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

    Gene ID: 54980, updated on 10-Dec-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, Dec 2024]
    Expression
    Broad expression in testis (RPKM 23.4), lymph node (RPKM 3.5) and 21 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (70149885..70191019, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (70161627..70202761, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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