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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
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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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Related articles in PubMed

  1. Up-regulation of NICE-3 as a novel EDC gene could contribute to human hepatocellular carcinoma. Wei YJ, et al. Asian Pac J Cancer Prev, 2012. PMID 23167344
  2. Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen. Jeng EE, et al. Cell Host Microbe, 2019 Oct 9. PMID 31540829, Free PMC Article
  3. Identification of human epidermal differentiation complex (EDC)-encoded genes by subtractive hybridization of entire YACs to a gridded keratinocyte cDNA library. Marenholz I, et al. Genome Res, 2001 Mar. PMID 11230159, Free PMC Article
  4. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Tao WA, et al. Nat Methods, 2005 Aug. PMID 16094384
  5. CD95/Fas suppresses NF-κB activation through recruitment of KPC2 in a CD95L/FasL-independent mechanism. Guégan JP, et al. iScience, 2021 Dec 17. PMID 34917906, Free PMC Article

See all (32) citations in PubMed

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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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

  • 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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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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