yes
Atha\COPT2
5 of 9
No
Yes
Atha\COPT5
5 of 9
No
No
Atha\COPT6
5 of 9
No
Yes
Atha\COPT4
3 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (3)
Scer\CTR2
11 of 15
Yes
Yes
Scer\CTR3
5 of 15
No
Yes
Scer\CTR1
1 of 15
No
Yes
Schizosaccharomyces pombe (Fission yeast) (3)
Spom\ctr6
8 of 12
Yes
No
Spom\ctr4
3 of 12
No
Yes
Spom\ctr5
3 of 12
No
Yes
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (2)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Ctr1A
9 of 10
Ctr1B
8 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    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
    Ctr1CdsRNA.UAS.cLa
    ameliorates  Alzheimer's disease
    modeled by Hsap\APPAβ42.UAS.Tag:SS(rPENK)
    (Lang et al., 2013)
    Disease Associations of Human Orthologs (via DIOPT v8.0 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
    9 of 15
    603085
         
        SLC31A2; solute carrier family 31 member 2
        7 of 15
        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
            Interactions Browser
            Summary of Genetic Interactions
            esyN Network Diagram
            esyN Network Key:
            Suppression
            Enhancement
            View in Interactions Browser
            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.
            MIST (genetic) - An integrated Molecular Interaction Database
            Pathways
            Signaling Pathways (FlyBase)
            Metabolic Pathways
            External Data
            Linkouts
            Genomic Location and Detailed Mapping Data
            Chromosome (arm)
            3R
            Recombination map
            3-102
            Cytogenetic map
            100B1-100B1
            Sequence location
            FlyBase Computed Cytological Location
            Cytogenetic map
            Evidence for location
            100B1-100B1
            Limits computationally determined from genome sequence between P{lacW}l(3)s2500s2500 and P{PZ}Aph-407028&P{PZ}dcorK215
            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)
            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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

            cDNA clones, fully sequenced
            BDGP DGC clones
            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.

              cDNA Clones, End Sequenced (ESTs)
              BDGP DGC clones
                Other clones
                  RNAi and Array Information
                  Linkouts
                  DRSC - Results frm RNAi screens
                  GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                  Antibody Information
                  Laboratory Generated Antibodies
                   

                  polyclonal

                  (Steiger et al., 2010)
                  Commercially Available Antibodies
                   
                  Other Information
                  Relationship to Other Genes
                  Source for database identify of
                  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-)
                  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)
                  Origin and Etymology
                  Discoverer
                  Etymology
                  Identification
                  External Crossreferences and Linkouts ( 30 )
                  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.
                  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.
                  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.
                  Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                  DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
                  EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
                  Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                  FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                  FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
                  Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
                  Flygut - An atlas of the Drosophila adult midgut
                  GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
                  InterPro - A database of protein families, domains and functional sites
                  KEGG Genes - Molecular building blocks of life in the genomic space.
                  MARRVEL_MODEL - MARRVEL (model organism gene)
                  modMine - A data warehouse for the modENCODE project
                  Linkouts
                  DroID - A comprehensive database of gene and protein interactions.
                  DRSC - Results frm RNAi screens
                  FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                  FlyMine - An integrated database for Drosophila genomics
                  MIST (genetic) - An integrated Molecular Interaction Database
                  Synonyms and Secondary IDs (5)
                  Datasets (0)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  Study result (0)
                  Result
                  Result Type
                  Title
                  References (37)