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KDM1B lysine demethylase 1B [ Homo sapiens (human) ]

Gene ID: 221656, updated on 28-Jan-2023

Summary

Official Symbol
KDM1Bprovided by HGNC
Official Full Name
lysine demethylase 1Bprovided by HGNC
Primary source
HGNC:HGNC:21577
See related
Ensembl:ENSG00000165097 MIM:613081; AllianceGenome:HGNC:21577
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AOF1; LSD2; C6orf193
Summary
Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009 [PubMed 19407342]).[supplied by OMIM, Oct 2009]
Expression
Broad expression in thyroid (RPKM 17.9), testis (RPKM 11.6) and 23 other tissues See more
Orthologs
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Genomic context

See KDM1B in Genome Data Viewer
Location:
6p22.3
Exon count:
23
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (18155422..18223854)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (18027575..18095996)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (18155653..18224085)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NHL repeat containing E3 ubiquitin protein ligase 1 Neighboring gene thiopurine S-methyltransferase Neighboring gene Sharpr-MPRA regulatory region 13525 Neighboring gene DEK proto-oncogene Neighboring gene uncharacterized LOC124901270

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ33898, FLJ34109, FLJ43328, DKFZp686I0412

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables FAD binding IDA
Inferred from Direct Assay
more info
PubMed 
enables FAD-dependent H3K4me/H3K4me3 demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables flavin adenine dinucleotide binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables histone demethylase activity TAS
Traceable Author Statement
more info
 
enables oxidoreductase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA methylation involved in gamete generation IEA
Inferred from Electronic Annotation
more info
 
involved_in histone H3-K4 demethylation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of DNA methylation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in regulation of gene expression by genomic imprinting ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
part_of nucleosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 

General protein information

Preferred Names
lysine-specific histone demethylase 2; lysine-specific histone demethylase 1B
Names
flavin-containing amine oxidase domain-containing protein 1
lysine (K)-specific demethylase 1B
NP_001351543.1
NP_694587.3
XP_005248982.1
XP_005248985.1
XP_011512687.1
XP_011512688.1
XP_016865929.1
XP_016865930.1
XP_016865931.1
XP_016865932.1
XP_016865934.1
XP_016865935.1
XP_047274308.1
XP_047274309.1
XP_047274310.1
XP_047274311.1
XP_047274312.1
XP_047274313.1
XP_047274314.1
XP_047274315.1
XP_047274316.1
XP_047274317.1
XP_047274318.1
XP_047274319.1
XP_047274320.1
XP_047274321.1
XP_047274322.1
XP_047274323.1
XP_047274324.1

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_001364614.2NP_001351543.1  lysine-specific histone demethylase 2 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL031774, AL589723
    Consensus CDS
    CCDS93866.1
    UniProtKB/Swiss-Prot
    Q96EL7
    Related
    ENSP00000499208.1, ENST00000650836.2
    Conserved Domains (2) summary
    pfam07496
    Location:138191
    zf-CW; CW-type Zinc Finger
    cl27535
    Location:302819
    Amino_oxidase; Flavin containing amine oxidoreductase
  2. NM_153042.4NP_694587.3  lysine-specific histone demethylase 2 isoform 2

    See identical proteins and their annotated locations for NP_694587.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant contains multiple differences, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AA332652, AJ420481, AK125318, AL031774, DA099422
    Consensus CDS
    CCDS34343.1
    UniProtKB/Swiss-Prot
    Q8NB78
    Related
    ENSP00000297792.5, ENST00000297792.9
    Conserved Domains (2) summary
    pfam01593
    Location:267587
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138191
    zf-CW; CW-type Zinc Finger

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    18155422..18223854
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010440.3XP_016865929.1  lysine-specific histone demethylase 1B isoform X1

  2. XM_017010441.3XP_016865930.1  lysine-specific histone demethylase 1B isoform X2

  3. XM_017010445.3XP_016865934.1  lysine-specific histone demethylase 1B isoform X8

  4. XM_047418357.1XP_047274313.1  lysine-specific histone demethylase 1B isoform X9

  5. XM_005248925.3XP_005248982.1  lysine-specific histone demethylase 1B isoform X3

    UniProtKB/TrEMBL
    H0Y6H0
    Related
    ENSP00000405669.2, ENST00000449850.2
    Conserved Domains (3) summary
    pfam01593
    Location:399820
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:281363
    SWIRM; SWIRM domain
    pfam07496
    Location:138191
    zf-CW; CW-type Zinc Finger
  6. XM_011514385.3XP_011512687.1  lysine-specific histone demethylase 1B isoform X10

    Conserved Domains (2) summary
    pfam01593
    Location:267688
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138191
    zf-CW; CW-type Zinc Finger
  7. XM_011514386.3XP_011512688.1  lysine-specific histone demethylase 1B isoform X11

    Conserved Domains (2) summary
    pfam01593
    Location:267687
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138191
    zf-CW; CW-type Zinc Finger
  8. XM_005248928.3XP_005248985.1  lysine-specific histone demethylase 1B isoform X12

    Conserved Domains (2) summary
    pfam01593
    Location:254675
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138174
    zf-CW; CW-type Zinc Finger
  9. XM_047418359.1XP_047274315.1  lysine-specific histone demethylase 1B isoform X13

  10. XM_017010442.3XP_016865931.1  lysine-specific histone demethylase 1B isoform X4

  11. XM_047418352.1XP_047274308.1  lysine-specific histone demethylase 1B isoform X5

  12. XM_047418353.1XP_047274309.1  lysine-specific histone demethylase 1B isoform X6

  13. XM_047418360.1XP_047274316.1  lysine-specific histone demethylase 1B isoform X14

  14. XM_047418361.1XP_047274317.1  lysine-specific histone demethylase 1B isoform X15

  15. XM_047418362.1XP_047274318.1  lysine-specific histone demethylase 1B isoform X16

  16. XM_017010443.3XP_016865932.1  lysine-specific histone demethylase 1B isoform X1

  17. XM_047418354.1XP_047274310.1  lysine-specific histone demethylase 1B isoform X2

  18. XM_047418355.1XP_047274311.1  lysine-specific histone demethylase 1B isoform X3

    UniProtKB/TrEMBL
    H0Y6H0
  19. XM_047418356.1XP_047274312.1  lysine-specific histone demethylase 1B isoform X7

    UniProtKB/Swiss-Prot
    Q96EL7
  20. XM_047418363.1XP_047274319.1  lysine-specific histone demethylase 1B isoform X10

  21. XM_047418364.1XP_047274320.1  lysine-specific histone demethylase 1B isoform X11

  22. XM_047418365.1XP_047274321.1  lysine-specific histone demethylase 1B isoform X13

  23. XM_047418358.1XP_047274314.1  lysine-specific histone demethylase 1B isoform X6

  24. XM_047418366.1XP_047274322.1  lysine-specific histone demethylase 1B isoform X17

  25. XM_047418367.1XP_047274323.1  lysine-specific histone demethylase 1B isoform X16

  26. XM_047418368.1XP_047274324.1  lysine-specific histone demethylase 1B isoform X19

  27. XM_017010446.2XP_016865935.1  lysine-specific histone demethylase 1B isoform X18

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    18027575..18095996
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)