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

    Gene ID: 257169, updated on 10-Dec-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
    mouse all
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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: 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. 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)

    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

      UniProtKB/TrEMBL
      B2R9P8

    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
      UniProtKB/TrEMBL
      B2R9P8

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

      UniProtKB/TrEMBL
      B2R9P8

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

      UniProtKB/Swiss-Prot
      Q8TAL5
      UniProtKB/TrEMBL
      B2R9P8

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

      UniProtKB/TrEMBL
      B2R9P8

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

      UniProtKB/TrEMBL
      B2R9P8

    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

    Gene LinkOut

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