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

    Gene ID: 221656, updated on 14-Nov-2024

    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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (18155422..18223854)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (18027575..18095996)
    RS_2024_09 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 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. Knockdown of KDM1B inhibits cell proliferation and induces apoptosis of pancreatic cancer cells. Wang Y, et al. Pathol Res Pract, 2019 May. PMID 30846414
    2. 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
    3. 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
    4. 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
    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 (58) 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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    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)

    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 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 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 transcription initiation-coupled chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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_2024_08

    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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