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

    Gene ID: 140873, updated on 28-Oct-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, Oct 2024]
    Expression
    Restricted expression toward testis (RPKM 5.0) See more
    Orthologs
    mouse all
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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

    Gene LinkOut

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

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