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

Summary

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

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_086030.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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

AA925036 (e-PCR)
- UniSTS:248459

D5Mit34 (e-PCR), detects polymorphism
- UniSTS:130486

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 histone demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor 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	IBA Inferred from Biological aspect of Ancestor 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 regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor 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

EC 1.14.11.27

XP_038945400.1

EC 1.14.11.27

XP_038945403.1

EC 1.14.11.27

XP_038945411.1

EC 1.14.11.27

XP_038945412.1

EC 1.14.11.27

XP_038945413.1

EC 1.14.11.27

XP_063127396.1

EC 1.14.11.27

XP_063127397.1

EC 1.14.11.27

XP_063127398.1

EC 1.14.11.27

XP_063127399.1

EC 1.14.11.27

XP_063127400.1

EC 1.14.11.27

XP_063127401.1

EC 1.14.11.27

XP_063127402.1

EC 1.14.11.27

XP_063127403.1

EC 1.14.11.27

XP_063127404.1

EC 1.14.11.27

XP_063127405.1

EC 1.14.11.27

XP_063127406.1

EC 1.14.11.27

XP_063127407.1

EC 1.14.11.27

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)

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

NC_086030.1 Reference GRCr8

Range

39224422..39362126

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063271329.1 → XP_063127399.1 lysine-specific demethylase 2B isoform X6
XM_063271328.1 → XP_063127398.1 lysine-specific demethylase 2B isoform X4
XM_063271330.1 → XP_063127400.1 lysine-specific demethylase 2B isoform X7
XM_063271327.1 → XP_063127397.1 lysine-specific demethylase 2B isoform X2
XM_063271326.1 → XP_063127396.1 lysine-specific demethylase 2B isoform X1

Related

ENSRNOP00000105523.1, ENSRNOT00000146321.1
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
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
XM_063271335.1 → XP_063127405.1 lysine-specific demethylase 2B isoform X10
XM_063271333.1 → XP_063127403.1 lysine-specific demethylase 2B isoform X10

Related

ENSRNOP00000101594.1, ENSRNOT00000163872.1
XM_063271334.1 → XP_063127404.1 lysine-specific demethylase 2B isoform X10
XM_063271331.1 → XP_063127401.1 lysine-specific demethylase 2B isoform X8
XM_063271332.1 → XP_063127402.1 lysine-specific demethylase 2B isoform X9

Related

ENSRNOP00000111972.1, ENSRNOT00000166421.1
XM_063271336.1 → XP_063127406.1 lysine-specific demethylase 2B isoform X11

Related

ENSRNOP00000050408.6, ENSRNOT00000044071.7
XM_063271337.1 → XP_063127407.1 lysine-specific demethylase 2B isoform X11
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
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
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