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C1orf54 chromosome 1 open reading frame 54 [ Homo sapiens (human) ]

Gene ID: 79630, updated on 5-Mar-2024

Summary

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Official Symbol
C1orf54provided by HGNC
Official Full Name
chromosome 1 open reading frame 54provided by HGNC
Primary source
HGNC:HGNC:26258
See related
Ensembl:ENSG00000118292 AllianceGenome:HGNC:26258
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
Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in spleen (RPKM 18.0), lymph node (RPKM 10.9) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
1q21.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (150268731..150280924)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (149393648..149405849)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150244687..150253335)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150208844-150209411 Neighboring gene RNA, U2 small nuclear 17, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150228359-150229053 Neighboring gene carbonic anhydrase 14 Neighboring gene small nucleolar RNA, C/D box 13C Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:150241516-150242127 Neighboring gene uncharacterized LOC124904414 Neighboring gene aph-1 homolog A, gamma-secretase subunit Neighboring gene Sharpr-MPRA regulatory region 3157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1679 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:150254031-150255230 Neighboring gene circadian associated repressor of transcription Neighboring gene uncharacterized LOC105371434

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. Tubular epithelial C1orf54 mediates protection and recovery from acute kidney injury. Xie H, et al. J Cell Mol Med, 2018 Oct. PMID 29999589, Free PMC Article
  2. Biological insights from 108 schizophrenia-associated genetic loci. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Nature, 2014 Jul 24. PMID 25056061, 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. DNA cloning using in vitro site-specific recombination. Hartley JL, et al. Genome Res, 2000 Nov. PMID 11076863, Free PMC Article

See all (11) 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
Biological insights from 108 schizophrenia-associated genetic loci.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • FLJ23221

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
uncharacterized protein C1orf54

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_001301039.1 → NP_001287968.1  uncharacterized protein C1orf54 isoform a precursor

    See identical proteins and their annotated locations for NP_001287968.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC242988
    Conserved Domains (1) summary
    pfam15465
    Location:1 → 130
    DUF4634; Domain of unknown function (DUF4634)

  2. NM_001301040.1 → NP_001287969.1  uncharacterized protein C1orf54 isoform b precursor

    See identical proteins and their annotated locations for NP_001287969.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a. Variants 2 and 3 encode the same isoform (b).
    Source sequence(s)
    AC242988
    Consensus CDS
    CCDS948.1
    UniProtKB/Swiss-Prot
    Q8WWF1, Q9H5P3
    Conserved Domains (1) summary
    pfam15465
    Location:1 → 129
    DUF4634; Domain of unknown function (DUF4634)

  3. NM_001301041.1 → NP_001287970.1  uncharacterized protein C1orf54 isoform c precursor

    See identical proteins and their annotated locations for NP_001287970.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AI004135, DA358536, W93038
    Conserved Domains (1) summary
    pfam15465
    Location:1 → 102
    DUF4634; Domain of unknown function (DUF4634)

  4. NM_001301042.1 → NP_001287971.1  uncharacterized protein C1orf54 isoform d precursor

    See identical proteins and their annotated locations for NP_001287971.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (d) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    AA095731, AI004135, AI342055, T82829
    Consensus CDS
    CCDS72905.1
    UniProtKB/TrEMBL
    Q5TB16
    Related
    ENSP00000358094.3, ENST00000369098.3
    Conserved Domains (1) summary
    pfam15465
    Location:1 → 100
    DUF4634; Domain of unknown function (DUF4634)

  5. NM_024579.4 → NP_078855.2  uncharacterized protein C1orf54 isoform b precursor

    See identical proteins and their annotated locations for NP_078855.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a. Variants 2 and 3 encode the same isoform (b).
    Source sequence(s)
    AI004135, AI342055, AK026874, BC017761
    Consensus CDS
    CCDS948.1
    UniProtKB/Swiss-Prot
    Q8WWF1, Q9H5P3
    Related
    ENSP00000358095.3, ENST00000369099.8
    Conserved Domains (1) summary
    pfam15465
    Location:1 → 129
    DUF4634; Domain of unknown function (DUF4634)

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    150268731..150280924
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047430446.1 → XP_047286402.1  uncharacterized protein C1orf54 isoform X1

  2. XM_047430455.1 → XP_047286411.1  uncharacterized protein C1orf54 isoform X2

    UniProtKB/Swiss-Prot
    Q8WWF1, Q9H5P3
    Related
    ENSP00000358098.1, ENST00000369102.5

  3. XM_047430461.1 → XP_047286417.1  uncharacterized protein C1orf54 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    149393648..149405849
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338735.1 → XP_054194710.1  uncharacterized protein C1orf54 isoform X1

  2. XM_054338736.1 → XP_054194711.1  uncharacterized protein C1orf54 isoform X2

    UniProtKB/Swiss-Prot
    Q8WWF1, Q9H5P3

  3. XM_054338737.1 → XP_054194712.1  uncharacterized protein C1orf54 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WWF1.1 GenPept UniProtKB/Swiss-Prot:Q8WWF1

Gene LinkOut

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

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