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    SINHCAF SIN3-HDAC complex associated factor [ Homo sapiens (human) ]

    Gene ID: 58516, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SINHCAFprovided by HGNC
    Official Full Name
    SIN3-HDAC complex associated factorprovided by HGNC
    Primary source
    HGNC:HGNC:30702
    See related
    Ensembl:ENSG00000139146 MIM:615027; AllianceGenome:HGNC:30702
    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
    L4; TERA; FAM60A; C12orf14
    Summary
    Involved in negative regulation of cell migration. Part of Sin3-type complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in endometrium (RPKM 24.9), lymph node (RPKM 18.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SINHCAF in Genome Data Viewer
    Location:
    12p11.21
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (31280584..31326150, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (31157116..31202680, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (31433518..31479084, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S3A pseudogene Neighboring gene Sharpr-MPRA regulatory region 11157 Neighboring gene melanoregulin pseudogene 1 Neighboring gene uncharacterized LOC124903109 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31478173-31479104 Neighboring gene uncharacterized LOC79857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31517453-31517952 Neighboring gene U6 spliceosomal RNA Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31523276-31523883 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31523884-31524492 Neighboring gene long intergenic non-protein coding RNA 2387 Neighboring gene DENN domain containing 5B Neighboring gene RNA, U6 small nuclear 618, pseudogene

    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. SIN3-HDAC complex-associated factor, a chromatin remodelling gene located in the 12p amplicon, is a potential germ cell tumour-specific oncogene. Jhuang YL, et al. J Pathol, 2022 Dec. PMID 36056608
    2. Restraint of FAM60A has a cancer-inhibiting role in pancreatic carcinoma via the effects on the Akt/GSK-3β/β-catenin signaling pathway. Zhang Y, et al. Environ Toxicol, 2022 Jun. PMID 35213078
    3. [Research Progress of FAM60A in the Regulation of Cellular Function]. Sun YH, et al. Zhongguo Yi Xue Ke Xue Yuan Xue Bao, 2021 Jun 30. PMID 34238425
    4. Integrative analysis of copy number and transcriptional expression profiles in esophageal cancer to identify a novel driver gene for therapy. Dong G, et al. Sci Rep, 2017 Feb 7. PMID 28169357, Free PMC Article
    5. FAM60A promotes cisplatin resistance in lung cancer cells by activating SKP2 expression. Hou Q, et al. Anticancer Drugs, 2020 Sep. PMID 32796403

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SIN3-HDAC complex-associated factor, a chromatin remodelling gene located in the 12p amplicon, is a potential germ cell tumour-specific oncogene.
      Title: SIN3-HDAC complex-associated factor, a chromatin remodelling gene located in the 12p amplicon, is a potential germ cell tumour-specific oncogene.
    2. Restraint of FAM60A has a cancer-inhibiting role in pancreatic carcinoma via the effects on the Akt/GSK-3beta/beta-catenin signaling pathway.
      Title: Restraint of FAM60A has a cancer-inhibiting role in pancreatic carcinoma via the effects on the Akt/GSK-3β/β-catenin signaling pathway.
    3. [Research Progress of FAM60A in the Regulation of Cellular Function].
      Title: [Research Progress of FAM60A in the Regulation of Cellular Function].
    4. FAM60A promotes cisplatin resistance in lung cancer cells by activating SKP2 expression.
      Title: FAM60A promotes cisplatin resistance in lung cancer cells by activating SKP2 expression.
    5. FAM60A act as a carcinogen and suggests that H. pylori-induced upregulation of FAM60A may contribute to the development of gastric cancer.
      Title: FAM60A, increased by Helicobacter pylori, promotes proliferation and suppresses apoptosis of gastric cancer cells by targeting the PI3K/AKT pathway.
    6. SINHCAF specifically represses HIF-2alpha mRNA and protein expression, via its interaction with the transcription factor SP1 (specificity protein 1) and recruitment of HDAC1 to the HIF-2alpha promoter.
      Title: SINHCAF/FAM60A and SIN3A specifically repress HIF-2α expression.
    7. FAM60A may act as a key transcriptional factor to regulate genes that are correlated with each cell cycle of tumor cells in esophageal cancer.
      Title: Integrative analysis of copy number and transcriptional expression profiles in esophageal cancer to identify a novel driver gene for therapy.
    8. studies reveal that loss of FAM60A or another component of the Sin3 complex, SDS3, leads to a change in cell morphology and an increase in cell migration
      Title: Human family with sequence similarity 60 member A (FAM60A) protein: a new subunit of the Sin3 deacetylase complex.
    9. Family with sequence similarity 60A (FAM60A) protein is a cell cycle-fluctuating regulator of the SIN3-HDAC1 histone deacetylase complex.
      Title: Family with sequence similarity 60A (FAM60A) protein is a cell cycle-fluctuating regulator of the SIN3-HDAC1 histone deacetylase complex.
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell migration NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Sin3-type complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Sin3-type complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Sin3-type complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SIN3-HDAC complex-associated factor
    Names
    family with sequence similarity 60 member A
    protein FAM60A
    tera protein 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_001135811.2 → NP_001129283.1  SIN3-HDAC complex-associated factor

