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SLC35C2 solute carrier family 35 member C2 [ Homo sapiens (human) ]

Gene ID: 51006, updated on 7-Apr-2024

Summary

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Official Symbol
SLC35C2provided by HGNC
Official Full Name
solute carrier family 35 member C2provided by HGNC
Primary source
HGNC:HGNC:17117
See related
Ensembl:ENSG00000080189 MIM:619530; AllianceGenome:HGNC:17117
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CGI-15; OVCOV1; C20orf5; BA394O2.1
Summary
This gene encodes a member of the triose-phosphate transporter protein family. This gene is regulated by oxygen tension, is induced in hypoxic trophoblast cells, and is overexpressed in ovarian cancer. Alternative splicing results in multiple transcript variants. A pseudogene of this gene has been defined on the X chromosome. [provided by RefSeq, Jul 2013]
Expression
Ubiquitous expression in testis (RPKM 9.5), placenta (RPKM 9.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
20q13.12
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (46345984..46364425, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (48082033..48100454, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (44974623..44993064, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-FlowFISH-validated CD40 regulatory element GRCh37_chr20:44746135-44748232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44781551-44782092 Neighboring gene CD40 molecule Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12973 Neighboring gene uncharacterized LOC124904916 Neighboring gene cadherin 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17968 Neighboring gene Sharpr-MPRA regulatory region 13247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44844486-44845022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44845561-44846096 Neighboring gene MPRA-validated peak4226 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44886736-44887236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44928578-44929078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44929079-44929579 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:44932028-44932246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44941853-44942801 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:44952422-44952611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44966161-44966662 Neighboring gene Sharpr-MPRA regulatory region 3506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44979919-44980510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44980511-44981101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44985189-44985688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12974 Neighboring gene uncharacterized LOC124904917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17971 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:45022873-45023372 Neighboring gene engulfment and cell motility 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr20:45034435-45035064 and GRCh37_chr20:45035065-45035694 Neighboring gene uncharacterized LOC105372633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17973 Neighboring gene NANOG hESC enhancer GRCh37_chr20:45052681-45053240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17974

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Oxygen as a regulator of cellular phenotypes in pregnancy and cancer. Lash GE, et al. Can J Physiol Pharmacol, 2002 Feb. PMID 11934252
  2. Assignment of OVCOV1 (alias CGI-15) to human chromosome 20 band q13.1-->q13.2 by fluorescent in situ hybridization. Leach R, et al. Cytogenet Cell Genet, 2001. PMID 11856893
  3. Whole-body gene expression by data mining. Pires Martins R, et al. Genomics, 2001 Feb 15. PMID 11247664
  4. Identification, molecular characterization, and tissue expression of OVCOV1. Leach RE, et al. Mamm Genome, 2002 Nov. PMID 12461647
  5. Slc35c2 promotes Notch1 fucosylation and is required for optimal Notch signaling in mammalian cells. Lu L, et al. J Biol Chem, 2010 Nov 12. PMID 20837470, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. In vivo evidence for GDP-fucose transport in the absence of transporter SLC35C1 and putative transporter SLC35C2.
    Title: In vivo evidence for GDP-fucose transport in the absence of transporter SLC35C1 and putative transporter SLC35C2.
  2. Assignment of OVCOV1 (alias CGI-15) to human chromosome 20 band q13.1-->q13.2 by fluorescent in situ hybridization
    Title: Assignment of OVCOV1 (alias CGI-15) to human chromosome 20 band q13.1-->q13.2 by fluorescent in situ hybridization.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ37039, FLJ46434, MGC20633, MGC32079, MGC39183

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in UDP-glucose transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in protein O-linked fucosylation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
is_active_in cis-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cis-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum-Golgi intermediate compartment IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum-Golgi intermediate compartment IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum-Golgi intermediate compartment membrane IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
solute carrier family 35 member C2
Names
ovarian cancer-overexpressed gene 1 protein
solute carrier family 35 (GDP-fucose transporter), member C2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001281457.2 → NP_001268386.1  solute carrier family 35 member C2 isoform c

    See identical proteins and their annotated locations for NP_001268386.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AL133227, BC021138, BM666377, DA820126, DB246755
    UniProtKB/TrEMBL
    B7Z6F2
    Conserved Domains (1) summary
    cd21092
    Location:1 → 213
    TPT_S35C2; solute carrier family 35 member C2, member of the triose-phosphate transporter family

