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C9orf78 chromosome 9 open reading frame 78 [ Homo sapiens (human) ]

Gene ID: 51759, updated on 2-Nov-2024

Summary

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Official Symbol
C9orf78provided by HGNC
Official Full Name
chromosome 9 open reading frame 78provided by HGNC
Primary source
HGNC:HGNC:24932
See related
Ensembl:ENSG00000136819 MIM:619569; AllianceGenome:HGNC:24932
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
CSU2; TLS1; HCA59; HSPC220; bA409K20.3
Summary
Enables U5 snRNA binding activity. Involved in mRNA cis splicing, via spliceosome and regulation of homologous chromosome segregation. Located in chromosome, centromeric region; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in bone marrow (RPKM 42.7), kidney (RPKM 29.7) and 25 other tissues See more
Orthologs
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Genomic context

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See C9orf78 in Genome Data Viewer
Location:
9q34.11
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129827290..129835275, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (142031858..142039846, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (132589569..132597554, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20389 Neighboring gene Sharpr-MPRA regulatory region 13743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29121 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29122 Neighboring gene torsin family 1 member B Neighboring gene Sharpr-MPRA regulatory region 5710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20391 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132597987-132598487 Neighboring gene torsin family 1 member A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132601680-132602180 Neighboring gene ubiquitin specific peptidase 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29123 Neighboring gene Sharpr-MPRA regulatory region 12255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132632499-132632998 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132636644-132637144 Neighboring gene Sharpr-MPRA regulatory region 12063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132647083-132647764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20393 Neighboring gene microRNA 6855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132651249-132652136 Neighboring gene Sharpr-MPRA regulatory region 3297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29128 Neighboring gene Sharpr-MPRA regulatory region 1290 Neighboring gene formin binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29133 Neighboring gene Sharpr-MPRA regulatory region 9235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29144 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:132786300-132786450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29146 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132796970-132797470 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132797471-132797971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132811133-132811633

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. C9ORF78 partially localizes to centromeres and plays a role in chromosome segregation. Koranne R, et al. Exp Cell Res, 2022 Apr 15. PMID 35167828
  2. Tls1 regulates splicing of shelterin components to control telomeric heterochromatin assembly and telomere length. Wang J, et al. Nucleic Acids Res, 2014 Oct. PMID 25245948, Free PMC Article
  3. Large scale identification of human hepatocellular carcinoma-associated antigens by autoantibodies. Wang Y, et al. J Immunol, 2002 Jul 15. PMID 12097419
  4. The Human Tau Interactome: Binding to the Ribonucleoproteome, and Impaired Binding of the Proline-to-Leucine Mutant at Position 301 (P301L) to Chaperones and the Proteasome. Gunawardana CG, et al. Mol Cell Proteomics, 2015 Nov. PMID 26269332, Free PMC Article
  5. Identification of substrates of SMURF1 ubiquitin ligase activity utilizing protein microarrays. Andrews PS, et al. Assay Drug Dev Technol, 2010 Aug. PMID 20804422

See all (52) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. C9ORF78 partially localizes to centromeres and plays a role in chromosome segregation.
    Title: C9ORF78 partially localizes to centromeres and plays a role in chromosome segregation.
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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables U5 snRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromosome segregation IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA cis splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of homologous chromosome segregation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in chromosome, centromeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
splicing factor C9orf78
Names
hepatocellular carcinoma-associated antigen 59
telomere length and silencing protein 1 homolog
uncharacterized protein C9orf78

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_016520.3 → NP_057604.1  splicing factor C9orf78

    See identical proteins and their annotated locations for NP_057604.1

    Status: VALIDATED

    Source sequence(s)
    AL158207, BC007664, BU674575, CB128496
    Consensus CDS
    CCDS6931.1
    UniProtKB/Swiss-Prot
    B3KPX8, Q8WVU6, Q9NT39, Q9NZ63
    Related
    ENSP00000361524.3, ENST00000372447.7
    Conserved Domains (1) summary
    pfam07052
    Location:101 → 196
    Hep_59; Hepatocellular carcinoma-associated antigen 59

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
    129827290..129835275 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    142031858..142039846 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NZ63.1 GenPept UniProtKB/Swiss-Prot:Q9NZ63

Gene LinkOut

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

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