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    C10orf90 chromosome 10 open reading frame 90 [ Homo sapiens (human) ]

    Gene ID: 118611, updated on 14-Nov-2024

    Summary

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    Official Symbol
    C10orf90provided by HGNC
    Official Full Name
    chromosome 10 open reading frame 90provided by HGNC
    Primary source
    HGNC:HGNC:26563
    See related
    Ensembl:ENSG00000154493 MIM:617735; AllianceGenome:HGNC:26563
    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
    FATS; bA422P15.2
    Summary
    Predicted to enable histone deacetylase binding activity; microtubule binding activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle process; and response to ionizing radiation. Located in cytoskeleton; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis (RPKM 1.4), brain (RPKM 1.2) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C10orf90 in Genome Data Viewer
    Location:
    10q26.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (126424997..126670693, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (127307175..127553313, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (128113566..128359262, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ADAM metallopeptidase domain 12 Neighboring gene secretion associated Ras related GTPase 1A pseudogene 2 Neighboring gene uncharacterized LOC112267914 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:128113684-128114883 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:128128268-128129467 Neighboring gene long intergenic non-protein coding RNA 601 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:128148161-128149360 Neighboring gene uncharacterized LOC728158 Neighboring gene uncharacterized LOC105378549 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:128209578-128210777 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:128249930-128250686 Neighboring gene uncharacterized LOC124902523 Neighboring gene uncharacterized LOC105378548 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:128361288-128361510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:128365437-128365977 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:128379081-128379804 Neighboring gene small nucleolar RNA SNORD60 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:128581076-128581576 Neighboring gene uncharacterized LOC105378550

    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. [Expression of FATS in non-small cell lung cancer and its relationship with prognosis]. Zhang TM, et al. Zhonghua Zhong Liu Za Zhi, 2019 Nov 23. PMID 31770849
    2. The value of FATS expression in predicting sensitivity to radiotherapy in breast cancer. Zhang J, et al. Oncotarget, 2017 Jun 13. PMID 28402275, Free PMC Article
    3. Expression level of novel tumor suppressor gene FATS is associated with the outcome of node positive breast cancer. Zhang J, et al. Chin Med J (Engl), 2011 Sep. PMID 22040499
    4. A functional genetic variant in fragile-site gene FATS modulates the risk of breast cancer in triparous women. Song F, et al. BMC Cancer, 2015 Jul 30. PMID 26223354, Free PMC Article
    5. FATS regulates polyamine biosynthesis by promoting ODC degradation in an ERβ-dependent manner in non-small-cell lung cancer. Qiu L, et al. Cell Death Dis, 2020 Oct 9. PMID 33037185, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The expression of FATS protein is associated with the development and is an independent prognostic factor of non-small cell lung cancer patients.
      Title: [Expression of FATS in non-small cell lung cancer and its relationship with prognosis].
    2. FATS status is a biomarker in breast cancer to identify individuals likely to benefit from radiotherapy
      Title: The value of FATS expression in predicting sensitivity to radiotherapy in breast cancer.
    3. Data identified a genetic variant in the FATS gene (905C > T, 262D/N) that is associated with susceptibility to breast cancer in a parity-dependent manner.
      Title: A functional genetic variant in fragile-site gene FATS modulates the risk of breast cancer in triparous women.
    4. FATS is an E2-independent ubiquitin ligase that stabilizes p53 and promotes its activation in response to DNA damage.
      Title: FATS is an E2-independent ubiquitin ligase that stabilizes p53 and promotes its activation in response to DNA damage.
    5. FATS is involved in the carcinogenesis and development of breast cancer and could be a potential biomarker and prognostic factor for breast cancer therapy.
      Title: Expression level of novel tumor suppressor gene FATS is associated with the outcome of node positive breast cancer.
    6. data suggest centrosomal functions for C10orf90 and KIAA1731 and new centriole-related functions for ALMS1
      Title: Centriolar association of ALMS1 and likely centrosomal functions of the ALMS motif-containing proteins C10orf90 and KIAA1731.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
    EBI GWAS Catalog

