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    Kdm2b lysine demethylase 2B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304495, updated on 9-Jul-2024

    Summary

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    Official Symbol
    Kdm2bprovided by RGD
    Official Full Name
    lysine demethylase 2Bprovided by RGD
    Primary source
    RGD:1310217
    See related
    Ensembl:ENSRNOG00000025702 AllianceGenome:RGD:1310217
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Fbxl10
    Summary
    Predicted to enable several functions, including histone H3-methyl-lysine-36 demethylase activity; sequence-specific DNA binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including brain development; cellular protein modification process; and embryonic morphogenesis. Predicted to act upstream of or within several processes, including histone H3-K36 demethylation; negative regulation of transcription by RNA polymerase II; and positive regulation of stem cell population maintenance. Predicted to be located in nucleus. Predicted to be part of PcG protein complex. Orthologous to human KDM2B (lysine demethylase 2B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 65.4), Testes (RPKM 62.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Kdm2b in Genome Data Viewer
    Location:
    12q16
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (39224422..39362126)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (33566530..33701366)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (39021924..39161954)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134481296 Neighboring gene uncharacterized LOC102546488 Neighboring gene ORAI calcium release-activated calcium modulator 1 Neighboring gene ring finger protein 34 Neighboring gene uncharacterized LOC120095970

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Members of a family of JmjC domain-containing oncoproteins immortalize embryonic fibroblasts via a JmjC domain-dependent process. Pfau R, et al. Proc Natl Acad Sci U S A, 2008 Feb 12. PMID 18250326, Free PMC Article
    2. FBXL10 regulates cardiac dysfunction in diabetic cardiomyopathy via the PKC β2 pathway. Yin L, et al. J Cell Mol Med, 2019 Apr. PMID 30701683, Free PMC Article
    3. KDM2b/JHDM1b, an H3K36me2-specific demethylase, is required for initiation and maintenance of acute myeloid leukemia. He J, et al. Blood, 2011 Apr 7. PMID 21310926, Free PMC Article
    4. MicroRNA-211-5p in extracellular vesicles derived from BMSCs facilitates the repair of rat frozen shoulder via regulating KDM2B/LACC1 axis. Mao X, et al. Tissue Cell, 2023 Apr. PMID 36610229
    5. KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs. Tzatsos A, et al. J Clin Invest, 2013 Feb. PMID 23321669, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MicroRNA-211-5p in extracellular vesicles derived from BMSCs facilitates the repair of rat frozen shoulder via regulating KDM2B/LACC1 axis.
      Title: MicroRNA-211-5p in extracellular vesicles derived from BMSCs facilitates the repair of rat frozen shoulder via regulating KDM2B/LACC1 axis.
    2. FBXL10 regulates cardiac dysfunction in diabetic cardiomyopathy via the PKC beta2 pathway.
      Title: FBXL10 regulates cardiac dysfunction in diabetic cardiomyopathy via the PKC β2 pathway.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K36 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables unmethylated CpG binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in embryonic camera-type eye morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in forebrain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in fourth ventricle development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in hindbrain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in initiation of neural tube closure ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in lateral ventricle development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in midbrain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in midbrain-hindbrain boundary morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of neural precursor cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of cell growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of stem cell population maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in third ventricle development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of PcG protein complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 2B
    Names
    F-box and leucine-rich repeat protein 10
    lysine (K)-specific demethylase 2B
    NP_001094149.1
    XP_038945400.1
    XP_038945403.1
    XP_038945411.1
    XP_038945412.1
    XP_038945413.1
    XP_063127396.1
    XP_063127397.1
    XP_063127398.1
    XP_063127399.1
    XP_063127400.1
    XP_063127401.1
    XP_063127402.1
    XP_063127403.1
    XP_063127404.1
    XP_063127405.1
    XP_063127406.1
    XP_063127407.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001100679.1 → NP_001094149.1  lysine-specific demethylase 2B

      See identical proteins and their annotated locations for NP_001094149.1

      Status: VALIDATED

      Source sequence(s)
      CH473973
      UniProtKB/TrEMBL
      A0A8I5ZKW7, A0A8I6ABR9, A6J173
      Related
      ENSRNOP00000107970.1, ENSRNOT00000165085.1
      Conserved Domains (10) summary
      PTZ00449
      Location:689 → 922
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd09293
      Location:1087 → 1276
      AMN1; Antagonist of mitotic exit network protein 1
      smart00558
      Location:151 → 226
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00034
      Location:1071 → 1095
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15644
      Location:630 → 691
      PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
      pfam02008
      Location:584 → 620
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:1037 → 1075
      F-box-like
      pfam17811
      Location:303 → 338
      JHD; Jumonji helical domain
      cl40423
      Location:198 → 304
      cupin_RmlC-like; RmlC-like cupin superfamily
      cl40435
      Location:476 → 542
      CTD_KDM2A_2B-like; C-terminal domain found in lysine-specific demethylase KDM2A, KDM2B, and similar proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086030.1 Reference GRCr8

      Range
      39224422..39362126
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063271329.1 → XP_063127399.1  lysine-specific demethylase 2B isoform X6

      UniProtKB/TrEMBL
      A0A8I5ZKW7

    2. XM_063271328.1 → XP_063127398.1  lysine-specific demethylase 2B isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZKW7

