Human Gene BAZ2A (ENST00000551812.5) from GENCODE V44
  Description: Homo sapiens bromodomain adjacent to zinc finger domain 2A (BAZ2A), transcript variant 1, mRNA. (from RefSeq NM_013449)
Gencode Transcript: ENST00000551812.5
Gencode Gene: ENSG00000076108.12
Transcript (Including UTRs)
   Position: hg38 chr12:56,595,930-56,636,379 Size: 40,450 Total Exon Count: 29 Strand: -
Coding Region
   Position: hg38 chr12:56,598,618-56,636,185 Size: 37,568 Coding Exon Count: 29 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:56,595,930-56,636,379)mRNA (may differ from genome)Protein (1905 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode
GeneCardsHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BAZ2A_HUMAN
DESCRIPTION: RecName: Full=Bromodomain adjacent to zinc finger domain protein 2A; AltName: Full=Transcription termination factor I-interacting protein 5; Short=TTF-I-interacting protein 5; Short=Tip5; AltName: Full=hWALp3;
FUNCTION: Essential component of the NoRC (nucleolar remodeling complex) complex, a complex that mediates silencing of a fraction of rDNA by recruiting histone-modifying enzymes and DNA methyltransferases, leading to heterochromatin formation and transcriptional silencing. In the complex, it plays a central role by being recruited to rDNA and by targeting chromatin modifying enzymes such as HDAC1, leading to repress RNA polymerase I transcription. Recruited to rDNA via its interaction with TTF1 and its ability to recognize and bind histone H4 acetylated on 'Lys- 16' (H4K16ac), leading to deacetylation of H4K5ac, H4K8ac, H4K12ac but not H4K16ac. Specifically binds pRNAs, 150-250 nucleotide RNAs that are complementary in sequence to the rDNA promoter; pRNA- binding is required for heterochromatin formation and rDNA silencing (By similarity).
SUBUNIT: Component of the NoRC complex, at least composed of SMARCA5/SNF2H and BAZ2A/TIP5. Interacts with TTF1; required for recruitment of the NoRC complex to rDNA. Interacts with DNMT1, DNM3B, HDAC1 and SIN3A (By similarity).
INTERACTION: P16333:NCK1; NbExp=2; IntAct=EBI-934890, EBI-389883;
SUBCELLULAR LOCATION: Nucleus, nucleolus (By similarity). Note=Colocalizes with the basal RNA polymerase I transcription factor UBF in the nucleolus (By similarity).
TISSUE SPECIFICITY: Expressed at moderate levels in most tissues analyzed, including heart, brain, placenta, lung, skeletal muscle, kidney and pancreas.
DOMAIN: The bromo domain and the PHD-type zinc finger recognize and bind histone H4 acetylated on 'Lys-16' (H4K16ac). These 2 domains play a central role in the recritment of chromatin silencing proteins such as DNMT1, DNMT3B and HDAC1.
DOMAIN: The MBD (methyl-CpG-binding) domain, also named TAM domain, specifically recognizes and binds a conserved stem-loop structure the association within pRNA. Binding to pRNA induces a conformational change of BAZ2A/TIP5 and is essential for targeting the NoRC complex to the nucleolus (By similarity).
PTM: Acetylation at Lys-680 by KAT8/MOF promotes its dissociation from pRNA, affecting heterochromatin formation, nucleosome positioning and rDNA silencing. Deacetylation by SIRT1 in late S phase enhances pRNA-binding, allowing de novo DNA methylation and heterochromatin formation. Acetylation is high during S phase and declines to background levels in late S phase when the silent copies of rRNA genes are replicated (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the WAL family.
SIMILARITY: Contains 4 A.T hook DNA-binding domains.
SIMILARITY: Contains 1 bromo domain.
SIMILARITY: Contains 1 DDT domain.
SIMILARITY: Contains 1 MBD (methyl-CpG-binding) domain.
SIMILARITY: Contains 1 PHD-type zinc finger.
SEQUENCE CAUTION: Sequence=AAB60864.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAG51228.1; Type=Erroneous termination; Positions=168; Note=Translated as Tyr;

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.02 RPKM in Testis
Total median expression: 788.03 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 -73.70194-0.380 Picture PostScript Text
3' UTR -875.902688-0.326 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
IPR017956 - AT_hook_DNA-bd_motif
IPR001487 - Bromodomain
IPR018359 - Bromodomain_CS
IPR004022 - DDT_dom
IPR018500 - DDT_dom_subgr
IPR018501 - DDT_dom_superfamily
IPR016177 - DNA-bd_integrase-typ
IPR001739 - Methyl_CpG_DNA-bd
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00439 - Bromodomain
PF02791 - DDT domain
PF01429 - Methyl-CpG binding domain
PF00628 - PHD-finger

