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

Gene ID: 84077, updated on 5-Mar-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, Apr 2022]
Expression
Broad expression in testis (RPKM 2.5), bone marrow (RPKM 0.5) and 17 other tissues See more
Orthologs
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Genomic context

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Location:
3p25.1
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (14675141..14773036)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (14677557..14775453)
105.20220307 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
  • 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 (14) 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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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

  • DKFZp434N1817

Gene Ontology Provided by GOA

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_2023_10

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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