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    YAF2 YY1 associated factor 2 [ Homo sapiens (human) ]

    Gene ID: 10138, updated on 3-Apr-2024

    Summary

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    Official Symbol
    YAF2provided by HGNC
    Official Full Name
    YY1 associated factor 2provided by HGNC
    Primary source
    HGNC:HGNC:17363
    See related
    Ensembl:ENSG00000015153 MIM:607534; AllianceGenome:HGNC:17363
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes a zinc finger containing protein that functions in the regulation of transcription. This protein was identified as an interacting partner of transcriptional repressor protein Yy1, and also interacts with other transcriptional regulators, including Myc and Polycomb. This protein can promote proteolysis of Yy1. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Feb 2016]
    Expression
    Ubiquitous expression in heart (RPKM 3.8), brain (RPKM 3.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q12
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (42157104..42238248, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (42115009..42196195, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (42550906..42632050, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378247 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4356 Neighboring gene ATP synthase subunit C lysine N-methyltransferase-like Neighboring gene glucoside xylosyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4357 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6209 Neighboring gene MPRA-validated peak1683 silencer Neighboring gene MPRA-validated peak1686 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:42631341-42631842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4361 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4362 Neighboring gene uncharacterized LOC124902920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4363 Neighboring gene insulin like growth factor 2 mRNA binding protein 2 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
    • 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. YAF2 exerts anti-apoptotic effect in human tumor cells in a FANK1- and phosphorylation-dependent manner. Zhang S, et al. Biochem Biophys Res Commun, 2021 May 21. PMID 33784512
    2. miR-34b inhibits the migration/invasion and promotes apoptosis of non-small-cell lung cancer cells by YAF2. Zhuang XF, et al. Eur Rev Med Pharmacol Sci, 2019 Mar. PMID 30915747
    3. NEAT1 enhances MPP(+) -induced pyroptosis in a cell model of Parkinson's disease via targeting miR-5047/YAF2 signaling. Shen H, et al. Immun Inflamm Dis, 2023 Jun. PMID 37382256, Free PMC Article
    4. A LINC00341-mediated regulatory pathway supports chondrocyte survival and may prevent osteoarthritis progression. Yang Q, et al. J Cell Biochem, 2019 Jun. PMID 30672021
    5. Functional interaction of Yaf2 with the central region of MycN. Bannasch D, et al. Oncogene, 2001 Sep 13. PMID 11593398

    See all (51) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NEAT1 enhances MPP[+] -induced pyroptosis in a cell model of Parkinson's disease via targeting miR-5047/YAF2 signaling.
      Title: NEAT1 enhances MPP(+) -induced pyroptosis in a cell model of Parkinson's disease via targeting miR-5047/YAF2 signaling.
    2. YAF2 exerts anti-apoptotic effect in human tumor cells in a FANK1- and phosphorylation-dependent manner.
      Title: YAF2 exerts anti-apoptotic effect in human tumor cells in a FANK1- and phosphorylation-dependent manner.
    3. miR-34b inhibits the migration/invasion and promotes apoptosis of non-small-cell lung cancer cells by YAF2.
      Title: miR-34b inhibits the migration/invasion and promotes apoptosis of non-small-cell lung cancer cells by YAF2.
    4. LINC00341 interacts with miR-141 to suppress its functional binding to the 3'-untranslated region of YAF2 messenger RNA whereby supporting chondrocyte survival and preventing osteoarthritis progression.
      Title: A LINC00341-mediated regulatory pathway supports chondrocyte survival and may prevent osteoarthritis progression.
    5. These findings uncovered an apoptotic signaling cascade linking YAF2, PDCD5, and TP53 during genotoxic stress responses.
      Title: YAF2 promotes TP53-mediated genotoxic stress response via stabilization of PDCD5.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    8. YEAF1/RYBP and YAF-2 are functionally distinct members of a cofactor family for the YY1 and E4TF1/hGABP transcription factors.
      Title: YEAF1/RYBP and YAF-2 are functionally distinct members of a cofactor family for the YY1 and E4TF1/hGABP transcription factors.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC41856, DKFZp779H1820

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription corepressor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    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
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    YY1-associated factor 2

    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_001190977.3 → NP_001177906.1  YY1-associated factor 2 isoform 3

      See identical proteins and their annotated locations for NP_001177906.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two consecutive in-frame exons compared to variant 1. The resulting isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC020629, AK294260, BC037777
      Consensus CDS
      CCDS53778.1
      UniProtKB/Swiss-Prot
      Q8IY57
      Related
      ENSP00000370167.4, ENST00000380790.4
      Conserved Domains (1) summary
      pfam17219
      Location:60 → 92
      YAF2_RYBP; Yaf2/RYBP C-terminal binding motif

    2. NM_001190979.3 → NP_001177908.1  YY1-associated factor 2 isoform 1

      See identical proteins and their annotated locations for NP_001177908.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC020629, BC037777, HY111766
      Consensus CDS
      CCDS53779.1
      UniProtKB/Swiss-Prot
      Q8IY57
      Related
      ENSP00000328004.5, ENST00000327791.8
      Conserved Domains (3) summary
      sd00029
      Location:23 → 42
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam00641
      Location:20 → 43
      zf-RanBP; Zn-finger in Ran binding protein and others
      pfam17219
      Location:126 → 158
      YAF2_RYBP; Yaf2/RYBP C-terminal binding motif

