ENSMUSG00000029475


Mus musculus

Features
Gene ID: ENSMUSG00000029475
  
Biological name :Kdm2b
  
Synonyms : Kdm2b / Lysine-specific demethylase 2B / Q6P1G2
  
Possible biological names infered from orthology : lysine demethylase 2B / Q8NHM5
  
Species: Mus musculus
  
Chr. number: 5
Strand: -1
Band: F
Gene start: 122870665
Gene end: 122989823
  
Corresponding Affymetrix probe sets: 10533569 (MoGene1.0st)   1452198_at (Mouse Genome 430 2.0 Array)   1459861_s_at (Mouse Genome 430 2.0 Array)   
  
Cross references: Ensembl peptide - ENSMUSP00000083376
Ensembl peptide - ENSMUSP00000114049
Ensembl peptide - ENSMUSP00000120912
Ensembl peptide - ENSMUSP00000119746
Ensembl peptide - ENSMUSP00000118488
Ensembl peptide - ENSMUSP00000114731
Ensembl peptide - ENSMUSP00000114052
Ensembl peptide - ENSMUSP00000031435
Ensembl peptide - ENSMUSP00000038229
NCBI entrez gene - 30841     See in Manteia.
MGI - MGI:1354737
RefSeq - XM_011248209
RefSeq - XM_011248211
RefSeq - XM_011248212
RefSeq - XM_011248213
RefSeq - XM_011248214
RefSeq - XM_011248215
RefSeq - XM_011248216
RefSeq - XM_011248217
RefSeq - NM_013910
RefSeq - XM_011248208
RefSeq - XM_011248210
RefSeq - NM_001003953
RefSeq - XM_006530376
RefSeq Peptide - NP_001003953
RefSeq Peptide - NP_038938
swissprot - Q6P1G2
swissprot - D6RHM8
swissprot - D3YVU7
swissprot - D3YVU4
swissprot - D3YV31
swissprot - F6QTG9
swissprot - D3YUE3
swissprot - E9QL25
Ensembl - ENSMUSG00000029475
  
See expression report in BioGPS
See gene description in Wikigenes
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 kdm2bbENSDARG00000046010Danio rerio
 KDM2BENSGALG00000004225Gallus gallus
 KDM2BENSG00000089094Homo sapiens


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
Kdm2a / lysine demethylase 2A / Q9Y2K7*ENSMUSG0000005461148
Fbxl19 / Q6PB97 / F-box/LRR-repeat protein 19 / Q6PCT2* / F-box and leucine rich repeat protein 19*ENSMUSG0000003081124
Phf8 / Q80TJ7 / Histone lysine demethylase PHF8 / Q9UPP1* / PHD finger protein 8*ENSMUSG0000004122919
Phf2 / Q9WTU0 / Lysine-specific demethylase PHF2 / O75151* / PHD finger protein 2*ENSMUSG0000003802518
Kdm7a / Q3UWM4 / Lysine-specific demethylase 7A / Q6ZMT4* / lysine demethylase 7A*ENSMUSG0000004259916
4921501E09Rik / RIKEN cDNA 4921501E09 geneENSMUSG0000002335016


Protein motifs (from Interpro)
Interpro ID Name
 IPR001810  F-box domain
 IPR001965  Zinc finger, PHD-type
 IPR002857  Zinc finger, CXXC-type
 IPR003347  JmjC domain
 IPR006553  Leucine-rich repeat, cysteine-containing subtype
 IPR011011  Zinc finger, FYVE/PHD-type
 IPR013083  Zinc finger, RING/FYVE/PHD-type
 IPR019787  Zinc finger, PHD-finger
 IPR032675  Leucine-rich repeat domain superfamily


