Human Gene INO80B (uc002slg.3) Description and Page Index
  Description: Homo sapiens INO80 complex subunit B (INO80B), mRNA.
RefSeq Summary (NM_031288): This gene encodes a subunit of an ATP-dependent chromatin remodeling complex, INO80, which plays a role in DNA and nucleosome-activated ATPase activity and ATP-dependent nucleosome sliding. Readthrough transcription of this gene into the neighboring downstream gene, which encodes WW domain-binding protein 1, generates a non-coding transcript. [provided by RefSeq, Feb 2011]. ##Evidence-Data-START## Transcript exon combination :: BC064425.1, ERR279845.3562.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000233331.12/ ENSP00000233331.7 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr2:74,682,150-74,685,087 Size: 2,938 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr2:74,682,244-74,684,991 Size: 2,748 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:74,682,150-74,685,087)mRNA (may differ from genome)Protein (356 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=INO80 complex subunit B; AltName: Full=High mobility group AT-hook 1-like 4; AltName: Full=IES2 homolog; Short=hIes2; AltName: Full=PAP-1-associated protein 1; Short=PAPA-1; AltName: Full=Zinc finger HIT domain-containing protein 4;
FUNCTION: Induces growth and cell cycle arrests at the G1 phase of the cell cycle.
FUNCTION: Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.
SUBUNIT: Component of the chromatin remodeling INO80 complex; specifically part of a complex module associated with the helicase ATP-binding and the helicase C-terminal domain of INO80. Interacts with RP9.
INTERACTION: P18065:IGFBP2; NbExp=4; IntAct=EBI-715611, EBI-2504392;
SUBCELLULAR LOCATION: Nucleus. Nucleus, nucleolus.
SIMILARITY: Contains 1 HIT-type zinc finger.
SEQUENCE CAUTION: Sequence=BAB21111.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 40.70 RPKM in Pituitary
Total median expression: 1155.98 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 -24.9094-0.265 Picture PostScript Text
3' UTR -13.3696-0.139 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
IPR006880 - PAPA1
IPR007529 - Znf_HIT

Pfam Domains:
PF04438 - HIT zinc finger
PF04795 - PAPA-1-like conserved region

ModBase Predicted Comparative 3D Structure on Q9C086
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006974 cellular response to DNA damage stimulus
GO:0016579 protein deubiquitination

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0031011 Ino80 complex

-  Descriptions from all associated GenBank mRNAs
  LF207227 - JP 2014500723-A/14730: Polycomb-Associated Non-Coding RNAs.
AK295889 - Homo sapiens cDNA FLJ52945 complete cds, highly similar to Zinc finger HIT domain-containing protein 4.
AK055333 - Homo sapiens cDNA FLJ30771 fis, clone FEBRA2000740.
AK295901 - Homo sapiens cDNA FLJ59544 complete cds, highly similar to Zinc finger HIT domain-containing protein 4.
BC039617 - Homo sapiens INO80 complex subunit B, mRNA (cDNA clone IMAGE:5770045).
BC064425 - Homo sapiens INO80 complex subunit B, mRNA (cDNA clone MGC:70669 IMAGE:5760624), complete cds.
AB054538 - Homo sapiens mRNA for PAPA-1, complete cds.
BC050666 - Homo sapiens INO80 complex subunit B, mRNA (cDNA clone IMAGE:6527060), partial cds.
JD497534 - Sequence 478558 from Patent EP1572962.
LF207229 - JP 2014500723-A/14732: Polycomb-Associated Non-Coding RNAs.
JD125163 - Sequence 106187 from Patent EP1572962.
LF383538 - JP 2014500723-A/191041: Polycomb-Associated Non-Coding RNAs.
MA619115 - JP 2018138019-A/191041: Polycomb-Associated Non-Coding RNAs.
MA442804 - JP 2018138019-A/14730: Polycomb-Associated Non-Coding RNAs.
MA442806 - JP 2018138019-A/14732: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9C086 (Reactome details) participates in the following event(s):

R-HSA-5689544 UCHL5 binds INO80 complex
R-HSA-5689603 UCH proteinases
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: HMGA1L4, IN80B_HUMAN, NM_031288, NP_112578, PAPA1, Q9C086, ZNHIT4
UCSC ID: uc002slg.3
RefSeq Accession: NM_031288
Protein: Q9C086 (aka IN80B_HUMAN)
CCDS: CCDS1942.2

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_031288.3
exon count: 5CDS single in 3' UTR: no RNA size: 1266
ORF size: 1071CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2244.50frame shift in genome: no % Coverage: 99.61
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 100# strange splices: 0
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.