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C20orf173 chromosome 20 open reading frame 173 [ Homo sapiens (human) ]

Gene ID: 140873, updated on 2-Nov-2024

Summary

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Official Symbol
C20orf173provided by HGNC
Official Full Name
chromosome 20 open reading frame 173provided by HGNC
Primary source
HGNC:HGNC:16166
See related
Ensembl:ENSG00000125975 AllianceGenome:HGNC:16166
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
Also known as
dJ477O4.4
Summary
Predicted to enable beta-galactoside (CMP) alpha-2,3-sialyltransferase activity. Predicted to be involved in ganglioside biosynthetic process via lactosylceramide; protein glycosylation; and sialylation. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Restricted expression toward testis (RPKM 5.0) See more
Orthologs
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Genomic context

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See C20orf173 in Genome Data Viewer
Location:
20q11.22
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35520741..35529652, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37241634..37250546, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34108569..34117481, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene growth differentiation factor 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17783 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12858 Neighboring gene microRNA 1289-1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12859 Neighboring gene centrosomal protein 250 Neighboring gene CEP250 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17786 Neighboring gene ERGIC and golgi 3 Neighboring gene ribosomal protein L36 pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:34145795-34145976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:34146815-34147316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:34147317-34147816 Neighboring gene fer-1 like family member 4 (pseudogene) Neighboring gene ReSE screen-validated silencer GRCh37_chr20:34164928-34165090 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:34176389-34176889 Neighboring gene ribosomal protein L37 pseudogene 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 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 CRISPR screens using isogenic cells reveal vulnerabilities conferred by loss of tumor suppressors. Feng X, et al. Sci Adv, 2022 May 13. PMID 35559673, Free PMC Article
  2. The DNA sequence and comparative analysis of human chromosome 20. Deloukas P, et al. Nature, 2001 Dec 20-27. PMID 11780052
  3. The sequence of the human genome. Venter JC, et al. Science, 2001 Feb 16. PMID 11181995
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

See all (9) 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

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

  • FLJ25360, MGC138265, MGC138267

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables beta-galactoside (CMP) alpha-2,3-sialyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in ganglioside biosynthetic process via lactosylceramide IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein glycosylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sialylation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
uncharacterized protein C20orf173

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_001145350.2 → NP_001138822.1  uncharacterized protein C20orf173 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the protein.
    Source sequence(s)
    FO393401
    Consensus CDS
    CCDS46594.1
    UniProtKB/Swiss-Prot
    Q96LM9
    Related
    ENSP00000403566.1, ENST00000444723.3

RNA

  1. NR_026933.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate 3' splice pattern, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK310337, DV080387, DW009696, FO393401

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    35520741..35529652 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439907.1 → XP_047295863.1  uncharacterized protein C20orf173 isoform X1

  2. XM_047439906.1 → XP_047295862.1  uncharacterized protein C20orf173 isoform X1

  3. XM_047439904.1 → XP_047295860.1  uncharacterized protein C20orf173 isoform X1

  4. XM_047439905.1 → XP_047295861.1  uncharacterized protein C20orf173 isoform X1

  5. XM_047439908.1 → XP_047295864.1  uncharacterized protein C20orf173 isoform X1

  6. XM_047439909.1 → XP_047295865.1  uncharacterized protein C20orf173 isoform X1

  7. XM_047439910.1 → XP_047295866.1  uncharacterized protein C20orf173 isoform X2

  8. XM_047439911.1 → XP_047295867.1  uncharacterized protein C20orf173 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    37241634..37250546 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054323031.1 → XP_054179006.1  uncharacterized protein C20orf173 isoform X1

  2. XM_054323030.1 → XP_054179005.1  uncharacterized protein C20orf173 isoform X1

  3. XM_054323028.1 → XP_054179003.1  uncharacterized protein C20orf173 isoform X1

  4. XM_054323029.1 → XP_054179004.1  uncharacterized protein C20orf173 isoform X1

  5. XM_054323032.1 → XP_054179007.1  uncharacterized protein C20orf173 isoform X1

  6. XM_054323033.1 → XP_054179008.1  uncharacterized protein C20orf173 isoform X1

  7. XM_054323034.1 → XP_054179009.1  uncharacterized protein C20orf173 isoform X2

  8. XM_054323035.1 → XP_054179010.1  uncharacterized protein C20orf173 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_080828.1: Suppressed sequence

    Description
    NM_080828.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96LM9.1 GenPept UniProtKB/Swiss-Prot:Q96LM9

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