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HBD Gene

protein-coding   GIFtS: 54

GC11M005210
hemoglobin, delta
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
Delta-globin 3
OTTHUMP00000069639 2
Descriptions
Hemoglobin delta chain 3
delta globin 2
delta-globin chain 2
hemoglobin, delta 2
External Ids
HGNC: 48291
Entrez Gene: 30452
UniProtKB: P020423
Ensembl: ENSG000001881707
Search outside databases for aliases for HBD gene

Previous GC identifers: GC11M005996 GC11M005549 GC11M005206 GC11M005213 GC11M005217 GC11M005204

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

EntrezGene summary for HBD:
The delta (HBD) and beta (HBB) genes are normally expressed in the adult: two alpha chains plus two
beta chains constitute HbA, which in normal adult life comprises about 97% of the total
hemoglobin. Two alpha chains plus two delta chains constitute HbA-2, which with HbF comprises the
remaining 3% of adult hemoglobin. Five beta-like globin genes are found within a 45 kb cluster on
chromosome 11 in the following order: 5'-epsilon--Ggamma--Agamma--delta--beta-3'.
Mutations in the delta-globin gene are associated with beta-thalassemia. [provided by RefSeq]

UniProtKB/Swiss-Prot: HBD_HUMAN, P02042
Function: Involved in oxygen transport from the lung to the various peripheral tissues

Gene Wiki entry for HBD

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the HBD gene  

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

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

GeneLoc gene densities for chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M005210:     (about GC identifiers)

Start:
5,210,484 bp from pter
End:
5,212,434 bp from pter
Size:
1,951 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000011.8  NT_009237.17  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: HBD_HUMAN, P02042 (See protein sequence)
Recommended Name: Hemoglobin subunit delta  
Size: 147 amino acids; 16055 Da
Subunit: Heterotetramer of two alpha chains and two delta chains in adult hemoglobin A2 (HbA2).
HbA2 represents less than 3.5% of adult hemoglobin
PDB structure from and Proteopedia :
1SHR (3D)    1SI4 (3D)    
Secondary accessions: Q3Y5H3 Q8WXT7

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_000510.1  

    ENSEMBL proteins: 
    ENSP00000292901 ENSP00000369654 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Sigma-Aldrich Proteins for HBD  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Browse Abcam for Recombinant Proteins
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    1 Gene Ontology (GO) cellular component term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005833 hemoglobin complex TAS7555018
    About this table

    Antibodies for HBD: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse Antibodies at Sigma-Aldrich
    Browse R&D Systems for Antibodies
    Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for HBD

    Assays for HBD: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    3 InterPro domains/families:
     IPR012292 Globin
     IPR000971 Globin_subset
     IPR002337 Haemoglobin_b


       GeneDecks  HBD for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry P02042

    ProtoNet protein and cluster: P02042

    1 Blocks protein family: IPB002337 Beta haemoglobin signature

    UniProtKB/Swiss-Prot: HBD_HUMAN, P02042
    Similarity: Belongs to the globin family

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (HBD)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (HBD)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_000519

                  Applied Biosystems Silencer® siRNAs for HBD

                  Sigma-Aldrich siRNA for HBD  
                         Sigma-Aldrich shRNA for HBD  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for HBD
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_000519
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_000519
                                     untagged cDNA clone in CMV expression vector: NM_000519 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_000519

    UniProtKB/Swiss-Prot: HBD_HUMAN, P02042
    Function: Involved in oxygen transport from the lung to the various peripheral tissues

    Genatlas biochemistry entry for HBD:
    hemoglobin,delta,adult

    4 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005344 oxygen transporter activity IEA--
    GO:0019825 oxygen binding IEA--
    GO:0020037 heme binding IEA--
    GO:0046872 metal ion binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


      --

    2 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810 transport IEA--
    GO:0015671 oxygen transport IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for HBD
    1 Novoseek chemical compound relationship for HBD gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    dihydrofolate 42.59 1 8612704 (1)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (HBD)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (HBD)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_000519

                  Sigma-Aldrich siRNA for HBD  
                         Sigma-Aldrich shRNA for HBD  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_000519  

    REFSEQ mRNAs for HBD gene: 

    NM_000519.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_000519  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_000519
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_000519
                                     untagged cDNA clone in CMV expression vector: NM_000519 

    Additional cDNA sequence: 

    AY034468.1 BC069307.1 BC070282.1 DQ655982.2 

    8 DOTS entries:

    DT.95198800  DT.95086395  DT.95086397  DT.95287469  DT.85101421  DT.92475803  DT.92476019  DT.99971801 

    6 AceView cDNA sequences:

    NM_000519 BC069307 BC070282 AY034468 BG941162 BG940533 

    highest scoring ESTs for HBD:

