Human Gene YAF2 (ENST00000534854.7_7) from GENCODE V47lift37
  Description: YY1 associated factor 2, transcript variant 2 (from RefSeq NM_005748.6)
Gencode Transcript: ENST00000534854.7_7
Gencode Gene: ENSG00000015153.15_9
Transcript (Including UTRs)
   Position: hg19 chr12:42,550,906-42,632,050 Size: 81,145 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr12:42,554,391-42,631,982 Size: 77,592 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:42,550,906-42,632,050)mRNA (may differ from genome)Protein (180 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: YAF2_HUMAN
DESCRIPTION: RecName: Full=YY1-associated factor 2;
FUNCTION: Binds to MYC and inhibits MYC-mediated transactivation. Also binds to MYCN and enhances MYCN-dependent transcriptional activation. Increases calpain 2-mediated proteolysis of YY1 in vitro. Component of the E2F6.com-1 complex, a repressive complex that methylates 'Lys-9' of histone H3, suggesting that it is involved in chromatin-remodeling.
SUBUNIT: Interacts with MYC, MYCN, RNF2/RING1B and YY1. Part of the E2F6.com-1 complex in G0 phase composed of E2F6, MGA, MAX, TFDP1, CBX3, BAT8, EUHMTASE1, RING1, RNF2, MBLR, L3MBTL2 and YAF2.
SUBCELLULAR LOCATION: Nucleus.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 RanBP2-type zinc finger.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.05 RPKM in Heart - Atrial Appendage
Total median expression: 223.71 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -18.8068-0.276 Picture PostScript Text
3' UTR -849.803485-0.244 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001876 - Znf_RanBP2

Pfam Domains:
PF00641 - Zn-finger in Ran binding protein and others
PF17219 - Yaf2/RYBP C-terminal binding motif

SCOP Domains:
90209 - Ran binding protein zinc finger-like
57783 - Zinc beta-ribbon

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2D9G - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q8IY57
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0070317 negative regulation of G0 to G1 transition

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC037777 - Homo sapiens YY1 associated factor 2, mRNA (cDNA clone MGC:41856 IMAGE:5276663), complete cds.
AK294260 - Homo sapiens cDNA FLJ59574 complete cds, highly similar to YY1-associated factor 2.
AK296191 - Homo sapiens cDNA FLJ57510 complete cds, highly similar to YY1-associated factor 2.
U72209 - Human YY1-associated factor 2 (YAF2) mRNA, complete cds.
AK291355 - Homo sapiens cDNA FLJ76409 complete cds, highly similar to Homo sapiens YY1 associated factor 2 (YAF2), mRNA.
CU691510 - Synthetic construct Homo sapiens gateway clone IMAGE:100020828 5' read YAF2 mRNA.
KJ898167 - Synthetic construct Homo sapiens clone ccsbBroadEn_07561 YAF2 gene, encodes complete protein.
EU446625 - Synthetic construct Homo sapiens clone IMAGE:100070061; IMAGE:100011834; FLH258256.01L YY1 associated factor 2 (YAF2) gene, encodes complete protein.
EU446756 - Synthetic construct Homo sapiens clone IMAGE:100069813; IMAGE:100011965; FLH258612.01L YY1 associated factor 2 (YAF2) gene, encodes complete protein.
AB527838 - Synthetic construct DNA, clone: pF1KB7919, Homo sapiens YAF2 gene for YY1 associated factor 2, without stop codon, in Flexi system.
JD249595 - Sequence 230619 from Patent EP1572962.
BX649019 - Homo sapiens mRNA; cDNA DKFZp779H1820 (from clone DKFZp779H1820).
AK127531 - Homo sapiens cDNA FLJ45624 fis, clone BRTHA3028339, moderately similar to Homo sapiens YY1 associated factor 2 (YAF2).

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8IY57 (Reactome details) participates in the following event(s):

R-HSA-9007283 CBX3 and PRC1.6 associate with E2F6.com-1
R-HSA-8953452 E2F6.com-1 complex binds the E2F1 gene promoter
R-HSA-8937989 RUNX1 binds PRC1 complexes
R-HSA-8953750 Transcriptional Regulation by E2F6
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-74160 Gene expression (Transcription)
R-HSA-8878171 Transcriptional regulation by RUNX1

-  Other Names for This Gene
  Alternate Gene Symbols: A8K5P0, B4DFU3, ENST00000534854.1, ENST00000534854.2, ENST00000534854.3, ENST00000534854.4, ENST00000534854.5, ENST00000534854.6, G3V465, NM_005748, Q8IY57, Q99710, uc324nks.1, uc324nks.2, YAF2_HUMAN
UCSC ID: ENST00000534854.7_7
RefSeq Accession: NM_005748.6
Protein: Q8IY57 (aka YAF2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.