    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

    • FLJ32938

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ubiquitin protein ligase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein polyubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein stabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of centriole replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    (E2-independent) E3 ubiquitin-conjugating enzyme FATS
    Names
    E2/E3 hybrid ubiquitin-protein ligase FATS
    centrosomal protein C10orf90
    fragile-site associated tumor suppressor homolog

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001004298.4 → NP_001004298.2  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform 2

      See identical proteins and their annotated locations for NP_001004298.2

      Status: VALIDATED

      Source sequence(s)
      AF435960, AK297577, AL705062, BC034828, CA423069, DB076049
      Consensus CDS
      CCDS31310.1
      UniProtKB/Swiss-Prot
      B9EIQ9, Q5JRP6, Q5T023, Q8NCV5, Q8WU75, Q96M02
      UniProtKB/TrEMBL
      A0A0A0MSX2
      Related
      ENSP00000284694.7, ENST00000284694.11
      Conserved Domains (1) summary
      pfam15309
      Location:568 → 697
      ALMS_motif; ALMS motif

    2. NM_001350921.2 → NP_001337850.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL392108, AL583860, AL589787
      Consensus CDS
      CCDS91374.1
      UniProtKB/TrEMBL
      B4DMQ6, S4R3N7
      Related
      ENSP00000474558.3, ENST00000488181.3
      Conserved Domains (1) summary
      pfam15309
      Location:665 → 794
      ALMS_motif; ALMS motif

    3. NM_001350922.2 → NP_001337851.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL392108, AL583860, AL589787
      UniProtKB/TrEMBL
      B4DMQ6
      Conserved Domains (1) summary
      pfam15309
      Location:568 → 697
      ALMS_motif; ALMS motif

    4. NM_001350923.2 → NP_001337852.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL392108, AL583860, AL589787

    RNA

    1. NR_146939.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL392108, AL583860, AL589787

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      126424997..126670693 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424560.1 → XP_047280516.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    2. XM_047424556.1 → XP_047280512.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X1

    3. XM_047424559.1 → XP_047280515.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    4. XM_047424558.1 → XP_047280514.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    5. XM_047424557.1 → XP_047280513.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    6. XM_011539217.2 → XP_011537519.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X2

      UniProtKB/TrEMBL
      A0A0A0MSX2
      Conserved Domains (2) summary
      pfam15309
      Location:596 → 723
      ALMS_motif; ALMS motif
      pfam17730
      Location:79 → 590
      Centro_C10orf90; Centrosomal C10orf90

    7. XM_047424561.1 → XP_047280517.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    8. XM_011539223.3 → XP_011537525.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

      See identical proteins and their annotated locations for XP_011537525.1

      UniProtKB/TrEMBL
      Q5T025
      Related
      ENSP00000349318.3, ENST00000356858.7
      Conserved Domains (2) summary
      pfam15309
      Location:522 → 649
      ALMS_motif; ALMS motif
      pfam17730
      Location:5 → 516
      Centro_C10orf90; Centrosomal C10orf90

    9. XM_047424563.1 → XP_047280519.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X5

    10. XM_047424564.1 → XP_047280520.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X6

    11. XM_047424562.1 → XP_047280518.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      127307175..127553313 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054364698.1 → XP_054220673.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    2. XM_054364692.1 → XP_054220667.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X1

    3. XM_054364696.1 → XP_054220671.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    4. XM_054364697.1 → XP_054220672.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    5. XM_054364695.1 → XP_054220670.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    6. XM_054364694.1 → XP_054220669.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    7. XM_054364693.1 → XP_054220668.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X2

    8. XM_054364699.1 → XP_054220674.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    9. XM_054364700.1 → XP_054220675.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X3

    10. XM_054364702.1 → XP_054220677.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X5

    11. XM_054364703.1 → XP_054220678.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X6

    12. XM_054364701.1 → XP_054220676.1  (E2-independent) E3 ubiquitin-conjugating enzyme FATS isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96M02.2 GenPept UniProtKB/Swiss-Prot:Q96M02

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