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C9orf85 chromosome 9 open reading frame 85 [ Homo sapiens (human) ]

Gene ID: 138241, updated on 16-Mar-2024

Summary

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Official Symbol
C9orf85provided by HGNC
Official Full Name
chromosome 9 open reading frame 85provided by HGNC
Primary source
HGNC:HGNC:28784
See related
Ensembl:ENSG00000155621 MIM:620761; AllianceGenome:HGNC:28784
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
Ubiquitous expression in urinary bladder (RPKM 3.1), testis (RPKM 2.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
9q21.13
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (71911639..71986058)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (84061989..84136715)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (74526555..74600974)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene glucosamine-6-phosphate deaminase 2 pseudogene Neighboring gene abhydrolase domain containing 17B, depalmitoylase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28457 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74534388-74534894 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74535401-74535906 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:74535907-74536412 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:74536413-74536918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74568411-74569057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74578682-74579426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:74579427-74580171 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:74604827-74606026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:74622307-74622838 Neighboring gene Sharpr-MPRA regulatory region 3495 Neighboring gene heat shock protein family B (small) member 1 pseudogene 1 Neighboring gene uncharacterized LOC101927108 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:74663139-74664338 Neighboring gene chromosome 9 open reading frame 57

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
  • 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. Single-gene knockout-coupled omics analysis identifies C9orf85 and CXorf38 as two uncharacterized human proteins associated with ZIP8 malfunction. Tan HW, et al. Front Mol Biosci, 2022. PMID 36330220, Free PMC Article
  2. DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article
  3. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. Wang AG, et al. Biochem Biophys Res Commun, 2006 Jul 7. PMID 16712791
  4. TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions. Banks CA, et al. Mol Cell Proteomics, 2016 Nov. PMID 27609421, Free PMC Article
  5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Lamesch P, et al. Genomics, 2007 Mar. PMID 17207965, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

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

  • MGC61599

General protein information

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Preferred Names
uncharacterized protein C9orf85

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_001365053.2 → NP_001351982.1  uncharacterized protein C9orf85 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL138751
    Consensus CDS
    CCDS94421.1
    UniProtKB/Swiss-Prot
    Q5W0N1, Q5W0N3, Q6PJW9, Q86U95, Q96MD7
    Related
    ENSP00000366230.3, ENST00000377031.7
    Conserved Domains (1) summary
    pfam10217
    Location:14 → 102
    DUF2039; Uncharacterized conserved protein (DUF2039)

  2. NM_001365055.2 → NP_001351984.1  uncharacterized protein C9orf85 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AA442437, BC010179, BC052375, BQ020559, BQ431408, CB113688
    Conserved Domains (1) summary
    pfam10217
    Location:8 → 83
    DUF2039; Uncharacterized conserved protein (DUF2039)

  3. NM_001365057.2 → NP_001351986.1  uncharacterized protein C9orf85 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL138751, BC028019
    UniProtKB/TrEMBL
    F6X0R3
    Conserved Domains (1) summary
    pfam10217
    Location:14 → 69
    DUF2039; Uncharacterized conserved protein (DUF2039)

  4. NM_182505.5 → NP_872311.2  uncharacterized protein C9orf85 isoform 2

    See identical proteins and their annotated locations for NP_872311.2

    Status: VALIDATED

    Source sequence(s)
    BC010179, BC052375, BQ020559, BQ431408, CB113688
    Consensus CDS
    CCDS6639.1
    UniProtKB/Swiss-Prot
    Q96MD7
    Related
    ENSP00000334289.2, ENST00000334731.7
    Conserved Domains (1) summary
    pfam10217
    Location:14 → 102
    DUF2039; Uncharacterized conserved protein (DUF2039)

RNA

  1. NR_157408.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AK311206, AL138751

  2. NR_157409.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL138751

  3. NR_157410.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL138751

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    71911639..71986058
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422767.1 → XP_047278723.1  uncharacterized protein C9orf85 isoform X1

  2. XM_047422768.1 → XP_047278724.1  uncharacterized protein C9orf85 isoform X2

  3. XM_047422769.1 → XP_047278725.1  uncharacterized protein C9orf85 isoform X3

    UniProtKB/TrEMBL
    F6X0R3

RNA

  1. XR_007061245.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    84061989..84136715
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054361973.1 → XP_054217948.1  uncharacterized protein C9orf85 isoform X1

  2. XM_054361974.1 → XP_054217949.1  uncharacterized protein C9orf85 isoform X2

  3. XM_054361975.1 → XP_054217950.1  uncharacterized protein C9orf85 isoform X3

    UniProtKB/TrEMBL
    F6X0R3

RNA

  1. XR_008487940.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_198394.1: Suppressed sequence

    Description
    NM_198394.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96MD7.1 GenPept UniProtKB/Swiss-Prot:Q96MD7

Gene LinkOut

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