    3. NM_001190980.3 → NP_001177909.1  YY1-associated factor 2 isoform 4

      See identical proteins and their annotated locations for NP_001177909.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks several 3' exons, and contains an alternate 3' exon, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (4) is shorter and has a distinct C-terminus, as compared to isoform (1).
      Source sequence(s)
      AC020629, AK127531
      Consensus CDS
      CCDS53780.1
      UniProtKB/Swiss-Prot
      Q8IY57
      Related
      ENSP00000451626.2, ENST00000555248.2
      Conserved Domains (2) summary
      sd00029
      Location:23 → 42
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam00641
      Location:20 → 43
      zf-RanBP; Zn-finger in Ran binding protein and others

    4. NM_001320080.2 → NP_001307009.1  YY1-associated factor 2 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate exon and initiates translation at an alternate downstream start codon compared to variant 1. The resulting isoform (5) has a distinct N-terminus and is shorter, compared to isoform 1.
      Source sequence(s)
      AC020629, AK296191
      UniProtKB/TrEMBL
      B4DJQ9
      Conserved Domains (1) summary
      pfam17219
      Location:93 → 125
      YAF2_RYBP; Yaf2/RYBP C-terminal binding motif

    5. NM_005748.6 → NP_005739.2  YY1-associated factor 2 isoform 2

      See identical proteins and their annotated locations for NP_005739.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon compared to variant 1. The resulting isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AA789222, AC020629, DA011078
      Consensus CDS
      CCDS31775.1
      UniProtKB/Swiss-Prot
      A8K5P0, B4DFU3, G3V465, Q8IY57, Q99710
      Related
      ENSP00000439256.2, ENST00000534854.7
      Conserved Domains (3) summary
      sd00029
      Location:23 → 42
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam00641
      Location:20 → 43
      zf-RanBP; Zn-finger in Ran binding protein and others
      pfam17219
      Location:102 → 134
      YAF2_RYBP; Yaf2/RYBP C-terminal binding motif

    RNA

    1. NR_135139.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains two alternate internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC020629, CB993159, DA491895, HY111766

    2. NR_135140.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) contains two alternate internal exons and uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC020629, BC037777, CB963485, DA491895, HY111766

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      42157104..42238248 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011537728.4 → XP_011536030.1  YY1-associated factor 2 isoform X1

      Conserved Domains (2) summary
      sd00029
      Location:23 → 42
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam00641
      Location:20 → 43
      zf-RanBP; Zn-finger in Ran binding protein and others

    2. XM_047428049.1 → XP_047284005.1  YY1-associated factor 2 isoform X4

    3. XM_047428048.1 → XP_047284004.1  YY1-associated factor 2 isoform X2

    4. XM_006719185.4 → XP_006719248.1  YY1-associated factor 2 isoform X3

      Conserved Domains (1) summary
      pfam17219
      Location:99 → 131
      YAF2_RYBP; Yaf2/RYBP C-terminal binding motif

    5. XM_011537729.3 → XP_011536031.1  YY1-associated factor 2 isoform X5

      Conserved Domains (1) summary
      pfam17219
      Location:81 → 113
      YAF2_RYBP; Yaf2/RYBP C-terminal binding motif

    6. XM_017018670.3 → XP_016874159.1  YY1-associated factor 2 isoform X6

      UniProtKB/TrEMBL
      G3V212
      Related
      ENSP00000450097.1, ENST00000552928.5
      Conserved Domains (2) summary
      sd00029
      Location:23 → 42
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam00641
      Location:20 → 43
      zf-RanBP; Zn-finger in Ran binding protein and others

    RNA

    1. XR_944467.4 RNA Sequence

    2. XR_007063026.1 RNA Sequence

    3. XR_001748538.2 RNA Sequence

    4. XR_001748537.2 RNA Sequence

    5. XR_002957279.2 RNA Sequence

    6. XR_007063027.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      42115009..42196195 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370722.1 → XP_054226697.1  YY1-associated factor 2 isoform X1

    2. XM_054370723.1 → XP_054226698.1  YY1-associated factor 2 isoform X2

    3. XM_054370724.1 → XP_054226699.1  YY1-associated factor 2 isoform X3

    4. XM_054370725.1 → XP_054226700.1  YY1-associated factor 2 isoform X5

    5. XM_054370726.1 → XP_054226701.1  YY1-associated factor 2 isoform X6

      UniProtKB/TrEMBL
      G3V212

    RNA

    1. XR_008488502.1 RNA Sequence

    2. XR_008488504.1 RNA Sequence

    3. XR_008488503.1 RNA Sequence

    4. XR_008488505.1 RNA Sequence

    5. XR_008488501.1 RNA Sequence

    6. XR_008488506.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001012424.1: Suppressed sequence

      Description
      NM_001012424.1: 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
    Q8IY57.3 GenPept UniProtKB/Swiss-Prot:Q8IY57

    Gene LinkOut

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

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