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KDM2B lysine demethylase 2B [ Homo sapiens (human) ]

Gene ID: 84678, updated on 24-Nov-2020

Summary

Official Symbol
KDM2Bprovided by HGNC
Official Full Name
lysine demethylase 2Bprovided by HGNC
Primary source
HGNC:HGNC:13610
See related
Ensembl:ENSG00000089094 MIM:609078
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CXXC2; Fbl10; PCCX2; FBXL10; JHDM1B
Summary
This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class. Multiple alternatively spliced transcript variants have been found for this gene, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 6.6), appendix (RPKM 5.9) and 25 other tissues See more
Orthologs

Genomic context

See KDM2B in Genome Data Viewer
Location:
12q24.31
Exon count:
29
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (121402288..121582268, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (121866899..122019110, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene calcium/calmodulin dependent protein kinase kinase 2 Neighboring gene anaphase promoting complex subunit 5 Neighboring gene ring finger protein 34 Neighboring gene microRNA 7107 Neighboring gene uncharacterized LOC105370033 Neighboring gene KDM2B divergent transcript Neighboring gene RNA, U6 small nuclear 1004, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding NAS
Non-traceable Author Statement
more info
 
RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity TAS
Traceable Author Statement
more info
PubMed 
histone demethylase activity (H3-K36 specific) IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
rRNA binding IEA
Inferred from Electronic Annotation
more info
 
transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
unmethylated CpG binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
embryonic camera-type eye morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
forebrain development ISS
Inferred from Sequence or Structural Similarity
more info
 
fourth ventricle development ISS
Inferred from Sequence or Structural Similarity
more info
 
hindbrain development ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H2A monoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K36 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
initiation of neural tube closure ISS
Inferred from Sequence or Structural Similarity
more info
 
lateral ventricle development ISS
Inferred from Sequence or Structural Similarity
more info
 
midbrain development ISS
Inferred from Sequence or Structural Similarity
more info
 
midbrain-hindbrain boundary morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of neural precursor cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of neuron apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell growth IEA
Inferred from Electronic Annotation
more info
 
positive regulation of stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
protein demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
third ventricle development ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
colocalizes_with PcG protein complex IDA
Inferred from Direct Assay
more info
PubMed 
chromatin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromosome IEA
Inferred from Electronic Annotation
more info
 
nucleolus IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
 

General protein information

Preferred Names
lysine-specific demethylase 2B
Names
CXXC-type zinc finger protein 2
F-box and leucine-rich repeat protein 10
F-box protein FBL10
F-box/LRR-repeat protein 10
JEMMA (Jumonji domain, EMSY-interactor, methyltransferase motif) protein
[Histone-H3]-lysine-36 demethylase 1B
jmjC domain-containing histone demethylation protein 1B
jumonji C domain-containing histone demethylase 1B
lysine (K)-specific demethylase 2B
protein-containing CXXC domain 2
NP_001005366.1
NP_115979.3
XP_005254012.1
XP_005254013.1
XP_005254018.1
XP_011537169.1
XP_011537170.1
XP_011537171.1
XP_011537177.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_033820.1 RefSeqGene

    Range
    4993..156920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001005366.2NP_001005366.1  lysine-specific demethylase 2B isoform b

    See identical proteins and their annotated locations for NP_001005366.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, 3' UTR and coding region, as compared to variant 1. The encoded isoform b has alternate N- and C-termini and lacks an internal segment, as compared to isoform a.
    Source sequence(s)
    AA504464, AK127328, BC028612
    Consensus CDS
    CCDS41849.1
    UniProtKB/Swiss-Prot
    Q8NHM5
    Related
    ENSP00000366269.3, ENST00000377069.8
    Conserved Domains (7) summary
    cd09293
    Location:10491238
    AMN1; Antagonist of mitotic exit network protein 1
    smart00558
    Location:151226
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam02008
    Location:584620
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:10331057
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15644
    Location:630691
    PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
    pfam12937
    Location:9991039
    F-box-like; F-box-like
    cl21464
    Location:198304
    cupin_like; Conserved domain found in cupin and related proteins
  2. NM_032590.5NP_115979.3  lysine-specific demethylase 2B isoform a