      See identical proteins and their annotated locations for NP_001129283.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same protein.
      Source sequence(s)
      AF087885, BC000024, BC004462, DR763430
      Consensus CDS
      CCDS8723.1
      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50
      UniProtKB/TrEMBL
      B7Z287
      Conserved Domains (1) summary
      pfam15396
      Location:2 → 198
      FAM60A; Protein Family FAM60A

    2. NM_001135812.2 → NP_001129284.1  SIN3-HDAC complex-associated factor

      See identical proteins and their annotated locations for NP_001129284.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks a segment in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same protein.
      Source sequence(s)
      AK026932, BC004462, DA741767, DR763430
      Consensus CDS
      CCDS8723.1
      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50
      UniProtKB/TrEMBL
      B7Z287
      Related
      ENSP00000337477.4, ENST00000337682.9
      Conserved Domains (1) summary
      pfam15396
      Location:2 → 198
      FAM60A; Protein Family FAM60A

    3. NM_021238.3 → NP_067061.1  SIN3-HDAC complex-associated factor

      See identical proteins and their annotated locations for NP_067061.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses a different splice site in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same protein.
      Source sequence(s)
      BC000024, BC004462, DR763430
      Consensus CDS
      CCDS8723.1
      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50
      UniProtKB/TrEMBL
      B7Z287
      Conserved Domains (1) summary
      pfam15396
      Location:2 → 198
      FAM60A; Protein Family FAM60A

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      31280584..31326150 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017019762.3 → XP_016875251.1  SIN3-HDAC complex-associated factor isoform X1

      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50
      UniProtKB/TrEMBL
      B7Z287
      Conserved Domains (1) summary
      pfam15396
      Location:2 → 198
      FAM60A; Protein Family FAM60A

    2. XM_047429272.1 → XP_047285228.1  SIN3-HDAC complex-associated factor isoform X1

      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50

    3. XM_011520803.3 → XP_011519105.2  SIN3-HDAC complex-associated factor isoform X1

      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50
      Related
      ENSP00000393279.2, ENST00000454658.6

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187587.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      171378..216944 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328933.1 → XP_054184908.1  SIN3-HDAC complex-associated factor isoform X1

      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50

    2. XM_054328932.1 → XP_054184907.1  SIN3-HDAC complex-associated factor isoform X1

      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50

    3. XM_054328931.1 → XP_054184906.1  SIN3-HDAC complex-associated factor isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      31157116..31202680 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372776.1 → XP_054228751.1  SIN3-HDAC complex-associated factor isoform X1

      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50

    2. XM_054372775.1 → XP_054228750.1  SIN3-HDAC complex-associated factor isoform X1

      UniProtKB/Swiss-Prot
      D3DUV8, Q9BSZ8, Q9NP50

    3. XM_054372774.1 → XP_054228749.1  SIN3-HDAC complex-associated factor isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NP50.1 GenPept UniProtKB/Swiss-Prot:Q9NP50

    Gene LinkOut

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

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