ModBase Predicted Comparative 3D Structure on Q9UIF9
FrontTopSide
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001164 RNA polymerase I CORE element sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0016922 ligand-dependent nuclear receptor binding
GO:0042393 histone binding
GO:0046872 metal ion binding
GO:0070577 lysine-acetylated histone binding

Biological Process:
GO:0000183 chromatin silencing at rDNA
GO:0001188 RNA polymerase I transcriptional preinitiation complex assembly
GO:0006306 DNA methylation
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0016575 histone deacetylation

Cellular Component:
GO:0005634 nucleus
GO:0005677 chromatin silencing complex
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0016607 nuclear speck
GO:0033553 rDNA heterochromatin


-  Descriptions from all associated GenBank mRNAs
  AB032254 - Homo sapiens BAZ2A mRNA for bromodomain adjacent to zinc finger domain 2A, complete cds.
LF208948 - JP 2014500723-A/16451: Polycomb-Associated Non-Coding RNAs.
MA444525 - JP 2018138019-A/16451: Polycomb-Associated Non-Coding RNAs.
CR749379 - Homo sapiens mRNA; cDNA DKFZp781B109 (from clone DKFZp781B109).
AK023842 - Homo sapiens cDNA FLJ13780 fis, clone PLACE4000450, highly similar to Homo sapiens BAZ2A mRNA for bromodomain adjacent to zinc finger domain 2A.
AK303327 - Homo sapiens cDNA FLJ54813 complete cds, highly similar to Homo sapiens bromodomain adjacent to zinc finger domain, 2A (BAZ2A), mRNA.
LF384695 - JP 2014500723-A/192198: Polycomb-Associated Non-Coding RNAs.
MA620272 - JP 2018138019-A/192198: Polycomb-Associated Non-Coding RNAs.
AB002312 - Homo sapiens mRNA for KIAA0314 protein, partial cds.
AK127775 - Homo sapiens cDNA FLJ45876 fis, clone OCBBF3008392, highly similar to Homo sapiens bromodomain adjacent to zinc finger domain, 2A (BAZ2A).
JD280508 - Sequence 261532 from Patent EP1572962.
LF324443 - JP 2014500723-A/131946: Polycomb-Associated Non-Coding RNAs.
MA560020 - JP 2018138019-A/131946: Polycomb-Associated Non-Coding RNAs.
BC065914 - Homo sapiens cDNA clone IMAGE:4363504, partial cds.
LF324442 - JP 2014500723-A/131945: Polycomb-Associated Non-Coding RNAs.
MA560019 - JP 2018138019-A/131945: Polycomb-Associated Non-Coding RNAs.
JD054698 - Sequence 35722 from Patent EP1572962.
LF324441 - JP 2014500723-A/131944: Polycomb-Associated Non-Coding RNAs.
MA560018 - JP 2018138019-A/131944: Polycomb-Associated Non-Coding RNAs.
JD559792 - Sequence 540816 from Patent EP1572962.
JD336883 - Sequence 317907 from Patent EP1572962.
JD297683 - Sequence 278707 from Patent EP1572962.
JD561801 - Sequence 542825 from Patent EP1572962.
JD424612 - Sequence 405636 from Patent EP1572962.
JD494876 - Sequence 475900 from Patent EP1572962.
JD306014 - Sequence 287038 from Patent EP1572962.
JD449997 - Sequence 431021 from Patent EP1572962.
LF324440 - JP 2014500723-A/131943: Polycomb-Associated Non-Coding RNAs.
MA560017 - JP 2018138019-A/131943: Polycomb-Associated Non-Coding RNAs.
JD250581 - Sequence 231605 from Patent EP1572962.
JD181506 - Sequence 162530 from Patent EP1572962.
JD434594 - Sequence 415618 from Patent EP1572962.
JD538881 - Sequence 519905 from Patent EP1572962.
JD367398 - Sequence 348422 from Patent EP1572962.
JD189717 - Sequence 170741 from Patent EP1572962.
JD218961 - Sequence 199985 from Patent EP1572962.
JD186249 - Sequence 167273 from Patent EP1572962.
