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

Gene ID: 221656, updated on 23-Nov-2023

Summary

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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

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See KDM1B in Genome Data Viewer
Location:
6p22.3
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (18155422..18223854)
RS_2023_10 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 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:18146951-18148150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24117 Neighboring gene MPRA-validated peak5710 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24118 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24119 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:18227006-18227518 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:18227519-18228032 Neighboring gene Sharpr-MPRA regulatory region 13525 Neighboring gene DEK proto-oncogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24120 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:18263885-18264436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16973 Neighboring gene uncharacterized LOC124901270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16974

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Lysine demethylase 1B (Kdm1b) enhances somatic reprogramming through inducing pluripotent gene expression and promoting cell proliferation. Hou C, et al. Exp Cell Res, 2022 Nov 1. PMID 36075448
  2. Expression profile of H3K4 demethylases with their clinical and pathological correlation in patients with clear cell renal cell carcinoma. Kumar A, et al. Gene, 2020 May 20. PMID 32097694
  3. Knockdown of KDM1B inhibits cell proliferation and induces apoptosis of pancreatic cancer cells. Wang Y, et al. Pathol Res Pract, 2019 May. PMID 30846414
  4. Lysine-specific demethylase 2 suppresses lipid influx and metabolism in hepatic cells. Nagaoka K, et al. Mol Cell Biol, 2015 Apr. PMID 25624347, Free PMC Article
  5. Inhibition of histone demethylase, LSD2 (KDM1B), attenuates DNA methylation and increases sensitivity to DNMT inhibitor-induced apoptosis in breast cancer cells. Katz TA, et al. Breast Cancer Res Treat, 2014 Jul. PMID 24924415

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CircKDM1B promotes hepatocellular carcinoma progression through regulating miR-1322/PRC1 axis.
    Title: CircKDM1B promotes hepatocellular carcinoma progression through regulating miR-1322/PRC1 axis.
  2. Lysine demethylase 1B (Kdm1b) enhances somatic reprogramming through inducing pluripotent gene expression and promoting cell proliferation.
    Title: Lysine demethylase 1B (Kdm1b) enhances somatic reprogramming through inducing pluripotent gene expression and promoting cell proliferation.
  3. The Role of LSD1 and LSD2 in Cancers of the Gastrointestinal System: An Update.
    Title: The Role of LSD1 and LSD2 in Cancers of the Gastrointestinal System: An Update.
  4. Histone demethylase AMX-1 is necessary for proper sensitivity to interstrand crosslink DNA damage.
    Title: Histone demethylase AMX-1 is necessary for proper sensitivity to interstrand crosslink DNA damage.
  5. In vitro evidence of NLRP3 inflammasome regulation by histone demethylase LSD2 in renal cancer: a pilot study.
    Title: In vitro evidence of NLRP3 inflammasome regulation by histone demethylase LSD2 in renal cancer: a pilot study.
  6. [Expression and Clinical Significance of MiR-215 and KDM1B in Patients with Diffuse Large B Cell Lymphoma].
    Title: [Expression and Clinical Significance of MiR-215 and KDM1B in Patients with Diffuse Large B Cell Lymphoma].
  7. Reduction in H3K4me patterns due to aberrant expression of methyltransferases and demethylases in renal cell carcinoma: prognostic and therapeutic implications.
    Title: Reduction in H3K4me patterns due to aberrant expression of methyltransferases and demethylases in renal cell carcinoma: prognostic and therapeutic implications.
  8. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.
    Title: A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.
  9. The expression of LSD2 was associated with higher TNM stage and metastasis of the tumor and thus, might serve as a useful marker for Clear cell renal cell carcinoma (ccRCC) progression.
    Title: Expression profile of H3K4 demethylases with their clinical and pathological correlation in patients with clear cell renal cell carcinoma.
  10. our findings provided new insights into the critical and multifaceted roles of KDM1B in the regulation of cell proliferation and apoptosis, and offered a potentially novel target in preventing the progression of pancreatic cancer.
    Title: Knockdown of KDM1B inhibits cell proliferation and induces apoptosis of pancreatic cancer cells.
Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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
  
enables flavin adenine dinucleotide binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in epigenetic programing of female pronucleus IEA
Inferred from Electronic Annotation
more info
  
involved_in genomic imprinting 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
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
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