  2. NM_001281458.2 → NP_001268387.1  solute carrier family 35 member C2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (d) has a longer and distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AK301022, AL133227, BC021138, BM666377, DA820126
    Consensus CDS
    CCDS63292.1
    UniProtKB/Swiss-Prot
    Q9NQQ7
    Related
    ENSP00000318960.9, ENST00000317734.12
    Conserved Domains (1) summary
    pfam03151
    Location:45 → 342
    TPT; Triose-phosphate Transporter family

  3. NM_001281459.2 → NP_001268388.1  solute carrier family 35 member C2 isoform e

    See identical proteins and their annotated locations for NP_001268388.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has multiple differences in the 5' UTR and 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (e) is shorter, compared to isoform a.
    Source sequence(s)
    AL133227, BC021138, BI831689, BM666377, DA820126
    UniProtKB/TrEMBL
    B7Z6F2, B7Z6R4
    Conserved Domains (1) summary
    cd21092
    Location:1 → 192
    TPT_S35C2; solute carrier family 35 member C2, member of the triose-phosphate transporter family

  4. NM_001281460.2 → NP_001268389.1  solute carrier family 35 member C2 isoform a

    See identical proteins and their annotated locations for NP_001268389.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 7 encode the same isoform (a).
    Source sequence(s)
    AL133227, BC025277, BM666377, DA820126, DB023133
    Consensus CDS
    CCDS13396.1
    UniProtKB/Swiss-Prot
    B7Z6V6, E1P5T0, Q53GK3, Q5JW05, Q96CJ8, Q9NQQ7, Q9Y304
    Related
    ENSP00000361301.1, ENST00000372227.5
    Conserved Domains (1) summary
    cd21092
    Location:80 → 327
    TPT_S35C2; solute carrier family 35 member C2, member of the triose-phosphate transporter family

  5. NM_015945.12 → NP_057029.8  solute carrier family 35 member C2 isoform a

    See identical proteins and their annotated locations for NP_057029.8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 7 encode the same isoform (a).
    Source sequence(s)
    AK222928, AL133227, BC014191, BM666377, DA820126
    Consensus CDS
    CCDS13396.1
    UniProtKB/Swiss-Prot
    B7Z6V6, E1P5T0, Q53GK3, Q5JW05, Q96CJ8, Q9NQQ7, Q9Y304
    Related
    ENSP00000361304.5, ENST00000372230.10
    Conserved Domains (1) summary
    cd21092
    Location:80 → 327
    TPT_S35C2; solute carrier family 35 member C2, member of the triose-phosphate transporter family

  6. NM_173073.4 → NP_775096.1  solute carrier family 35 member C2 isoform b

    See identical proteins and their annotated locations for NP_775096.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (b) is shorter, compared to isoform a.
    Source sequence(s)
    AL133227, BC014191, BM666377, DA820126
    Consensus CDS
    CCDS13397.1
    UniProtKB/Swiss-Prot
    Q9NQQ7
    Related
    ENSP00000439974.2, ENST00000543605.5
    Conserved Domains (1) summary
    cl26744
    Location:16 → 292
    TPT; Triose-phosphate Transporter family

  7. NM_173179.4 → NP_775271.1  solute carrier family 35 member C2 isoform a

    See identical proteins and their annotated locations for NP_775271.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a. Variants 1, 2, and 7 encode the same isoform.
    Source sequence(s)
    AL133227, BC021138, BM666377, DA820126
    Consensus CDS
    CCDS13396.1
    UniProtKB/Swiss-Prot
    B7Z6V6, E1P5T0, Q53GK3, Q5JW05, Q96CJ8, Q9NQQ7, Q9Y304
    Related
    ENSP00000243896.2, ENST00000243896.6
    Conserved Domains (1) summary
    cd21092
    Location:80 → 327
    TPT_S35C2; solute carrier family 35 member C2, member of the triose-phosphate transporter family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    46345984..46364425 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    48082033..48100454 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NQQ7.2 GenPept UniProtKB/Swiss-Prot:Q9NQQ7

Gene LinkOut

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