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    C3orf20 chromosome 3 open reading frame 20 [ Homo sapiens (human) ]

    Gene ID: 84077, updated on 2-Nov-2024

    Summary

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    Official Symbol
    C3orf20provided by HGNC
    Official Full Name
    chromosome 3 open reading frame 20provided by HGNC
    Primary source
    HGNC:HGNC:25320
    See related
    Ensembl:ENSG00000131379 MIM:619992; AllianceGenome:HGNC:25320
    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 cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 2.5), bone marrow (RPKM 0.5) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C3orf20 in Genome Data Viewer
    Location:
    3p25.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (14675141..14773036)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (14677557..14775453)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (14716648..14814543)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909347 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:14692810-14693468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19515 Neighboring gene uncharacterized LOC124906215 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:14712491-14713690 Neighboring gene coiled-coil domain containing 174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19517 Neighboring gene MPRA-validated peak4545 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19521 Neighboring gene meiotic recombination hotspot H Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14838036-14838969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14845672-14846414 Neighboring gene long intergenic non-protein coding RNA 2011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14852491-14852991 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:14855464-14855666 Neighboring gene FYVE, RhoGEF and PH domain containing 5 Neighboring gene Sharpr-MPRA regulatory region 8692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14905091-14905672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14920327-14920828 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14941355-14942238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:14942239-14943121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14955453-14956275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14956276-14957097 Neighboring gene uncharacterized LOC105376963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:14962633-14963132 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:14963648-14964847

    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 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. Associations between the C3orf20 rs12496846 Polymorphism and Both Postoperative Analgesia after Orthognathic and Abdominal Surgeries and C3orf20 Gene Expression in the Brain. Nishizawa D, et al. Pharmaceutics, 2022 Mar 28. PMID 35456561, Free PMC Article
    2. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. Simpson JC, et al. EMBO Rep, 2000 Sep. PMID 11256614, Free PMC Article
    3. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article
    4. From ORFeome to biology: a functional genomics pipeline. Wiemann S, et al. Genome Res, 2004 Oct. PMID 15489336, Free PMC Article
    5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Wiemann S, et al. Genome Res, 2001 Mar. PMID 11230166, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp434N1817

    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 cytoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    uncharacterized protein C3orf20

    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_001184957.2 → NP_001171886.1  uncharacterized protein C3orf20 isoform 2

      See identical proteins and their annotated locations for NP_001171886.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Both variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AC090957, AL136781, BC038406, DB064418
      Consensus CDS
      CCDS54555.1
      Related
      ENSP00000396081.1, ENST00000412910.1
      Conserved Domains (1) summary
      pfam14977
      Location:239 → 442
      FAM194; FAM194 protein

    2. NM_001184958.2 → NP_001171887.1  uncharacterized protein C3orf20 isoform 2

      See identical proteins and their annotated locations for NP_001171887.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1. Both variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AC090957, BC030599, BC038406, BG718869, DB064418
      Consensus CDS
      CCDS54555.1
      Related
      ENSP00000402933.1, ENST00000435614.5
      Conserved Domains (1) summary
      pfam14977
      Location:239 → 442
      FAM194; FAM194 protein

    3. NM_032137.5 → NP_115513.4  uncharacterized protein C3orf20 isoform 1

      See identical proteins and their annotated locations for NP_115513.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC090957, BC038406, DB064418
      Consensus CDS
      CCDS33706.1
      UniProtKB/Swiss-Prot
      Q7L0U6, Q8NCP2, Q8ND61, Q9H0I7
      Related
      ENSP00000253697.3, ENST00000253697.8
      Conserved Domains (1) summary
      pfam14977
      Location:361 → 564
      FAM194; FAM194 protein

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      14675141..14773036
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006713341.3 → XP_006713404.1  uncharacterized protein C3orf20 isoform X1

      See identical proteins and their annotated locations for XP_006713404.1

      Conserved Domains (1) summary
      pfam14977
      Location:361 → 564
      FAM194; FAM194 protein

    2. XM_011534153.4 → XP_011532455.1  uncharacterized protein C3orf20 isoform X1

      See identical proteins and their annotated locations for XP_011532455.1

      Conserved Domains (1) summary
      pfam14977
      Location:361 → 564
      FAM194; FAM194 protein

    3. XM_006713342.2 → XP_006713405.1  uncharacterized protein C3orf20 isoform X1

      See identical proteins and their annotated locations for XP_006713405.1

      Conserved Domains (1) summary
      pfam14977
      Location:361 → 564
      FAM194; FAM194 protein

    4. XM_011534154.4 → XP_011532456.1  uncharacterized protein C3orf20 isoform X2

      Conserved Domains (1) summary
      pfam14977
      Location:239 → 442
      FAM194; FAM194 protein

    5. XM_006713343.3 → XP_006713406.1  uncharacterized protein C3orf20 isoform X3

      Conserved Domains (1) summary
      pfam14977
      Location:361 → 564
      FAM194; FAM194 protein

    6. XM_011534158.3 → XP_011532460.1  uncharacterized protein C3orf20 isoform X6

      Conserved Domains (1) summary
      pfam14977
      Location:361 → 539
      FAM194; FAM194 protein

    7. XM_017007310.2 → XP_016862799.1  uncharacterized protein C3orf20 isoform X5

    8. XM_011534157.3 → XP_011532459.1  uncharacterized protein C3orf20 isoform X4

      Conserved Domains (1) summary
      pfam14977
      Location:57 → 260
      FAM194; FAM194 protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      14677557..14775453
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348072.1 → XP_054204047.1  uncharacterized protein C3orf20 isoform X1

    2. XM_054348074.1 → XP_054204049.1  uncharacterized protein C3orf20 isoform X1

    3. XM_054348073.1 → XP_054204048.1  uncharacterized protein C3orf20 isoform X1

    4. XM_054348075.1 → XP_054204050.1  uncharacterized protein C3orf20 isoform X2

    5. XM_054348077.1 → XP_054204052.1  uncharacterized protein C3orf20 isoform X3

    6. XM_054348080.1 → XP_054204055.1  uncharacterized protein C3orf20 isoform X6

    7. XM_054348079.1 → XP_054204054.1  uncharacterized protein C3orf20 isoform X5

    8. XM_054348076.1 → XP_054204051.1  uncharacterized protein C3orf20 isoform X7

    9. XM_054348078.1 → XP_054204053.1  uncharacterized protein C3orf20 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8ND61.2 GenPept UniProtKB/Swiss-Prot:Q8ND61

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