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Preferred Names
lysine-specific histone demethylase 2
Names
flavin-containing amine oxidase domain-containing protein 1
lysine (K)-specific demethylase 1B
lysine-specific histone 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
XP_054210575.1
XP_054210576.1
XP_054210577.1
XP_054210578.1
XP_054210579.1
XP_054210580.1
XP_054210581.1
XP_054210582.1
XP_054210583.1
XP_054210584.1
XP_054210585.1
XP_054210586.1
XP_054210587.1
XP_054210588.1
XP_054210589.1
XP_054210590.1
XP_054210591.1
XP_054210592.1
XP_054210593.1
XP_054210594.1
XP_054210595.1
XP_054210596.1
XP_054210597.1
XP_054210598.1
XP_054210599.1
XP_054210600.1
XP_054210601.1

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_001364614.2 → NP_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
    A2A2C5, A2A2C6, Q5TGV3, Q6AI15, Q6ZUU4, Q8N258, Q8NB78, Q96EL7
    Related
    ENSP00000499208.1, ENST00000650836.2
    Conserved Domains (2) summary
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger
    cl27535
    Location:302 → 819
    Amino_oxidase; Flavin containing amine oxidoreductase

  2. NM_153042.4 → NP_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:267 → 587
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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_017010440.3 → XP_016865929.1  lysine-specific histone demethylase 2 isoform X1

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

  3. XM_017010445.3 → XP_016865934.1  lysine-specific histone demethylase 2 isoform X8

  4. XM_047418357.1 → XP_047274313.1  lysine-specific histone demethylase 2 isoform X9

  5. XM_005248925.3 → XP_005248982.1  lysine-specific histone demethylase 2 isoform X3

    UniProtKB/TrEMBL
    H0Y6H0
    Related
    ENSP00000405669.2, ENST00000449850.2
    Conserved Domains (3) summary
    pfam01593
    Location:399 → 820
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:281 → 363
    SWIRM; SWIRM domain
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger

  6. XM_011514385.3 → XP_011512687.1  lysine-specific histone demethylase 2 isoform X10

    Conserved Domains (2) summary
    pfam01593
    Location:267 → 688
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger

  7. XM_011514386.3 → XP_011512688.1  lysine-specific histone demethylase 2 isoform X11

    Conserved Domains (2) summary
    pfam01593
    Location:267 → 687
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger

  8. XM_005248928.3 → XP_005248985.1  lysine-specific histone demethylase 2 isoform X12

    Conserved Domains (2) summary
    pfam01593
    Location:254 → 675
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138 → 174
    zf-CW; CW-type Zinc Finger

  9. XM_047418359.1 → XP_047274315.1  lysine-specific histone demethylase 2 isoform X13

  10. XM_017010442.3 → XP_016865931.1  lysine-specific histone demethylase 2 isoform X4

  11. XM_047418352.1 → XP_047274308.1  lysine-specific histone demethylase 2 isoform X5

  12. XM_047418353.1 → XP_047274309.1  lysine-specific histone demethylase 2 isoform X6

  13. XM_047418360.1 → XP_047274316.1  lysine-specific histone demethylase 2 isoform X14

  14. XM_047418361.1 → XP_047274317.1  lysine-specific histone demethylase 2 isoform X15

  15. XM_047418362.1 → XP_047274318.1  lysine-specific histone demethylase 2 isoform X16

  16. XM_017010443.3 → XP_016865932.1  lysine-specific histone demethylase 2 isoform X1

  17. XM_047418354.1 → XP_047274310.1  lysine-specific histone demethylase 2 isoform X2

  18. XM_047418355.1 → XP_047274311.1  lysine-specific histone demethylase 2 isoform X3

    UniProtKB/TrEMBL
    H0Y6H0

  19. XM_047418356.1 → XP_047274312.1  lysine-specific histone demethylase 2 isoform X7

    UniProtKB/Swiss-Prot
    A2A2C5, A2A2C6, Q5TGV3, Q6AI15, Q6ZUU4, Q8N258, Q8NB78, Q96EL7