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0000122 negative regulation of transcription by RNA polymerase II IMP
 biological_processGO:0006325 chromatin organization IEA
 biological_processGO:0006351 transcription, DNA-templated IEA
 biological_processGO:0006355 regulation of transcription, DNA-templated IEA
 biological_processGO:0007283 spermatogenesis IMP
 biological_processGO:0021555 midbrain-hindbrain boundary morphogenesis IMP
 biological_processGO:0021592 fourth ventricle development IMP
 biological_processGO:0021670 lateral ventricle development IMP
 biological_processGO:0021678 third ventricle development IMP
 biological_processGO:0021993 initiation of neural tube closure IMP
 biological_processGO:0030307 positive regulation of cell growth IDA
 biological_processGO:0030900 forebrain development IMP
 biological_processGO:0030901 midbrain development IMP
 biological_processGO:0030902 hindbrain development IMP
 biological_processGO:0035518 histone H2A monoubiquitination ISO
 biological_processGO:0043524 negative regulation of neuron apoptotic process IMP
 biological_processGO:0048596 embryonic camera-type eye morphogenesis IMP
 biological_processGO:0055114 oxidation-reduction process IEA
 biological_processGO:0070544 histone H3-K36 demethylation IDA
 biological_processGO:1902459 positive regulation of stem cell population maintenance IDA
 biological_processGO:2000178 negative regulation of neural precursor cell proliferation IMP
 cellular_componentGO:0005634 nucleus IEA
 cellular_componentGO:0005730 nucleolus IEA
 cellular_componentGO:0031519 PcG protein complex ISO
 molecular_functionGO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA
 molecular_functionGO:0003677 DNA binding IEA
 molecular_functionGO:0003723 RNA binding IEA
 molecular_functionGO:0005515 protein binding IEA
 molecular_functionGO:0008270 zinc ion binding IEA
 molecular_functionGO:0016491 oxidoreductase activity IEA
 molecular_functionGO:0019843 rRNA binding IEA
 molecular_functionGO:0032452 histone demethylase activity TAS
 molecular_functionGO:0046872 metal ion binding IEA
 molecular_functionGO:0051213 dioxygenase activity IEA
 molecular_functionGO:0051864 histone demethylase activity (H3-K36 specific) IEA


Pathways (from Reactome)
Pathway description
HDMs demethylate histones


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 MP:0000266 abnormal cardiac morphology "anomalies in the hollow, muscular organ that maintains the circulation of the blood" [MeSH:National Library of Medicine - Medical Subject Headings , 2003]
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Allelic Composition: Foxo1tm1Rdp/Foxo1tm1.1Rdp,Foxo3tm1Rdp/Foxo3tm1.1Rdp,Ptentm1Hwu/Ptentm1Hwu,Tg(CYP19A1-cre)1Jri/0
Genetic Background: involves: 129S4/SvJae * 129S6/SvEvTac

 MP:0000914 exencephaly "neurocranial defects resulting in exposure or extrusion of the brain" [Stedman s Medical Dictionary:ISBN 0-683-40008-8, J:49840]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0000928 incomplete cephalic closure "arrest of the fusion of the cephalic neural folds" [J:12622]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0000929 open neural tube "incomplete invagination and fusion of the neuroepithelial layer in early development" [MGI:CLS, J:53370, J:62571]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

Allelic Composition: Kdm2bGt(RRT043)Byg/Kdm2bGt(RRT043)Byg
Genetic Background: B6.129P2-Kdm2bGt(RRT043)Byg

 MP:0001265 reduced body size "smaller than average body weight, height and/or length of an organism compared to controls" [Stedman s Medical Dictionary , 27th edition:ISBN 0-683-40008-8, J:23170]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0001325 abnormal retina morphology "structural or developmental anomaly of the thin layer of neural tissue lining the back of the eyeball which contains visual receptors " [cwg:Carroll-Ann W. Goldsmith , Mouse Genome Informatics curator]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0001688 abnormal somite development "anomalous formation of any of the paired, metamerically arranged cell masses formed in the embryonic paraxial mesoderm" [Stedman s Medical Dictionary:ISBN 0-683-40008-8]
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Allelic Composition: Foxo1tm1Rdp/Foxo1tm1.1Rdp,Foxo3tm1Rdp/Foxo3tm1.1Rdp,Ptentm1Hwu/Ptentm1Hwu,Tg(CYP19A1-cre)1Jri/0
Genetic Background: involves: 129S4/SvJae * 129S6/SvEvTac