    3. XM_063271330.1 → XP_063127400.1  lysine-specific demethylase 2B isoform X7

      UniProtKB/TrEMBL
      A0A8I5ZKW7

    4. XM_063271327.1 → XP_063127397.1  lysine-specific demethylase 2B isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZKW7

    5. XM_063271326.1 → XP_063127396.1  lysine-specific demethylase 2B isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZKW7
      Related
      ENSRNOP00000105523.1, ENSRNOT00000146321.1

    6. XM_039089475.2 → XP_038945403.1  lysine-specific demethylase 2B isoform X5

      UniProtKB/TrEMBL
      A0A8I5ZKW7
      Related
      ENSRNOP00000091279.2, ENSRNOT00000107393.2
      Conserved Domains (9) summary
      cd09293
      Location:1049 → 1238
      AMN1; Antagonist of mitotic exit network protein 1
      smart00558
      Location:151 → 226
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00034
      Location:1033 → 1057
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15644
      Location:630 → 691
      PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
      pfam02008
      Location:584 → 620
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:999 → 1037
      F-box-like
      pfam17811
      Location:303 → 338
      JHD; Jumonji helical domain
      cd21785
      Location:476 → 542
      CTD_KDM2B; C-terminal domain found in Lysine-specific demethylase 2B
      cl40423
      Location:198 → 304
      cupin_RmlC-like; RmlC-like cupin superfamily

    7. XM_039089472.2 → XP_038945400.1  lysine-specific demethylase 2B isoform X3

      UniProtKB/TrEMBL
      A0A8I5ZKW7, A0A8I6A9S6
      Related
      ENSRNOP00000089414.1, ENSRNOT00000106205.2
      Conserved Domains (10) summary
      PTZ00449
      Location:683 → 916
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd09293
      Location:1081 → 1270
      AMN1; Antagonist of mitotic exit network protein 1
      smart00558
      Location:145 → 220
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00034
      Location:1065 → 1089
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15644
      Location:624 → 685
      PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
      pfam02008
      Location:578 → 614
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:1031 → 1069
      F-box-like
      pfam17811
      Location:297 → 332
      JHD; Jumonji helical domain
      cd21785
      Location:470 → 536
      CTD_KDM2B; C-terminal domain found in Lysine-specific demethylase 2B
      cl40423
      Location:192 → 298
      cupin_RmlC-like; RmlC-like cupin superfamily

    8. XM_063271335.1 → XP_063127405.1  lysine-specific demethylase 2B isoform X10

      UniProtKB/TrEMBL
      F1LLW9

    9. XM_063271333.1 → XP_063127403.1  lysine-specific demethylase 2B isoform X10

      UniProtKB/TrEMBL
      F1LLW9
      Related
      ENSRNOP00000101594.1, ENSRNOT00000163872.1

    10. XM_063271334.1 → XP_063127404.1  lysine-specific demethylase 2B isoform X10

      UniProtKB/TrEMBL
      F1LLW9

    11. XM_063271331.1 → XP_063127401.1  lysine-specific demethylase 2B isoform X8

      UniProtKB/TrEMBL
      F1LLW9

    12. XM_063271332.1 → XP_063127402.1  lysine-specific demethylase 2B isoform X9

      UniProtKB/TrEMBL
      F1LLW9
      Related
      ENSRNOP00000111972.1, ENSRNOT00000166421.1

    13. XM_063271336.1 → XP_063127406.1  lysine-specific demethylase 2B isoform X11

      UniProtKB/TrEMBL
      F1LLW9
      Related
      ENSRNOP00000050408.6, ENSRNOT00000044071.7

    14. XM_063271337.1 → XP_063127407.1  lysine-specific demethylase 2B isoform X11

      UniProtKB/TrEMBL
      F1LLW9

    15. XM_039089483.2 → XP_038945411.1  lysine-specific demethylase 2B isoform X12

      Conserved Domains (6) summary
      PTZ00449
      Location:160 → 396
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd09293
      Location:561 → 750
      AMN1; Antagonist of mitotic exit network protein 1
      sd00034
      Location:545 → 569
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15644
      Location:101 → 162
      PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
      pfam02008
      Location:55 → 91
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:511 → 549
      F-box-like

    16. XM_039089485.2 → XP_038945413.1  lysine-specific demethylase 2B isoform X14

      Conserved Domains (5) summary
      cd09293
      Location:520 → 709
      AMN1; Antagonist of mitotic exit network protein 1
      sd00034
      Location:504 → 528
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15644
      Location:101 → 162
      PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
      pfam02008
      Location:55 → 91
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:470 → 508
      F-box-like

    17. XM_039089484.2 → XP_038945412.1  lysine-specific demethylase 2B isoform X13

      UniProtKB/TrEMBL
      A0A8I5ZXA0
      Related
      ENSRNOP00000082558.1, ENSRNOT00000119628.2
      Conserved Domains (6) summary
      PTZ00449
      Location:160 → 393
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cd09293
      Location:558 → 747
      AMN1; Antagonist of mitotic exit network protein 1
      sd00034
      Location:542 → 566
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15644
      Location:101 → 162
      PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
      pfam02008
      Location:55 → 91
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:508 → 546
      F-box-like
    Nucleotide Protein Strain
    Heading Accession and Version

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