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KDM3B Gene

protein-coding   GIFtS: 51

GC05P137717
lysine (K)-specific demethylase 3B
(Previous names: chromosome 5 open reading frame 7, jumonji domain containing 1B )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbols: C5orf7, JMJD1B)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
5qNCA 2
C5orf7 2, 3
EC 1.14.11.- 3
JHDM2B 3
JMJD1B 2, 3
KIAA1082 1, 2, 3
Descriptions
JmjC domain-containing histone demethylation protein 2B 3
Jumonji domain-containing protein 1B 3
Nuclear protein 5qNCA 2, 3
chromosome 5 open reading frame 7 1
jumonji domain containing 1B 1, 2
lysine (K)-specific demethylase 3B 2
lysine-specific demethylase 3B 1
External Ids
HGNC: 13371
Entrez Gene: 517802
UniProtKB: Q7LBC63
Ensembl: ENSG000001207337
Search outside databases for aliases for KDM3B gene

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

UniProtKB/Swiss-Prot: KDM3B_HUMAN, Q7LBC6
Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing
a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate.
May have tumor suppressor activity

Gene Wiki entry for KDM3B (JMJD1B)

(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

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.2   HGNC cytogenetic band: 5q31

KDM3B 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 5         GeneLoc Exon Structure

GeneLoc location for GC05P137717:     (about GC identifiers)

Start:
137,716,184 bp from pter
End:
137,800,615 bp from pter
Size:
84,432 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000005.8  NT_034772.5  
(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: KDM3B_HUMAN, Q7LBC6 (See protein sequence)
Recommended Name: Lysine-specific demethylase 3B  
Size: 1761 amino acids; 191611 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subcellular location: Nucleus (By similarity)
Miscellaneous: Its gene is located in the 5q region of the genome which is deleted in del(5q)
interstitial deletion, a frequent deletion found in myeloid leukemias and myelodysplasias,
suggesting that it may be a good candidate for the del(5q) tumor suppressor gene
Secondary accessions: Q9BVH6 Q9BW93 Q9BZ52 Q9NYF4 Q9UPS0
Alternative splicing: 3 isoforms:  Q7LBC6-1   Q7LBC6-2   Q7LBC6-3   

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_057688.2  

    ENSEMBL proteins: 
    ENSP00000326563 ENSP00000378335 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (KDM3B / JMJD1B)
    Human Recombinant Proteins from Abnova (JMJD1B)
                    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:0005634 nucleus IEA--
    About this table

    Antibodies for KDM3B: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for KDM3B
    Browse R&D Systems for Antibodies
    Cell Signaling Technology (CST) Antibodies for KDM3B (JHDM2B, JMJD1B)
    Antibodies from Abcam (KDM3B / JMJD1B), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (JMJD1B)
    Novus Biologicals Antibodies for JMJD1B

    Assays for KDM3B: 
    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

    2 InterPro domains/families:
     IPR013129 TF_JmjC
     IPR003347 TF_JmjC_AAH


       GeneDecks  KDM3B for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q7LBC6

    ProtoNet protein and cluster: Q7LBC6

    1 Blocks protein family: IPB003347 Transcription factor jumonji

    UniProtKB/Swiss-Prot: KDM3B_HUMAN, Q7LBC6
    Domain: Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear
    receptors (By similarity)
    Similarity: Belongs to the JHDM2 histone demethylase family
    Similarity: Contains 1 JmjC domain

    (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 (KDM3B)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_016604

                  Applied Biosystems Silencer® siRNAs for KDM3B

                  Sigma-Aldrich siRNA for KDM3B  
                         Sigma-Aldrich shRNA for KDM3B  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for KDM3B
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_016604
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_016604
                                     untagged cDNA clone in CMV expression vector: NM_016604 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_016604

    UniProtKB/Swiss-Prot: KDM3B_HUMAN, Q7LBC6
    Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing
    a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate.
    May have tumor suppressor activity
    Enzyme Number (IUBMB): EC 1.14.11.- 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005506 iron ion binding IEA--
    GO:0008270 zinc ion binding IEA--
    GO:0016491 oxidoreductase activity IEA--
    GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen 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



    1 Interacting protein for KDM3B (Q7LBC62) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ZNF512BQ96KM62MINT-60808
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006350 transcription IEA--
    GO:0006355 regulation of transcription, DNA-dependent IEA--
    GO:0016568 chromatin modification IEA--
    GO:0055114 oxidation reduction 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 KDM3B
    2 Novoseek chemical compound relationships for KDM3B gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    zinc 68.59 20 16323267 (2), 18030324 (2), 11180958 (1), 1720570 (1) (see all 16)
    abscisic acid 49.87 3 16925600 (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 (KDM3B)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_016604

                  Sigma-Aldrich siRNA for KDM3B  
                         Sigma-Aldrich shRNA for KDM3B  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_016604  

    REFSEQ mRNAs for KDM3B gene: 

    NM_016604.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_016604  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_016604
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_016604
                                     untagged cDNA clone in CMV expression vector: NM_016604 

    Additional cDNA sequence: 

    AB029005.2 AF251039.1 AF338242.1 AK025755.1 AK304371.1 BC000539.2 BC001202.1 BC073869.1 
    BC117692.1 BC117693.1 BC146788.1 CR596928.1 CR615541.1 

    12 DOTS entries:

    DT.87009767  DT.95190557  DT.92447513  DT.95352632  DT.100795486  DT.40245180  DT.440580  DT.100795487 
    DT.100795492  DT.40191866  DT.92447515  DT.75125761 

