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C18orf21 chromosome 18 open reading frame 21 [ Homo sapiens (human) ]

Gene ID: 83608, updated on 3-Apr-2024

Summary

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Official Symbol
C18orf21provided by HGNC
Official Full Name
chromosome 18 open reading frame 21provided by HGNC
Primary source
HGNC:HGNC:28802
See related
Ensembl:ENSG00000141428 AllianceGenome:HGNC:28802
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
XTP13; HsT3108; PNAS-124; PNAS-131
Expression
Ubiquitous expression in testis (RPKM 16.8), bone marrow (RPKM 16.7) and 25 other tissues See more
Orthologs
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Genomic context

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See C18orf21 in Genome Data Viewer
Location:
18q12.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (35972679..35979278)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (36164179..36170780)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (33552642..33559241)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr18:33522236-33522395 Neighboring gene microRNA 3929 Neighboring gene uncharacterized LOC105372066 Neighboring gene Sharpr-MPRA regulatory region 2053 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33552432-33553324 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:33564018-33565217 Neighboring gene regulation of nuclear pre-mRNA domain containing 1A Neighboring gene Sharpr-MPRA regulatory region 15530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:33647245-33647760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:33664612-33665166 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:33666275-33666828 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:33678780-33678940 Neighboring gene solute carrier family 39 member 6 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33709101-33709606

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. Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes. Behr ER, et al. PLoS One, 2013. PMID 24223155, Free PMC Article
  2. A whole genome screen for HIV restriction factors. Liu L, et al. Retrovirology, 2011 Nov 14. PMID 22082156, Free PMC Article
  3. Spindle Assembly Checkpoint Inhibition Can Resensitize p53-Null Stem Cells to Cancer Chemotherapy. Liu C, et al. Cancer Res, 2019 May 1. PMID 30862715, Free PMC Article
  4. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Beausoleil SA, et al. Nat Biotechnol, 2006 Oct. PMID 16964243
  5. SMYD3 Impedes Small Cell Lung Cancer Sensitivity to Alkylation Damage through RNF113A Methylation-Phosphorylation Cross-talk. Lukinović V, et al. Cancer Discov, 2022 Sep 2. PMID 35819319, Free PMC Article

See all (22) 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 analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes.
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)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of chromosome 18 open reading frame 21 (C18orf21) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC131953

General protein information

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Preferred Names
UPF0711 protein C18orf21
Names
HBV X-transactivated gene 13 protein
HBV X-transactivated protein 13
HBV XAg-transactivated protein 13

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_001201474.2 → NP_001188403.1  UPF0711 protein C18orf21 isoform b

    See identical proteins and their annotated locations for NP_001188403.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AA648431, AW967900, BC108730, W84353
    Consensus CDS
    CCDS56064.1
    UniProtKB/TrEMBL
    L7N2F3
    Related
    ENSP00000480486.1, ENST00000610527.4
    Conserved Domains (1) summary
    pfam15719
    Location:1 → 126
    DUF4674; Domain of unknown function (DUF4674)

  2. NM_001201475.2 → NP_001188404.1  UPF0711 protein C18orf21 isoform b

    See identical proteins and their annotated locations for NP_001188404.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AA648431, BC025950, BC108730, W84353
    Consensus CDS
    CCDS56064.1
    UniProtKB/TrEMBL
    L7N2F3
    Related
    ENSP00000329492.5, ENST00000333234.5
    Conserved Domains (1) summary
    pfam15719
    Location:1 → 126
    DUF4674; Domain of unknown function (DUF4674)

  3. NM_001201476.2 → NP_001188405.1  UPF0711 protein C18orf21 isoform c

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon compared to variant 1, that causes a frameshift. The resulting isoform (c) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    DN991579, W84353
    Consensus CDS
    CCDS74212.1
    UniProtKB/TrEMBL
    A0A087X0E7
    Related
    ENSP00000483334.1, ENST00000618334.1
    Conserved Domains (1) summary
    pfam15719
    Location:27 → 100
    DUF4674; Domain of unknown function (DUF4674)

  4. NM_031446.5 → NP_113634.3  UPF0711 protein C18orf21 isoform a

    See identical proteins and their annotated locations for NP_113634.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AA648431, BC108730
    Consensus CDS
    CCDS11916.2
    UniProtKB/Swiss-Prot
    Q32NC0, Q6GW03, Q9BXV6, Q9BXW2
    UniProtKB/TrEMBL
    Q8TBS0
    Related
    ENSP00000465517.1, ENST00000592875.6
    Conserved Domains (1) summary
    pfam15719
    Location:27 → 214
    DUF4674; Domain of unknown function (DUF4674)

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    35972679..35979278
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005258364.6 → XP_005258421.1  UPF0711 protein C18orf21 isoform X1

    UniProtKB/TrEMBL
    Q8TBS0
    Conserved Domains (1) summary
    pfam15719
    Location:33 → 220
    DUF4674; Domain of unknown function (DUF4674)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    36164179..36170780
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319255.1 → XP_054175230.1  UPF0711 protein C18orf21 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q32NC0.1 GenPept UniProtKB/Swiss-Prot:Q32NC0

Gene LinkOut

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