Human Gene CENPBD1 (uc002fpr.3) Description and Page Index
  Description: Homo sapiens CENPB DNA-binding domains containing 1 (CENPBD1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr16:90,036,183-90,039,240 Size: 3,058 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr16:90,037,767-90,038,330 Size: 564 Coding Exon Count: 1 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:90,036,183-90,039,240)mRNA (may differ from genome)Protein (187 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
PubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=CENPB DNA-binding domain-containing protein 1;
SUBCELLULAR LOCATION: Nucleus (Potential).
SIMILARITY: Contains 1 HTH CENPB-type DNA-binding domain.
SIMILARITY: Contains 1 HTH psq-type DNA-binding domain.

-  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: 6.66 RPKM in Pituitary
Total median expression: 168.64 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -416.69910-0.458 Picture PostScript Text
3' UTR -554.031584-0.350 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
IPR009057 - Homeodomain-like
IPR006600 - HTH_CenpB_DNA-bd_dom
IPR007889 - HTH_Psq

Pfam Domains:
PF03221 - Tc5 transposase DNA-binding domain
PF04218 - CENP-B N-terminal DNA-binding domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on B2RD01
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 Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  BC040698 - Homo sapiens hypothetical protein MGC16385, mRNA (cDNA clone IMAGE:6155608).
AK074351 - Homo sapiens cDNA FLJ23771 fis, clone HEP19402.
BC005105 - Homo sapiens hypothetical protein MGC16385, mRNA (cDNA clone IMAGE:3636649).
JD506552 - Sequence 487576 from Patent EP1572962.
JD272116 - Sequence 253140 from Patent EP1572962.
JD334819 - Sequence 315843 from Patent EP1572962.
JD383335 - Sequence 364359 from Patent EP1572962.
JD347695 - Sequence 328719 from Patent EP1572962.
JD066333 - Sequence 47357 from Patent EP1572962.
JD336123 - Sequence 317147 from Patent EP1572962.
JD165877 - Sequence 146901 from Patent EP1572962.
JD052395 - Sequence 33419 from Patent EP1572962.
JD086256 - Sequence 67280 from Patent EP1572962.
BC009263 - Homo sapiens hypothetical protein MGC16385, mRNA (cDNA clone IMAGE:3937996), with apparent retained intron.
JD376277 - Sequence 357301 from Patent EP1572962.
AK056131 - Homo sapiens cDNA FLJ31569 fis, clone NT2RI2001621.
JD251479 - Sequence 232503 from Patent EP1572962.
JD292602 - Sequence 273626 from Patent EP1572962.
JD461450 - Sequence 442474 from Patent EP1572962.
JD406766 - Sequence 387790 from Patent EP1572962.
JD523429 - Sequence 504453 from Patent EP1572962.
JD351743 - Sequence 332767 from Patent EP1572962.
JD448342 - Sequence 429366 from Patent EP1572962.
JD332356 - Sequence 313380 from Patent EP1572962.
JD175915 - Sequence 156939 from Patent EP1572962.
JD138304 - Sequence 119328 from Patent EP1572962.
JD472155 - Sequence 453179 from Patent EP1572962.
JD256974 - Sequence 237998 from Patent EP1572962.
JD180061 - Sequence 161085 from Patent EP1572962.
JD085879 - Sequence 66903 from Patent EP1572962.
JD047641 - Sequence 28665 from Patent EP1572962.
JD439153 - Sequence 420177 from Patent EP1572962.
JD556313 - Sequence 537337 from Patent EP1572962.
JD181405 - Sequence 162429 from Patent EP1572962.
JD340816 - Sequence 321840 from Patent EP1572962.
JD179686 - Sequence 160710 from Patent EP1572962.
JD481349 - Sequence 462373 from Patent EP1572962.
JD236872 - Sequence 217896 from Patent EP1572962.
DQ600479 - Homo sapiens piRNA piR-38545, complete sequence.
JD102362 - Sequence 83386 from Patent EP1572962.
JD542085 - Sequence 523109 from Patent EP1572962.
JD247929 - Sequence 228953 from Patent EP1572962.
JD555217 - Sequence 536241 from Patent EP1572962.
AK315352 - Homo sapiens cDNA, FLJ96397.
JD073572 - Sequence 54596 from Patent EP1572962.
JD438535 - Sequence 419559 from Patent EP1572962.
JD116671 - Sequence 97695 from Patent EP1572962.
JD540578 - Sequence 521602 from Patent EP1572962.
JD257379 - Sequence 238403 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RD01, CENP1_HUMAN, NM_145039, NP_659476
UCSC ID: uc002fpr.3
RefSeq Accession: NM_145039
Protein: B2RD01 (aka CENP1_HUMAN)
CCDS: CCDS45556.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_145039.3
exon count: 1CDS single in 3' UTR: no RNA size: 3061
ORF size: 564CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 833.00frame shift in genome: no % Coverage: 99.90
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: 0# 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.