    24/262 AceView cDNA sequences (see all 262 ):

    BF445534 BI917674 AI439064 AA337372 BC000539 H03250 BI768210 AL561650 
    CD671660 BE082546 CR615541 BQ023995 F03931 BM802414 BM457347 CR596928 
    AF338242 BE265035 BE048898 AL698902 BX477892 BQ311965 AI560465 AI219862 

    Unigene Cluster for KDM3B:

    Lysine (K)-specific demethylase 3B
    Hs.714832  [show with all ESTs]
    Unigene Representative Sequence: NM_016604


    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for KDM3B (see all 7 )

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18a · 18b ^ 19a · 19b ^
    SP1:                                            -                                                           -                                               -   
    SP2:                                            -                                                           -                                               -   
    SP3:                                                                                                                                                            
    SP4:                                                                                                        -                                                   
    SP5:                                                                                                                                                            

    ExUns: 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26
    SP1:  -                                             
    SP2:  -                                             
    SP3:                                                
    SP4:                                                
    SP5:                                                

    About this scheme

    ECgene alternative splicing isoforms for KDM3B

    2 Ensembl transcripts including schematic representations:
    ENST00000314358  ENST00000394866  
    (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

    KDM3B expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for KDM3B

    1 / 2

    6 probe-sets matching KDM3B gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    84982_at2 U95-D 1 1.00 1.00 0.74 0.38 -- -- -- -- --

    33870_at2 U95-A 1 1.00 1.00 1.00 1.00 -- -- -- -- --

    210878_s_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

    201643_x_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

    210878_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    201643_x_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: TTCTTATTAA

    SOURCE GeneReport for Unigene cluster: Hs.714832

    UniProtKB/Swiss-Prot: KDM3B_HUMAN, Q7LBC6
    Tissue specificity: Ubiquitous. Highly expressed in placenta, skeletal muscle, kidney, heart and
    liver

    (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 KDM3B gene from 5/8 species (see all 8 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    JMJD1B1   -- jumonji domain containing 1B 93.94(n)
    97.32(a)
    474695  XM_531921.2  XP_531921.2 
    chimpanzee
    (Pan troglodytes)
    JMJD1B1   -- jumonji domain containing 1B 99.75(n)
    99.83(a)
    462095  XM_517956.2  XP_517956.2 
    cow
    (Bos taurus)
    JMJD1B1   -- jumonji domain containing 1B 93.63(n)
    96.59(a)
    534005  XM_867954.2  XP_873047.2 
    mouse
    (Mus musculus)
    Kdm3b5
    Jmjd1b1
    185
    KDM3B lysine (K)-specific demethylase 3B5
    jumonji domain containing 1B1
    89.8(n)1
    93.7(a)1
    2772501  NM_001081256.11  NP_001074725.11 
     AA5167435  AA8401265  (see all 21)
    zebrafish
    (Danio rerio)
    wufa12c092   -- wufa12c09 78.17(n) 335041  57059800 
    About this table        Species with no ortholog for KDM3B

    ENSEMBL Gene Tree for KDM3B
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for KDM3B gene
    JMJD1C2  KDM3A2  HR2  

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


    10/374 NCBI SNPs in KDM3B are shown (see all 374 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 90)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 5 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs113341,2
    C,F,H,O137800195(+) GGTGTG/CTTCCC 1 -- ut31 ese39Minor allele frequency- C:0.45MN EA EU WA NA 2450
    rs77066141,2
    A,C,F,H137782707(+) AAATAG/ACAATA 1 N/S mis116Minor allele frequency- A:0.06NA EU EA WA 1468
    rs68654721,2
    C,F,H137745164(+) ATTCAA/GCGCCT 1 T/A mis1 ese38Minor allele frequency- G:0.02EU EA WA 838
    rs48357931,2
    A,C137799646(+) AGTGGA/GAATGT 1 -- ut310--------
    rs37981511,2
    F137799396(+) AGCCAG/ATGTGG 1 -- ut31 ese31Minor allele frequency- A:0.01EA 1486
    rs285619311,2
    C137782697(+) GTTCGG/TCATCA 1 A/S mis1 ese31Minor allele frequency- T:0.01NA 72
    rs77262341,2
    A,C,F,H137782594(+) TCTGGC/TGGAGG 1 G/G syn1 ese38Minor allele frequency- T:0.34MN NA EU EA WA 734
    rs100739221,2
    A,C,F,H137745112(+) GGTGAG/AATCAA 1 E/E syn115Minor allele frequency- A:0.26NA EA EU WA 1340
    rs48356781,2
    A,C,F,H137736333(+) GTTATT/CGTGCT 1 I/I syn116Minor allele frequency- C:0.31EA NA EU WA 1452
    rs172945631,2
    C,F137761790(+) GGGGTA/GCTCCG 1 V/V syn1 ese35Minor allele frequency- G:0.14NA MN 404
    About this table

    HapMap Linkage Disequilibrium images for KDM3B (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: 609373

    1 Novoseek disease relationship for KDM3B gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    tumors 0.00 2 11687974 (2)
    About this table

    (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

    10/35 PubMed articles for KDM3B gene (see all 35 ):
    (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: 51780 HGNC: 1337 AceView: JMJD1B Ensembl:ENSG00000120733 euGenes: HUgn51780
    ECgene: KDM3B H-InvDB: KDM3B
    (According to HUGE)
    About This Section

    HUGE: KIAA1082
    (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

      --
    (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 KDM3B:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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