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C9orf43 chromosome 9 open reading frame 43 [ Homo sapiens (human) ]

Gene ID: 257169, updated on 10-Oct-2024

Summary

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Official Symbol
C9orf43provided by HGNC
Official Full Name
chromosome 9 open reading frame 43provided by HGNC
Primary source
HGNC:HGNC:23570
See related
Ensembl:ENSG00000157653 AllianceGenome:HGNC:23570
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
Expression
Restricted expression toward testis (RPKM 20.2) See more
Orthologs
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Genomic context

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See C9orf43 in Genome Data Viewer
Location:
9q32
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (113410747..113429690)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (125609564..125628508)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (116173027..116191970)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28837 Neighboring gene haloacid dehalogenase like hydrolase domain containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116162720-116163300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20204 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:116171753-116172952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116173655-116174554 Neighboring gene aminolevulinate dehydratase Neighboring gene DNA polymerase epsilon 3, accessory subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116224910-116225864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116225865-116226819 Neighboring gene regulator of G protein signaling 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116265604-116266246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116266247-116266887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28846 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116286687-116287497 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116298300-116299051 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:116303397-116303896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116304621-116305136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116305137-116305652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116326740-116327461 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116327462-116328182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116344249-116344757 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116349073-116349850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116351247-116351748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:116351749-116352248 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:116361196-116361362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116361689-116362612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20206 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:116375197-116375698 Neighboring gene uncharacterized LOC105376222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116383205-116384076 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:116384948-116385819

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. Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. Letra A, et al. Am J Med Genet A, 2010 Jul. PMID 20583170, Free PMC Article
  2. mTOR Inhibition via Rapamycin Treatment Partially Reverts the Deficit in Energy Metabolism Caused by FH Loss in RPE Cells. Merle DA, et al. Antioxidants (Basel), 2021 Dec 3. PMID 34943047, Free PMC Article
  3. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. Virok DP, et al. J Proteome Res, 2011 Apr 1. PMID 21244100
  4. DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article
  5. Phospho-tyrosine dependent protein-protein interaction network. Grossmann A, et al. Mol Syst Biol, 2015 Mar 26. PMID 25814554, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate.
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

  • MGC17358

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
uncharacterized protein C9orf43

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_001278629.2 → NP_001265558.1  uncharacterized protein C9orf43 isoform 1

    See identical proteins and their annotated locations for NP_001265558.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and represents use of an alternate promoter, compared to variant 1. Both variants 1 and 2 encode the same isoform 1.
    Source sequence(s)
    AK313867, AL137066
    Consensus CDS
    CCDS6796.1
    UniProtKB/Swiss-Prot
    Q8TAL5
    UniProtKB/TrEMBL
    B2R9P8
    Related
    ENSP00000363280.1, ENST00000374165.6
    Conserved Domains (1) summary
    pfam15504
    Location:1 → 446
    DUF4647; Domain of unknown function (DUF4647)

  2. NM_001278630.2 → NP_001265559.1  uncharacterized protein C9orf43 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' most exon which results in the use of an alternate upstream AUG, compared to isoform 1. The encoded isoform (2) has a longer and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AK301872, AL137066
    UniProtKB/TrEMBL
    B4DX97
    Conserved Domains (1) summary
    pfam15504
    Location:19 → 464
    DUF4647; Domain of unknown function (DUF4647)

  3. NM_152786.3 → NP_689999.1  uncharacterized protein C9orf43 isoform 1

    See identical proteins and their annotated locations for NP_689999.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform (1). Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AL137066, BC026884
    Consensus CDS
    CCDS6796.1
    UniProtKB/Swiss-Prot
    Q8TAL5
    UniProtKB/TrEMBL
    B2R9P8
    Related
    ENSP00000288462.4, ENST00000288462.4
    Conserved Domains (1) summary
    pfam15504
    Location:1 → 446
    DUF4647; Domain of unknown function (DUF4647)

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    113410747..113429690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447490.2 → XP_024303258.1  uncharacterized protein C9orf43 isoform X1

    UniProtKB/Swiss-Prot
    Q8TAL5
    UniProtKB/TrEMBL
    B2R9P8
    Conserved Domains (1) summary
    pfam15504
    Location:1 → 446
    DUF4647; Domain of unknown function (DUF4647)

  2. XM_047423157.1 → XP_047279113.1  uncharacterized protein C9orf43 isoform X2

  3. XM_024447491.2 → XP_024303259.1  uncharacterized protein C9orf43 isoform X1

    UniProtKB/Swiss-Prot
    Q8TAL5
    UniProtKB/TrEMBL
    B2R9P8
    Conserved Domains (1) summary
    pfam15504
    Location:1 → 446
    DUF4647; Domain of unknown function (DUF4647)

  4. XM_011518477.2 → XP_011516779.1  uncharacterized protein C9orf43 isoform X2

    UniProtKB/TrEMBL
    B2R9P8
    Conserved Domains (1) summary
    pfam15504
    Location:1 → 370
    DUF4647; Domain of unknown function (DUF4647)

  5. XM_005251885.4 → XP_005251942.1  uncharacterized protein C9orf43 isoform X3

    See identical proteins and their annotated locations for XP_005251942.1

    Conserved Domains (1) summary
    pfam15504
    Location:1 → 312
    DUF4647; Domain of unknown function (DUF4647)

  6. XM_011518479.3 → XP_011516781.1  uncharacterized protein C9orf43 isoform X3

    See identical proteins and their annotated locations for XP_011516781.1

    Conserved Domains (1) summary
    pfam15504
    Location:1 → 312
    DUF4647; Domain of unknown function (DUF4647)

RNA

  1. XR_007061270.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    125609564..125628508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362631.1 → XP_054218606.1  uncharacterized protein C9orf43 isoform X1

    UniProtKB/Swiss-Prot
    Q8TAL5

  2. XM_054362633.1 → XP_054218608.1  uncharacterized protein C9orf43 isoform X2

  3. XM_054362630.1 → XP_054218605.1  uncharacterized protein C9orf43 isoform X1

    UniProtKB/Swiss-Prot
    Q8TAL5

  4. XM_054362632.1 → XP_054218607.1  uncharacterized protein C9orf43 isoform X2

  5. XM_054362634.1 → XP_054218609.1  uncharacterized protein C9orf43 isoform X4

  6. XM_054362635.1 → XP_054218610.1  uncharacterized protein C9orf43 isoform X3

  7. XM_054362636.1 → XP_054218611.1  uncharacterized protein C9orf43 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TAL5.1 GenPept UniProtKB/Swiss-Prot:Q8TAL5

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