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C2orf42 chromosome 2 open reading frame 42 [ Homo sapiens (human) ]

Gene ID: 54980, updated on 5-Mar-2024

Summary

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Official Symbol
C2orf42provided by HGNC
Official Full Name
chromosome 2 open reading frame 42provided by HGNC
Primary source
HGNC:HGNC:26056
See related
Ensembl:ENSG00000115998 AllianceGenome:HGNC:26056
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 23.4), lymph node (RPKM 3.5) and 21 other tissues See more
Orthologs
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Genomic context

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See C2orf42 in Genome Data Viewer
Location:
2p13.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (70149885..70191019, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (70161627..70202761, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (70377017..70418151, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15991 Neighboring gene mitochondrial ribosomal protein L36 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15994 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70350131-70350936 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70350937-70351742 Neighboring gene Sharpr-MPRA regulatory region 3961 Neighboring gene long intergenic non-protein coding RNA 1816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70365403-70365944 Neighboring gene Sharpr-MPRA regulatory region 12614 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70368111-70368650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15999 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70376065-70376594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16004 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:70418013-70418598 Neighboring gene TIA1 cytotoxic granule associated RNA binding protein Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70474526-70475341 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70475342-70476156 Neighboring gene tRNA-Gly (anticodon CCC) 2-1

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. Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. Navarini AA, et al. Nat Commun, 2014 Jun 13. PMID 24927181
  2. Charting the landscape of tandem BRCT domain-mediated protein interactions. Woods NT, et al. Sci Signal, 2012 Sep 18. PMID 22990118, Free PMC Article
  3. Transcriptome analysis of human gastric cancer. Oh JH, et al. Mamm Genome, 2005 Dec. PMID 16341674
  4. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
  5. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

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

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

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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Homology

Clone Names

  • FLJ20558

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
uncharacterized protein C2orf42

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_001348758.2 → NP_001335687.1  uncharacterized protein C2orf42

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1-8 all encode the same protein.
    Source sequence(s)
    AC016700
    Consensus CDS
    CCDS1899.1
    UniProtKB/Swiss-Prot
    D6W5G3, Q9H629, Q9NWW7
    Conserved Domains (1) summary
    pfam14952
    Location:16 → 57
    zf-tcix; Putative treble-clef, zinc-finger, Zn-binding

  2. NM_001348759.2 → NP_001335688.1  uncharacterized protein C2orf42

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-8 all encode the same protein.
    Source sequence(s)
    AC016700
    Consensus CDS
    CCDS1899.1
    UniProtKB/Swiss-Prot
    D6W5G3, Q9H629, Q9NWW7
    Conserved Domains (1) summary
    pfam14952
    Location:16 → 57
    zf-tcix; Putative treble-clef, zinc-finger, Zn-binding

  3. NM_001348760.2 → NP_001335689.1  uncharacterized protein C2orf42

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1-8 all encode the same protein.
    Source sequence(s)
    AC016700
    Consensus CDS
    CCDS1899.1
    UniProtKB/Swiss-Prot
    D6W5G3, Q9H629, Q9NWW7
    Conserved Domains (1) summary
    pfam14952
    Location:16 → 57
    zf-tcix; Putative treble-clef, zinc-finger, Zn-binding

  4. NM_001348761.2 → NP_001335690.1  uncharacterized protein C2orf42

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1-8 all encode the same protein.
    Source sequence(s)
    AC016700
    Consensus CDS
    CCDS1899.1
    UniProtKB/Swiss-Prot
    D6W5G3, Q9H629, Q9NWW7
    Conserved Domains (1) summary
    pfam14952
    Location:16 → 57
    zf-tcix; Putative treble-clef, zinc-finger, Zn-binding

  5. NM_001348762.2 → NP_001335691.1  uncharacterized protein C2orf42

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1-8 all encode the same protein.
    Source sequence(s)
    AC016700
    Consensus CDS
    CCDS1899.1
    UniProtKB/Swiss-Prot
    D6W5G3, Q9H629, Q9NWW7
    Related
    ENSP00000404515.1, ENST00000420306.1
    Conserved Domains (1) summary
    pfam14952
    Location:16 → 57
    zf-tcix; Putative treble-clef, zinc-finger, Zn-binding

  6. NM_001348763.2 → NP_001335692.1  uncharacterized protein C2orf42

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1. Variants 1-8 all encode the same protein.
    Source sequence(s)
    AC016700
    Consensus CDS
    CCDS1899.1
    UniProtKB/Swiss-Prot
    D6W5G3, Q9H629, Q9NWW7
    Conserved Domains (1) summary
    pfam14952
    Location:16 → 57
    zf-tcix; Putative treble-clef, zinc-finger, Zn-binding

  7. NM_001348764.2 → NP_001335693.1  uncharacterized protein C2orf42

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1. Variants 1-8 all encode the same protein.
    Source sequence(s)
    AC016700
    Consensus CDS
    CCDS1899.1
    UniProtKB/Swiss-Prot
    D6W5G3, Q9H629, Q9NWW7
    Conserved Domains (1) summary
    pfam14952
    Location:16 → 57
    zf-tcix; Putative treble-clef, zinc-finger, Zn-binding

  8. NM_017880.3 → NP_060350.1  uncharacterized protein C2orf42

    See identical proteins and their annotated locations for NP_060350.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-8 all encode the same protein.
    Source sequence(s)
    AK000565
    Consensus CDS
    CCDS1899.1
    UniProtKB/Swiss-Prot
    D6W5G3, Q9H629, Q9NWW7
    Related
    ENSP00000264434.2, ENST00000264434.7
    Conserved Domains (1) summary
    pfam14952
    Location:16 → 57
    zf-tcix; Putative treble-clef, zinc-finger, Zn-binding

RNA

  1. NR_145967.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC016700

  2. NR_145968.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC016700

  3. NR_145969.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC016700

  4. NR_145970.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC016700

  5. NR_145971.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC016700

  6. NR_145972.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC016700

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    70149885..70191019 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444838.1 → XP_047300794.1  uncharacterized protein C2orf42 isoform X1

    UniProtKB/Swiss-Prot
    D6W5G3, Q9H629, Q9NWW7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    70161627..70202761 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342685.1 → XP_054198660.1  uncharacterized protein C2orf42 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NWW7.1 GenPept UniProtKB/Swiss-Prot:Q9NWW7

Gene LinkOut

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