JD309617 - Sequence 290641 from Patent EP1572962.
JD465564 - Sequence 446588 from Patent EP1572962.
JD465563 - Sequence 446587 from Patent EP1572962.
LF324439 - JP 2014500723-A/131942: Polycomb-Associated Non-Coding RNAs.
MA560016 - JP 2018138019-A/131942: Polycomb-Associated Non-Coding RNAs.
LF324438 - JP 2014500723-A/131941: Polycomb-Associated Non-Coding RNAs.
MA560015 - JP 2018138019-A/131941: Polycomb-Associated Non-Coding RNAs.
JD120208 - Sequence 101232 from Patent EP1572962.
JD154007 - Sequence 135031 from Patent EP1572962.
JD299823 - Sequence 280847 from Patent EP1572962.
JD228750 - Sequence 209774 from Patent EP1572962.
JD049739 - Sequence 30763 from Patent EP1572962.
LF324437 - JP 2014500723-A/131940: Polycomb-Associated Non-Coding RNAs.
MA560014 - JP 2018138019-A/131940: Polycomb-Associated Non-Coding RNAs.
JD288243 - Sequence 269267 from Patent EP1572962.
JD399034 - Sequence 380058 from Patent EP1572962.
JD380225 - Sequence 361249 from Patent EP1572962.
JD466514 - Sequence 447538 from Patent EP1572962.
JD548594 - Sequence 529618 from Patent EP1572962.
JD393696 - Sequence 374720 from Patent EP1572962.
JD519927 - Sequence 500951 from Patent EP1572962.
JD465643 - Sequence 446667 from Patent EP1572962.
JD272683 - Sequence 253707 from Patent EP1572962.
JD358522 - Sequence 339546 from Patent EP1572962.
JD200946 - Sequence 181970 from Patent EP1572962.
JD150052 - Sequence 131076 from Patent EP1572962.
LF324436 - JP 2014500723-A/131939: Polycomb-Associated Non-Coding RNAs.
MA560013 - JP 2018138019-A/131939: Polycomb-Associated Non-Coding RNAs.
BC008965 - Homo sapiens bromodomain adjacent to zinc finger domain, 2A, mRNA (cDNA clone IMAGE:2959181), partial cds.
AK023830 - Homo sapiens cDNA FLJ13768 fis, clone PLACE4000211, highly similar to Bromodomain adjacent to zinc finger domain 2A.
JD052382 - Sequence 33406 from Patent EP1572962.
JD239186 - Sequence 220210 from Patent EP1572962.
JD411355 - Sequence 392379 from Patent EP1572962.
JD520965 - Sequence 501989 from Patent EP1572962.
JD230374 - Sequence 211398 from Patent EP1572962.
JD564225 - Sequence 545249 from Patent EP1572962.
JD287382 - Sequence 268406 from Patent EP1572962.
BC152739 - Synthetic construct Homo sapiens clone IMAGE:100015975, MGC:184123 bromodomain adjacent to zinc finger domain, 2A (BAZ2A) mRNA, encodes complete protein.
AB527356 - Synthetic construct DNA, clone: pF1KE0092, Homo sapiens BAZ2A gene for bromodomain adjacent to zinc finger domain, 2A, without stop codon, in Flexi system.
LF324435 - JP 2014500723-A/131938: Polycomb-Associated Non-Coding RNAs.
MA560012 - JP 2018138019-A/131938: Polycomb-Associated Non-Coding RNAs.
LF324434 - JP 2014500723-A/131937: Polycomb-Associated Non-Coding RNAs.
MA560011 - JP 2018138019-A/131937: Polycomb-Associated Non-Coding RNAs.
LF324433 - JP 2014500723-A/131936: Polycomb-Associated Non-Coding RNAs.
MA560010 - JP 2018138019-A/131936: Polycomb-Associated Non-Coding RNAs.
LF324432 - JP 2014500723-A/131935: Polycomb-Associated Non-Coding RNAs.
MA560009 - JP 2018138019-A/131935: Polycomb-Associated Non-Coding RNAs.
LF324431 - JP 2014500723-A/131934: Polycomb-Associated Non-Coding RNAs.
MA560008 - JP 2018138019-A/131934: Polycomb-Associated Non-Coding RNAs.
LF324430 - JP 2014500723-A/131933: Polycomb-Associated Non-Coding RNAs.
MA560007 - JP 2018138019-A/131933: Polycomb-Associated Non-Coding RNAs.
LF324429 - JP 2014500723-A/131932: Polycomb-Associated Non-Coding RNAs.