    See identical proteins and their annotated locations for NP_115979.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC145422, AJ459424, AK027692, BX648928, CA430876
    Consensus CDS
    CCDS41850.1
    UniProtKB/Swiss-Prot
    Q8NHM5
    Related
    ENSP00000366271.3, ENST00000377071.9
    Conserved Domains (7) summary
    cd09293
    Location:11181307
    AMN1; Antagonist of mitotic exit network protein 1
    smart00558
    Location:182257
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam02008
    Location:615651
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:11021126
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15644
    Location:661722
    PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
    pfam12937
    Location:10681108
    F-box-like; F-box-like
    cl21464
    Location:229335
    cupin_like; Conserved domain found in cupin and related proteins

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    121402288..121582268 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538867.3XP_011537169.1  lysine-specific demethylase 2B isoform X1

    Conserved Domains (7) summary
    cd09293
    Location:11211310
    AMN1; Antagonist of mitotic exit network protein 1
    smart00558
    Location:182257
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam02008
    Location:615651
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:11051129
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15644
    Location:661722
    PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
    pfam12937
    Location:10711111
    F-box-like; F-box-like
    cl21464
    Location:229335
    cupin_like; Conserved domain found in cupin and related proteins
  2. XM_011538868.3XP_011537170.1  lysine-specific demethylase 2B isoform X2

    Conserved Domains (7) summary
    cd09293
    Location:11211310
    AMN1; Antagonist of mitotic exit network protein 1
    smart00558
    Location:182257
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam02008
    Location:615651
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:11051129
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15644
    Location:661722
    PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
    pfam12937
    Location:10711111
    F-box-like; F-box-like
    cl21464
    Location:229335
    cupin_like; Conserved domain found in cupin and related proteins
  3. XM_005253955.4XP_005254012.1  lysine-specific demethylase 2B isoform X4

    Conserved Domains (7) summary
    cd09293
    Location:10871276
    AMN1; Antagonist of mitotic exit network protein 1
    smart00558
    Location:151226
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam02008
    Location:584620
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:10711095
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15644
    Location:630691
    PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
    pfam12937
    Location:10371077
    F-box-like; F-box-like
    cl21464
    Location:198304
    cupin_like; Conserved domain found in cupin and related proteins
  4. XM_005253956.4XP_005254013.1  lysine-specific demethylase 2B isoform X5

    Conserved Domains (7) summary
    cd09293
    Location:10811270
    AMN1; Antagonist of mitotic exit network protein 1
    smart00558
    Location:145220
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam02008
    Location:578614
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:10651089
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15644
    Location:624685
    PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
    pfam12937
    Location:10311071
    F-box-like; F-box-like
    cl21464
    Location:192298
    cupin_like; Conserved domain found in cupin and related proteins
  5. XM_005253961.5XP_005254018.1  lysine-specific demethylase 2B isoform X7

    Related
    ENSP00000437821.1, ENST00000542973.5
    Conserved Domains (5) summary
    cd09293
    Location:558747
    AMN1; Antagonist of mitotic exit network protein 1
    pfam02008
    Location:5591
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:542566
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15644
    Location:101162
    PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
    pfam12937
    Location:508548
    F-box-like; F-box-like
  6. XM_011538875.3XP_011537177.1  lysine-specific demethylase 2B isoform X6

    See identical proteins and their annotated locations for XP_011537177.1

    UniProtKB/TrEMBL
    B4DSN4
    Conserved Domains (5) summary
    cd09293
    Location:561750
    AMN1; Antagonist of mitotic exit network protein 1
    pfam02008
    Location:5591
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:545569
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15644
    Location:101162
    PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
    pfam12937
    Location:511551
    F-box-like; F-box-like
  7. XM_011538869.2XP_011537171.1  lysine-specific demethylase 2B isoform X3

    Conserved Domains (7) summary
    cd09293
    Location:11211310
    AMN1; Antagonist of mitotic exit network protein 1
    smart00558
    Location:182257
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam02008
    Location:615651
    zf-CXXC; CXXC zinc finger domain
    sd00034
    Location:11051129
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15644
    Location:661722
    PHD_KDM2B; PHD finger found in Lysine-specific demethylase 2B (KDM2B)
    pfam12937
    Location:10711111
    F-box-like; F-box-like
    cl21464
    Location:229335
    cupin_like; Conserved domain found in cupin and related proteins
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