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

Gene ID: 304495, updated on 2-Nov-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
EnsemblRapid: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 histone H3K36 demethylase activity; sequence-specific DNA binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including brain development; embryonic morphogenesis; and negative regulation of neuron apoptotic process. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II; positive regulation of cell growth; and positive regulation of stem cell population maintenance. Predicted to be located in nucleoplasm. Predicted to be part of PcG protein complex. Used to study T-cell non-Hodgkin lymphoma. Orthologous to human KDM2B (lysine demethylase 2B). [provided by Alliance of Genome Resources, Nov 2024]
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 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

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

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

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

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

    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

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

    Related
    ENSRNOP00000101594.1, ENSRNOT00000163872.1

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

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

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

    Related
    ENSRNOP00000111972.1, ENSRNOT00000166421.1

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

    Related
    ENSRNOP00000050408.6, ENSRNOT00000044071.7

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

  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
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