MA560006 - JP 2018138019-A/131932: Polycomb-Associated Non-Coding RNAs.
LF372275 - JP 2014500723-A/179778: Polycomb-Associated Non-Coding RNAs.
MA607852 - JP 2018138019-A/179778: Polycomb-Associated Non-Coding RNAs.
LF324428 - JP 2014500723-A/131931: Polycomb-Associated Non-Coding RNAs.
MA560005 - JP 2018138019-A/131931: Polycomb-Associated Non-Coding RNAs.
LF324427 - JP 2014500723-A/131930: Polycomb-Associated Non-Coding RNAs.
MA560004 - JP 2018138019-A/131930: Polycomb-Associated Non-Coding RNAs.
LF324426 - JP 2014500723-A/131929: Polycomb-Associated Non-Coding RNAs.
MA560003 - JP 2018138019-A/131929: Polycomb-Associated Non-Coding RNAs.
LF324425 - JP 2014500723-A/131928: Polycomb-Associated Non-Coding RNAs.
MA560002 - JP 2018138019-A/131928: Polycomb-Associated Non-Coding RNAs.
LF372269 - JP 2014500723-A/179772: Polycomb-Associated Non-Coding RNAs.
MA607846 - JP 2018138019-A/179772: Polycomb-Associated Non-Coding RNAs.
LF324424 - JP 2014500723-A/131927: Polycomb-Associated Non-Coding RNAs.
MA560001 - JP 2018138019-A/131927: Polycomb-Associated Non-Coding RNAs.
LF324423 - JP 2014500723-A/131926: Polycomb-Associated Non-Coding RNAs.
MA560000 - JP 2018138019-A/131926: Polycomb-Associated Non-Coding RNAs.
AF000422 - Homo sapiens TTF-I interacting peptide 5 mRNA, partial cds.
LF324422 - JP 2014500723-A/131925: Polycomb-Associated Non-Coding RNAs.
MA559999 - JP 2018138019-A/131925: Polycomb-Associated Non-Coding RNAs.
LF372268 - JP 2014500723-A/179771: Polycomb-Associated Non-Coding RNAs.
MA607845 - JP 2018138019-A/179771: Polycomb-Associated Non-Coding RNAs.
LF324421 - JP 2014500723-A/131924: Polycomb-Associated Non-Coding RNAs.
MA559998 - JP 2018138019-A/131924: Polycomb-Associated Non-Coding RNAs.
LF324420 - JP 2014500723-A/131923: Polycomb-Associated Non-Coding RNAs.
MA559997 - JP 2018138019-A/131923: Polycomb-Associated Non-Coding RNAs.
LF372267 - JP 2014500723-A/179770: Polycomb-Associated Non-Coding RNAs.
MA607844 - JP 2018138019-A/179770: Polycomb-Associated Non-Coding RNAs.
LF372265 - JP 2014500723-A/179768: Polycomb-Associated Non-Coding RNAs.
MA607842 - JP 2018138019-A/179768: Polycomb-Associated Non-Coding RNAs.
LF324419 - JP 2014500723-A/131922: Polycomb-Associated Non-Coding RNAs.
MA559996 - JP 2018138019-A/131922: Polycomb-Associated Non-Coding RNAs.
LF324418 - JP 2014500723-A/131921: Polycomb-Associated Non-Coding RNAs.
MA559995 - JP 2018138019-A/131921: Polycomb-Associated Non-Coding RNAs.
JD231730 - Sequence 212754 from Patent EP1572962.
JD268385 - Sequence 249409 from Patent EP1572962.
JD126369 - Sequence 107393 from Patent EP1572962.
JD052251 - Sequence 33275 from Patent EP1572962.

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

Protein Q9UIF9 (Reactome details) participates in the following event(s):

R-HSA-427409 Nucleolar Remodelling Complex (NoRC) binds intergenic region of rDNA
R-HSA-5227490 NoRC:HDAC:DNMT methylates cytosine of the rRNA genes
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B3KN66, BAZ2A_HUMAN, ENST00000551812.1, ENST00000551812.2, ENST00000551812.3, ENST00000551812.4, KIAA0314, NM_013449, O00536, O15030, Q68DI8, Q96H26, Q9UIF9, TIP5, uc001slq.1, uc001slq.2
UCSC ID: ENST00000551812.5
RefSeq Accession: NM_013449
Protein: Q9UIF9 (aka BAZ2A_HUMAN or BA2A_HUMAN)
CCDS: CCDS44924.1, CCDS73483.1

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