 MP:0001698 reduced embryo size "smaller proportions of embryo compared to littermates" [J:61790]
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Allelic Composition: Kdm2bGt(RRT043)Byg/Kdm2bGt(RRT043)Byg
Genetic Background: B6.129P2-Kdm2bGt(RRT043)Byg

 MP:0001915 intracranial hemorrhage "bleeding within the skull, including hemorrhage into the brain and within the cranial epidural, subdural, and subarachnoid spaces" [MeSH:National Library of Medicine - Medical Subject Headings , 2003]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0002687 oligozoospermia "reduced concentration of spermatozoa " [pvb:Pierre Vanden Borre , Mouse Genome Informatics Curator, J:57312]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0003051 curly tail "a loop or corkscrew-like curl in the tail" [csmith:Cynthia L. Smith, Mouse Genome Informatics Curator]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0003400 kinked neural tube "twists or kinks in the embryonic neural tube" [J:66514, anna:Anna Anagnostopoulos, Mouse Genome Informatics Curator]
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Allelic Composition: Kdm2bGt(RRT043)Byg/Kdm2bGt(RRT043)Byg
Genetic Background: B6.129P2-Kdm2bGt(RRT043)Byg

 MP:0004200 reduced fetal size "smaller proportions of a fetus compared to littermates (sensu Mus: from E14 through birth)" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0004948 abnormal neuronal precursor proliferation "any anomaly in the ability of a neuroblast population to undergo rapid expansion by cell division" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0010715 coloboma of the retina "congenital defect of the retina in which some part of the structure is absent" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0011098 complete embryonic lethality during organogenesis "death of all organisms of a given genotype in a population between embryo turning and the completion of organogenesis (Mus: E9 to less than E14)" [MGI:csmith]
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Allelic Composition: Kdm2bGt(RRT043)Byg/Kdm2bGt(RRT043)Byg
Genetic Background: B6.129P2-Kdm2bGt(RRT043)Byg

 MP:0011109 partial lethality throughout fetal growth and development "the appearance of lower than Mendelian ratios of organisms of a given genotype due to death of some, but not all of the organisms between the completion of organogenesis and birth (Mus: E14 to approximately E18.5)" [MGI:csmith]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0011110 partial preweaning lethality "the appearance of lower than Mendelian ratios of organisms of a given genotype due to death of some, but not all of the organisms between fertilization and weaning age (Mus: approximately 3-4 weeks of age)" [MGI:csmith]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0012091 increased midbrain size "greater than average size of the brain region derived from the middle of the three cerebral vesicles of the embryo; this region controls sensory and motor functions in the adult, including eye movement and coordination of auditory and visual reflexes" [MGI:anna, MGI:csmith]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0012265 increased hindbrain size "greater than average size of the part of the brain developed from the posterior of the three primary brain vesicles of the embryonic neural tube from which the metencephalon and myelencephalon are derived" [MGI:anna]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0012535 abnormal optic fissure closure "failure to initiate and/or complete closure of the transient gap in the ventral margin of the developing optic cup; fusion of the optic fissure begins with apposition of the inferior lips of the ventral-most optic cup and continues anteriorly toward its rim and posteriorly along the optic stalk; failure or late closure of the optic fissure prevents the establishment of normal fetal intraocular pressure and can result in microphthalmia associataed with colobomas" [MGI:anna]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0012678 absent fourth ventricle "absence of the irregularly shaped cavity in the rhombencephalon, normally located between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind; the fourth ventricle is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space" [MGI:anna]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0012701 increased embryonic neuroepithelium apoptosis "increase in the number of cells of the embryonic neuroepithelium undergoing programmed cell death" [MGI:anna]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0013000 absent cerebral aqueduct "absence of the channel in the mesencephalon that connects the third and fourth ventricles" [MGI:anna]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

 MP:0013199 increased head mesenchyme apoptosis "increase in the number of cells of the head mesenchyme undergoing programmed cell death" [MGI:anna]
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Allelic Composition: Fmr1tm1Cgr/Fmr1tm1Cgr
Genetic Background: B6.129P2-Fmr1tm1Cgr

  


Interacting proteins (from Reactome)
Interactor ID Name Interaction type
No match






 

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