    BF174264 BG940711 V00505 AV757270 AY034468 BC070282 BG942666 BG943559 BG944125 BQ446275 

    Unigene Cluster for HBD:

    Hemoglobin, delta
    Hs.699280  [show with all ESTs]
    Unigene Representative Sequence: AY034468


    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for HBD (see all 7 )

    ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8a · 8b
    SP1:                                                                                    
    SP2:                                                                                    
    SP3:                                                        -                           
    SP4:                                                                                    
    SP5:                          -     -                                                   

    About this scheme

    ECgene alternative splicing isoforms for HBD

    2 Ensembl transcripts including schematic representations:
    ENST00000292901  ENST00000380299  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    HBD expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for HBD

    1 / 2 / 3

    4 probe-sets matching HBD gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    33516_at2, 3 U95-A 2 1.00 0.94 0.97 0.71 V00505 0.20 1.00 0.72 1

    31687_f_at2, 3 U95-A 5 0.81 0.37 0.92 1.32 M25079 0.40 0.50 0.45 1

    206834_at2, 3 U133-A 1 1.00 1.00 -- -- NM_000519 0.40 0.50 0.45 1

    206834_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  HBD for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: GCAAGAAGGT

    SOURCE GeneReport for Unigene cluster: Hs.699280

    Expression variation in blood from EXPOLDB for HBD

    UniProtKB/Swiss-Prot: HBD_HUMAN, P02042
    Tissue specificity: Red blood cells

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for HBD gene from 1 species
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    mouse
    (Mus musculus)
    Gm57365 7 predicted gene 5736   -- BC147126 
    About this table        Species with no ortholog for HBD

    ENSEMBL Gene Tree for HBD
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for HBD gene
    HBB2  HBE12  HBG22  CYGB2  HBG12  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/90 NCBI SNPs in HBD are shown (see all 90 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 105)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 11 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs79484161,2
    A,C,F,H5213007(+) AAGTGC/AAAAGT 1 -- ng31 tfbs312Minor allele frequency- A:0.17EA NA EU WA 998
    --
    rs79486681,2
    A,C,F,H5213223(+) attgaG/Aggaaa 1 -- ng31 tfbs3 trp34Minor allele frequency- A:0.43EU EA WA 406
    rs38137271,2
    A,C,F,H5212488(-) ATATGC/TAGAGG 1 -- ng3111Minor allele frequency- T:0.38EA MN EU WA 2504
    rs38137261,2
    C,F,H5212565(-) AGCCTA/GAAACA 1 -- ng316Minor allele frequency- G:0.02MN EA EU WA 776
    rs169119981,2
    C,F,H5214276(+) GGTACG/AATAAA 1 -- ng3111Minor allele frequency- A:0.06NA EU EA WA 980
    rs79362531,2
    A,F,H5213506(+) gtggtG/Aatatg 1 -- ng314Minor allele frequency- A:0.08EU EA WA 420
    rs37590741,2
    C,F,H5214354(-) ATCCAC/TATATC 1 -- ng318Minor allele frequency- N:0.00NA EU EA WA 636
    rs71153751,2
    C,F,H5214385(+) AACCAG/TGTCAA 1 -- ng3111Minor allele frequency- T:0.04EU EA WA NA 980
    rs118221991,2
    F,H5210375(+) TAATCG/ATAGCA 1 -- ng514Minor allele frequency- A:0.03EU EA WA 416
    rs96659641,2
    F,H5213419(+) gaaaaG/Caaacg 1 -- ng31 trp34Minor allele frequency- C:0.06EU EA WA 412
    About this table

    HapMap Linkage Disequilibrium images for HBD (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 142000

    UniProtKB/Swiss-Prot: HBD_HUMAN, P02042

  • Elevated HbA2 level are characteristic of beta-thalassemia trait
  • 2 Novoseek disease relationships for HBD gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    thalassemia 63.11 1 11493481 (1)
    sickle cell disease 44.37 1 7708766 (1)
    About this table

    Genatlas disease: HBD
    thalassemia,delta

    Human Gene Mutation Database: HBD

    (Possibly Related Articles in Doctor's Guide)
    About This Section

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

    10/133 PubMed articles for HBD gene (see all 133 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 3045 HGNC: 4829 AceView: HBD Ensembl:ENSG00000188170 euGenes: HUgn3045
    ECgene: HBD H-InvDB: HBD
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    HbVarhttp://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=directlink&gene=HBD
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for HBD:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Explore super-pooled esiRNAs Proteins for HBD
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