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

    Gene ID: 79630, updated on 10-Dec-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, Dec 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 18.0), lymph node (RPKM 10.9) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C1orf54 in Genome Data Viewer
    Location:
    1q21.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (150268731..150280924)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (149393648..149405849)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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

    Process Evidence Code Pubs
    involved_in epithelial cell proliferation involved in renal tubule morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to wounding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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_2024_08

    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

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

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