Human Gene HBP1 (ENST00000222574.9_4) from GENCODE V47lift37
  Description: HMG-box transcription factor 1, transcript variant 2 (from RefSeq NM_012257.4)
Gencode Transcript: ENST00000222574.9_4
Gencode Gene: ENSG00000105856.14_14
Transcript (Including UTRs)
   Position: hg19 chr7:106,809,448-106,842,967 Size: 33,520 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr7:106,820,339-106,841,876 Size: 21,538 Coding Exon Count: 10 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:106,809,448-106,842,967)mRNA (may differ from genome)Protein (514 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HBP1_HUMAN
DESCRIPTION: RecName: Full=HMG box-containing protein 1; AltName: Full=HMG box transcription factor 1; AltName: Full=High mobility group box transcription factor 1;
FUNCTION: Transcriptional repressor that binds to the promoter region of target genes. Plays a role in the regulation of the cell cycle and of the Wnt pathway. Binds preferentially to the sequence 5'-TTCATTCATTCA-3'. Binding to the H1F0 promoter is enhanced by interaction with RB1. Disrupts the interaction between DNA and TCF4.
SUBUNIT: Binds the second PAH repeat of SIN3A (By similarity). Binds TCF4 and RB1.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Contains 1 AXH domain.
SIMILARITY: Contains 1 HMG box DNA-binding domain.
SEQUENCE CAUTION: Sequence=BAB85059.1; Type=Erroneous initiation;

-  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

+  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: 21.84 RPKM in Testis
Total median expression: 539.87 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 -74.90198-0.378 Picture PostScript Text
3' UTR -292.101091-0.268 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
IPR013723 - Ataxin-1_HBP1
IPR003652 - Ataxin_AXH_dom
IPR009071 - HMG_superfamily

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF08517 - Ataxin-1 and HBP1 module (AXH)
PF09011 - HMG-box domain

SCOP Domains:
47095 - HMG-box
102031 - AXH domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2E6O - NMR MuPIT 3QVE - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O60381
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007050 cell cycle arrest
GO:0016055 Wnt signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AK295910 - Homo sapiens cDNA FLJ56446 complete cds, highly similar to HMG box-containing protein 1.
AK298504 - Homo sapiens cDNA FLJ55129 complete cds, highly similar to HMG box-containing protein 1.
BC017069 - Homo sapiens HMG-box transcription factor 1, mRNA (cDNA clone MGC:9634 IMAGE:3914986), complete cds.
AK122785 - Homo sapiens cDNA FLJ16340 fis, clone TESTI2011575, highly similar to HMG box-containing protein 1.
AF182038 - Homo sapiens HMG box containing protein 1a mRNA, complete cds.
BC022329 - Homo sapiens HMG-box transcription factor 1, mRNA (cDNA clone MGC:22757 IMAGE:4278438), complete cds.
AF019214 - Homo sapiens HMG box containing protein 1 mRNA, complete cds.
CU677821 - Synthetic construct Homo sapiens gateway clone IMAGE:100017382 5' read HBP1 mRNA.
CU692562 - Synthetic construct Homo sapiens gateway clone IMAGE:100022320 5' read HBP1 mRNA.
AB463745 - Synthetic construct DNA, clone: pF1KB7788, Homo sapiens HBP1 gene for HMG-box transcription factor 1, without stop codon, in Flexi system.
DQ891576 - Synthetic construct clone IMAGE:100004206; FLH178293.01X; RZPDo839B07128D HMG-box transcription factor 1 (HBP1) gene, encodes complete protein.
KJ898644 - Synthetic construct Homo sapiens clone ccsbBroadEn_08038 HBP1-like gene, encodes complete protein.
AK074353 - Homo sapiens cDNA FLJ23773 fis, clone HEP20215, highly similar to Homo sapiens HMG box containing protein 1 mRNA.
JD407099 - Sequence 388123 from Patent EP1572962.
JD409494 - Sequence 390518 from Patent EP1572962.
JD485963 - Sequence 466987 from Patent EP1572962.
AK025284 - Homo sapiens cDNA: FLJ21631 fis, clone COL08155, highly similar to AF019214 Homo sapiens HMG box containing protein 1 mRNA.
JD053222 - Sequence 34246 from Patent EP1572962.
JD110012 - Sequence 91036 from Patent EP1572962.
JD184461 - Sequence 165485 from Patent EP1572962.
JD430043 - Sequence 411067 from Patent EP1572962.
JD024991 - Sequence 6015 from Patent EP1572962.
JD033602 - Sequence 14626 from Patent EP1572962.
JD241912 - Sequence 222936 from Patent EP1572962.
JD245184 - Sequence 226208 from Patent EP1572962.
JD284919 - Sequence 265943 from Patent EP1572962.
JD067097 - Sequence 48121 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KVB7, ENST00000222574.1, ENST00000222574.2, ENST00000222574.3, ENST00000222574.4, ENST00000222574.5, ENST00000222574.6, ENST00000222574.7, ENST00000222574.8, HBP1_HUMAN, NM_012257, O60381, Q8TBM1, Q8TE93, Q96AJ2, uc317dfg.1, uc317dfg.2
UCSC ID: ENST00000222574.9_4
RefSeq Accession: NM_012257.4
Protein: O60381 (aka HBP1_HUMAN)

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