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    C1orf43 chromosome 1 open reading frame 43 [ Homo sapiens (human) ]

    Gene ID: 25912, updated on 3-Nov-2024

    Summary

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    Official Symbol
    C1orf43provided by HGNC
    Official Full Name
    chromosome 1 open reading frame 43provided by HGNC
    Primary source
    HGNC:HGNC:29876
    See related
    Ensembl:ENSG00000143612 MIM:617428; AllianceGenome:HGNC:29876
    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
    NICE3; NICE-3; S863-3; HSPC012; NS5ATP4
    Summary
    Involved in phagocytosis. Located in Golgi apparatus; cytosol; and mitochondrion. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 53.9), fat (RPKM 47.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C1orf43 in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (154206720..154220590, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (153343930..153357787, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (154179196..154193066, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr1:154169885-154170114 Neighboring gene microRNA 190b Neighboring gene cilia and flagella associated protein 141 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154192439-154193186 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154193187-154193934 Neighboring gene ubiquitin associated protein 2 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154205661-154206160 Neighboring gene small nucleolar RNA, H/ACA box 58B Neighboring gene ReSE screen-validated silencer GRCh37_chr1:154244721-154244861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1775 Neighboring gene HCLS1 associated protein X-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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. our findings indicate that NICE-3 may contribute to human hepatocellular carcinoma by promoting cell proliferation.
      Title: Up-regulation of NICE-3 as a novel EDC gene could contribute to human hepatocellular carcinoma.
    Submit: New GeneRIF Correction

    Phenotypes

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    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC111001, DKFZp586G1722

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phagocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phagocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein C1orf43
    Names
    HCV NS5A-transactivated protein 4
    hepatitis C virus NS5A-transactivated protein 4
    uncharacterized protein C1orf43

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001098616.3 → NP_001092086.1  protein C1orf43 isoform 3

      See identical proteins and their annotated locations for NP_001092086.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate in-frame exon, compared to variant 1. The encoded isoform (3) is longer than isoform 1.
      Source sequence(s)
      BC000152, BU072807
      Consensus CDS
      CCDS41404.1
      UniProtKB/Swiss-Prot
      A8K3G8, D3DV72, D3DV74, Q5M801, Q5VU73, Q5VU83, Q96HP7, Q9BWL3, Q9UFU2, Q9UGL7, Q9UGL8, Q9Y2R6
      Related
      ENSP00000357507.4, ENST00000368521.10
      Conserved Domains (1) summary
      pfam07406
      Location:6 → 188
      NICE-3; NICE-3 protein

    2. NM_001297717.2 → NP_001284646.1  protein C1orf43 isoform 4

      See identical proteins and their annotated locations for NP_001284646.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate in-frame exon and lacks two exons, which results in a frameshift, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      BC088353, BU072807
      UniProtKB/TrEMBL
      A0A1W2PQP6
      Related
      ENSP00000492072.1, ENST00000640799.1
      Conserved Domains (1) summary
      pfam07406
      Location:6 → 151
      NICE-3; NICE-3 protein

    3. NM_001297718.2 → NP_001284647.1  protein C1orf43 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains multiple differences in the 5' region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (5) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      BC006514, BG478941, BU072807
      UniProtKB/Swiss-Prot
      Q9BWL3
      Conserved Domains (1) summary
      pfam07406
      Location:1 → 153
      NICE-3; NICE-3 protein

    4. NM_001297720.2 → NP_001284649.1  protein C1orf43 isoform 6

      See identical proteins and their annotated locations for NP_001284649.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) contains an alternate in-frame exon and lacks an in-frame exon, compared to variant 1. The encoded isoform (6) is longer than isoform 1.
      Source sequence(s)
      AJ243663, AL540989, BC000152, BU072807
      Consensus CDS
      CCDS72924.1
      UniProtKB/TrEMBL
      X6R6S3
      Related
      ENSP00000357505.1, ENST00000368519.5
      Conserved Domains (1) summary
      pfam07406
      Location:6 → 170
      NICE-3; NICE-3 protein

    5. NM_001297721.2 → NP_001284650.1  protein C1orf43 isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks a portion of the 3' coding region and its transcription extends past a splice site used in variant 1, resulting in a different 3' UTR. The encoded isoform (7) has a shorter C-terminus than isoform 1.
      Source sequence(s)
      AK290583, CD247026
      Consensus CDS
      CCDS76219.1
      UniProtKB/TrEMBL
      X6R6F3
      Related
      ENSP00000357502.1, ENST00000368516.1
      Conserved Domains (1) summary
      pfam07406
      Location:6 → 154
      NICE-3; NICE-3 protein

    6. NM_001297723.2 → NP_001284652.1  protein C1orf43 isoform 8

      See identical proteins and their annotated locations for NP_001284652.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) contains an alternate in-frame exon, lacks a portion of the 3' coding region, and its transcription extends past a splice site used in variant 1, resulting in a different 3' UTR. The encoded isoform (8) is shorter than isoform 1.
      Source sequence(s)
      AK290583, AL590431, BC008306
      Consensus CDS
      CCDS76220.1
      UniProtKB/TrEMBL
      A0A1W2PQP6
      Related
      ENSP00000357504.1, ENST00000368518.5
      Conserved Domains (1) summary
      pfam07406
      Location:6 → 188
      NICE-3; NICE-3 protein

    7. NM_015449.4 → NP_056264.1  protein C1orf43 isoform 1

      See identical proteins and their annotated locations for NP_056264.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      BC006514, BU072807
      Consensus CDS
      CCDS1061.1
      UniProtKB/TrEMBL
      Q09GN0
      Related
      ENSP00000271925.5, ENST00000350592.7
      Conserved Domains (1) summary
      pfam07406
      Location:6 → 154
      NICE-3; NICE-3 protein

    8. NM_138740.4 → NP_620077.1  protein C1orf43 isoform 2

      See identical proteins and their annotated locations for NP_620077.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AJ243663, BU072807
      Consensus CDS
      CCDS1062.1
      UniProtKB/Swiss-Prot
      Q9BWL3
      Related
      ENSP00000354496.4, ENST00000362076.8
      Conserved Domains (1) summary
      pfam07406
      Location:6 → 136
      NICE-3; NICE-3 protein

    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
      154206720..154220590 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417239.1 → XP_047273195.1  protein C1orf43 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      153343930..153357787 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BWL3.1 GenPept UniProtKB/Swiss-Prot:Q9BWL3

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