  20. XM_047418363.1 → XP_047274319.1  lysine-specific histone demethylase 2 isoform X10

  21. XM_047418364.1 → XP_047274320.1  lysine-specific histone demethylase 2 isoform X11

  22. XM_047418365.1 → XP_047274321.1  lysine-specific histone demethylase 2 isoform X13

  23. XM_047418358.1 → XP_047274314.1  lysine-specific histone demethylase 2 isoform X6

  24. XM_047418366.1 → XP_047274322.1  lysine-specific histone demethylase 2 isoform X17

  25. XM_047418367.1 → XP_047274323.1  lysine-specific histone demethylase 2 isoform X16

  26. XM_047418368.1 → XP_047274324.1  lysine-specific histone demethylase 2 isoform X19

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

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

mRNA and Protein(s)

  1. XM_054354600.1 → XP_054210575.1  lysine-specific histone demethylase 2 isoform X1

  2. XM_054354601.1 → XP_054210576.1  lysine-specific histone demethylase 2 isoform X2

  3. XM_054354610.1 → XP_054210585.1  lysine-specific histone demethylase 2 isoform X8

  4. XM_054354611.1 → XP_054210586.1  lysine-specific histone demethylase 2 isoform X9

  5. XM_054354602.1 → XP_054210577.1  lysine-specific histone demethylase 2 isoform X3

    UniProtKB/TrEMBL
    H0Y6H0

  6. XM_054354613.1 → XP_054210588.1  lysine-specific histone demethylase 2 isoform X10

  7. XM_054354614.1 → XP_054210589.1  lysine-specific histone demethylase 2 isoform X11

  8. XM_054354615.1 → XP_054210590.1  lysine-specific histone demethylase 2 isoform X12

  9. XM_054354616.1 → XP_054210591.1  lysine-specific histone demethylase 2 isoform X13

  10. XM_054354603.1 → XP_054210578.1  lysine-specific histone demethylase 2 isoform X4

  11. XM_054354604.1 → XP_054210579.1  lysine-specific histone demethylase 2 isoform X5

  12. XM_054354605.1 → XP_054210580.1  lysine-specific histone demethylase 2 isoform X6

  13. XM_054354617.1 → XP_054210592.1  lysine-specific histone demethylase 2 isoform X14

  14. XM_054354618.1 → XP_054210593.1  lysine-specific histone demethylase 2 isoform X15

  15. XM_054354619.1 → XP_054210594.1  lysine-specific histone demethylase 2 isoform X16

  16. XM_054354606.1 → XP_054210581.1  lysine-specific histone demethylase 2 isoform X1

  17. XM_054354607.1 → XP_054210582.1  lysine-specific histone demethylase 2 isoform X2

  18. XM_054354608.1 → XP_054210583.1  lysine-specific histone demethylase 2 isoform X3

    UniProtKB/TrEMBL
    H0Y6H0

  19. XM_054354609.1 → XP_054210584.1  lysine-specific histone demethylase 2 isoform X7

    UniProtKB/Swiss-Prot
    A2A2C5, A2A2C6, Q5TGV3, Q6AI15, Q6ZUU4, Q8N258, Q8NB78, Q96EL7

  20. XM_054354620.1 → XP_054210595.1  lysine-specific histone demethylase 2 isoform X10

  21. XM_054354621.1 → XP_054210596.1  lysine-specific histone demethylase 2 isoform X11

  22. XM_054354622.1 → XP_054210597.1  lysine-specific histone demethylase 2 isoform X13

  23. XM_054354612.1 → XP_054210587.1  lysine-specific histone demethylase 2 isoform X6

  24. XM_054354623.1 → XP_054210598.1  lysine-specific histone demethylase 2 isoform X17

  25. XM_054354624.1 → XP_054210599.1  lysine-specific histone demethylase 2 isoform X16

  26. XM_054354626.1 → XP_054210601.1  lysine-specific histone demethylase 2 isoform X19

  27. XM_054354625.1 → XP_054210600.1  lysine-specific histone demethylase 2 isoform X18

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NB78.3 GenPept UniProtKB/Swiss-Prot:Q8NB78

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