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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HBBP1 Gene

pseudogene   GIFtS: 31
GCID: GC11M005263

Hemoglobin, Beta Pseudogene 1

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 6.2

Aliases
Hemoglobin, Beta Pseudogene 11 2
HBB5

External Ids:    HGNC: 48281   Entrez Gene: 30442   Ensembl: ENSG000002299887   OMIM: 1419005   
ORGUL members:    fRNAdb10:FR042621 FR125407 FR265985 FR085101 FR147411      
H-InvDB12:HIT000194114 HIT000320809 HIT000194113 HIT000321980    
NCBI13:M11428 U01317 V00512 U01317 U01317 see all 8    
NONCODE14:n333955 n340951 n343029 n343032 n405380 see all 8      
Rfam:RF00621    
RNAdb15:LIT2039 HIV2553 LIT2038 EVF37699 LIT2037    

Export aliases for HBBP1 gene to outside databases

Previous GC identifers: GC11M006011 GC11U900033 GC11M005222 GC11M005227 GC11M005219 GC11M004924


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for HBBP1 Gene: 
HBBP1 (hemoglobin, beta pseudogene 1) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with HBBP1 include heinz body anemias, beta-, and thalassemia-beta, dominant inclusion-body.

fRNAdb sequence ontologies for HBBP1 - the ORGUL cluster for this gene includes several descriptions:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
mature_transcript - A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified.
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.
ribozyme - An RNA with catalytic activity.

View fRNAdb secondary structures for HBBP1

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000011.9  NC_018922.2  NT_009237.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HBBP1 gene promoter:
         TBP   TFIID   c-Myb   STAT3   IRF-1   GATA-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHBBP1 promoter sequence
   Search SABiosciences Chromatin IP Primers for HBBP1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HBBP1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11p15.5   Ensembl cytogenetic band:  11p15.4   HGNC cytogenetic band: 11p15.5

HBBP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HBBP1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M005263:  view genomic region     (about GC identifiers)

Start:
5,263,184 bp from pter      End:
5,264,822 bp from pter
Size:
1,639 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for HBBP1

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:
     Genatlas biochemistry entry for HBBP1:
hemoglobin,beta,pseudogene 1

Animal Models:
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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HBBP1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
5/7 fRNAdb Secondary structures (see all 7):


Unigene Cluster for HBBP1:

Hemoglobin, beta pseudogene 1
Hs.20205  [show with all ESTs]
Unigene Representative Sequence: BX109789
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000454892(uc001mag.3) ENST00000433329
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Additional mRNA sequence: NR_001589.1 

2 DOTS entries:

DT.410242  DT.410243 

1 AceView cDNA sequence:

NR_001589 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

HBBP1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
HBBP1 Expression
About this image


Genevestigator expression for HBBP1

SOURCE GeneReport for Unigene cluster: Hs.20205
    SABiosciences Custom PCR Arrays for HBBP1
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section
  --

ENSEMBL Gene Tree for HBBP1 (if available)
TreeFam Gene Tree for HBBP1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/111 SNPs in HBBP1 are shown (see all 111)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs110364151,2
C,F,A,H--5262782(+) TAAATC/AATAAA 1 -- ds500112Minor allele frequency- A:0.28NA WA CSA NS EA 728
rs1892498691,2
--5262789(+) TAAAAA/TATATG 1 -- ds50010--------
rs1822076851,2
--5262824(+) CTGCAA/GTCACC 1 -- ds50010--------
rs1872148411,2
--5262836(+) AATGAA/GCTATA 1 -- ds50010--------
rs118201141,2
C,F,H--5262843(+) TATATC/ACTGAG 1 -- ds50018Minor allele frequency- A:0.02NS EA NA 780
rs340337251,2
C--5262849(+) CTGAGT/-TTCAT 1 -- ds50012Minor allele frequency- -:0.13CSA NS 356
rs1817484251,2
--5262866(+) AATAGC/TCTATA 1 -- ds50010--------
rs752441711,2
C,F--5262990(+) AGAGAC/TGATTT 1 -- ds50012Minor allele frequency- T:0.02NS WA 488
rs169122031,2
C,F,H--5262991(+) GAGACG/AATTTC 1 -- ds500112Minor allele frequency- A:0.11NA NS EA WA CSA 1057
rs1856483791,2
--5263005(+) TTCCTA/GGGAGT 1 -- ds50010--------

HapMap Linkage Disequilibrium report for HBBP1 (5263184 - 5264822 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for HBBP1:    About this table     
Variant IDTypeSubtypePubMed ID
nsv896929CNV Loss21882294

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM gene information: 141900OMIM information: 194071 604499 607967 609270 609470 142200 602670    
OMIM disorders: 603903  604131  140700  603902  
8 diseases for HBBP1:    About MalaCards
heinz body anemias, beta-    thalassemia-beta, dominant inclusion-body    heinz body anemias    methemoglobinemia
hereditary persistence of fetal hemoglobin    sickle cell anemia    thalassemia    anemia


HBBP1 for disorders           About GeneDecksing

Genetic Association Database (GAD): HBBP1
Human Genome Epidemiology (HuGE) Navigator: HBBP1 (2 documents)

Export disorders for HBBP1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for HBBP1 gene, integrated from 9 sources (see all 19):
(articles sorted by number of sources associating them with HBBP1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A genome-wide association identified the common genet ic variants influence disease severity in beta0-thalassemia/hemoglobin E. (PubMed id 20183929)1, 4 Nuinoon M....Fucharoen S. (2010)
  2. A review of the molecular genetics of the human alpha-globin gene cluster. (PubMed id 2649166)1, 3 Higgs D.R....Weatherall D.J. (1989)
  3. GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children. (PubMed id 23263863)1 Li J....Sleiman P.M. (2013)
  4. A single nucleotide polymorphism in the HBBP1 gene in the human b-globin locus is associated with a mild b-thalassemia disease phenoty pe. (PubMed id 22943111)1 Giannopoulou E....Patrinos G.P. (2012)
  5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (2012)
  6. Influence of BCL11A, HBS1L-MYB, HBBP1 single nucleotid e polymorphisms and the HBG2 XmnI polymorphism On Hb F levels. (PubMed id 23094636)1 Roy P....Das M. (2012)
  7. A genome-wide association identified the common genet ic variants influence disease severity in beta(0)-thalassemia/hemoglobin E. (PubMed id 19924444)4 Nuinoon M....Fucharoen S. (2009)
  8. Real-time PCR for single-cell genotyping in sickle cell and thalassemia syndromes as a rapid, accurate, reliable, and widely applicable protocol for preimplantation genetic diagnosis. (PubMed id 15108284)1 Vrettou C....Kanavakis E. (2004)
  9. Isolation and nucleotide sequence analysis of the beta-type globin pseudogene from human, gorilla and chimpanzee. (PubMed id 6098690)1 Chang L.Y. and Slightom J.L. (1984)
  10. Confirmation of the potential usefulness of two human beta globin pseudogene markers to estimate gene flows to and from sub-Saharan Africans. (PubMed id 12030652)9 Ciminelli B.M....Pardo M.G. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
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  Query String
PubMed
OMIM
NCBI Bookshelf
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 3044 HGNC: 4828 AceView: HBBP1 Ensembl:ENSG00000229988 euGenes: HUgn3044
ECgene: HBBP1 H-InvDB: HBBP1

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for HBBP1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for HBBP1 gene:
Search GeneIP for patents involving HBBP1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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