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Aliases &
Descriptions
for KDM1
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase)
About This Section
|
| Aliases |
|---|
| AOF2 2, 3 | | BHC110 1, 2 | | EC 1.-.-.- 3 | | KIAA0601 1, 2, 3 | | LSD1 1, 2, 3 |
| | | Descriptions |
|---|
| BRAF35-HDAC complex protein BHC110 2, 3 | | FAD-binding protein BRAF35-HDAC complex, 110 kDa subunit 2 | | Flavin-containing amine oxidase domain-containing protein 2 3 | | amine oxidase (flavin containing) domain 2 1, 2 | | lysine (K)-specific demethylase 1 2 | | lysine-specific demethylase 1 1 | | lysine-specific histone demethylase 1 2 |
|
| |
Search outside databases for aliases for KDM1 gene |
Summaries
for KDM1(According to Entrez Gene,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| EntrezGene summary for KDM1:
This gene encodes a nuclear protein containing a SWIRM domain, a FAD-binding motif, and an amine
oxidase domain. This protein is a component of several histone deacetylase complexes, though it
silences genes by functioning as a histone demethylase. Alternative splicing results in multiple
transcript variants. [provided by RefSeq]
UniProtKB/Swiss-Prot: KDM1_HUMAN, O60341Function: Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for
epigenetic transcriptional activation, thereby acting as a corepressor. Acts by oxidizing the
substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates
both mono- and di-methylated 'Lys-4' of histone H3. May play a role in the repression of neuronal
genes. Alone, it is unable to demethylate H3 'Lys-4' on nucleosomes and requires the presence of
RCOR1/CoREST to achieve such activity. May also demethylate 'Lys-9' of histone H3, a specific tag
for epigenetic transcriptional repression, thereby leading to derepression of androgen receptor
target genes. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of
p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and
stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis |
Genomic Location
for KDM1
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to
UCSC and
Ensembl,
Transcription factor binding sites according to
SABiosciences)
About This Section
| Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 1p36.12 Ensembl cytogenetic band: 1p36.12 HGNC cytogenetic band: 1p36.12KDM1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc gene densities for chromosome 1 GeneLoc Exon Structure GeneLoc location for GC01P023219:
(about GC identifiers)
Start:
|
23,218,533 bp from pter |
End:
|
23,282,771 bp from pter |
Size:
|
64,239 bases |
Orientation:
|
plus strand |
RefSeq DNA sequence:- NC_000001.9 NT_004610.18
| Proteins
for KDM1
(According to
1UniProtKB,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Enzo Life Sciences,
Abnova,
OriGene and/or,
Abcam,
Biochemical Assays by
Invitrogen,
Millipore,
R&D Systems,
Cell Signaling Technology, and/or
Enzo Life Sciences,
Ontologies according to Gene
Ontology Consortium 01 Apr 2009 and
Entrez Gene,
Antibodies by Invitrogen,
Millipore,
Sigma-Aldrich,
R&D Systems,
Cell Signaling Technology,
Abcam,
Abnova, and/or
Novus Biologicals)
About This Section
| UniProtKB/Swiss-Prot: KDM1_HUMAN, O60341 (See
protein sequence)Recommended Name: Lysine-specific histone demethylase 1 Size: 852 amino acids; 92903 Da
Cofactor: FAD
Subunit: Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35,
KDM1, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1
and GTF2I. In the complex, RCOR1/CoREST strongly enhances the demethylase activity and protects it
from the proteasome while PHF21A/BHC80 inhibits the demethylase activity. Interacts with the
androgen receptor (AR)
Subcellular location: Nucleus
PDB structures from  and Proteopedia  :2COM (3D)
2DW4 (3D)
2EJR (3D)
2H94 (3D)
2HKO (3D)
2IW5 (3D)
2UXN (3D)
2UXX (3D)
2V1D (3D)
2Z3Y (3D)
2Z5U (3D)
Secondary accessions: Q5TH94 Q5TH95 Q86VT7 Q8IXK4 Q8NDP6 Q8TAZ3 Q96AW4Alternative splicing: 2 isoforms: O60341-1 O60341-2 Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins (2 alternative transcripts):
NP_001009999.1 NP_055828.2
ENSEMBL proteins: ENSP00000246149 ENSP00000383042 ENSP00000349049
Human Recombinant Proteins  Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 
2 Gene Ontology (GO) cellular component terms (links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005634 | nucleus |
IEA | -- | | GO:0005667 | transcription factor complex |
IEA | -- |
About this table
Antibodies for KDM1:
Assays for KDM1: | Protein
Domains/
Families
for KDM1(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| - Graphical View of Domain Structure for InterPro Entry O60341
ProtoNet protein and cluster: O60341 1 Blocks protein family: IPB007526 SWIRM
UniProtKB/Swiss-Prot: KDM1_HUMAN, O60341Domain: The SWIRN domain may act as an anchor site for a histone tailSimilarity: Belongs to the flavin monoamine oxidase familySimilarity: Contains 1 SWIRM domain | Gene Function
for KDM1
(According to MGI Jun 06 2009, UniProtKB,
IUBMB,and/or Genatlas,
shRNA from
OriGene,
Sigma-Aldrich, RNAi from
Sigma-Aldrich,
RNAi Products,
Clones, and
Q-PCR Products
from Invitrogen,
Millipore,
OriGene, and/or
Abnova,
siRNAs from
Applied Biosystems,
SYBR primers from OriGene,
Cell-based Assays from Millipore,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
| OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015013
 Applied Biosystems Silencer® siRNAs for KDM1
 Sigma-Aldrich siRNA and siRNA Panels for KDM1
Sigma-Aldrich shRNA for KDM1
Explore Sigma-Aldrich super-pooled esiRNAs
OriGene GFP tagged cDNA clone in CMV expression vector: NM_015013
Myc/DDK tagged cDNA clone in CMV expression vector: NM_015013
untagged cDNA clones in CMV expression vector (see all 2): NM_001009999
Primers:  Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
OriGene genome-wide validated SYBR primer pairs: NM_001009999
UniProtKB/Swiss-Prot: KDM1_HUMAN, O60341Function: Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for
epigenetic transcriptional activation, thereby acting as a corepressor. Acts by oxidizing the
substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates
both mono- and di-methylated 'Lys-4' of histone H3. May play a role in the repression of neuronal
genes. Alone, it is unable to demethylate H3 'Lys-4' on nucleosomes and requires the presence of
RCOR1/CoREST to achieve such activity. May also demethylate 'Lys-9' of histone H3, a specific tag
for epigenetic transcriptional repression, thereby leading to derepression of androgen receptor
target genes. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of
p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and
stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesisBiophysicochemical properties: Kinetic parameters: KM=3.0 uM for H3 monomethyl-K4; KM=4.2 uM for H3
dimethyl-K4; KM=3.9 uM for H3 monomethyl-K4-monomethyl-K9; KM=17.5 uM for monomethyl-K4-acetyl-K9;Enzyme Number (IUBMB): EC 1.-.-.- 7 MGI mutant phenotypes (inferred from 6 alleles ) (MGI details for Kdm1):
5 Gene Ontology (GO) molecular function terms (links to tree view): About this table | Pathways & Interactions
for KDM1
(Pathways according to Invitrogen
(maps by GeneGo),
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Proteins Network according to
SABiosciences,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene.)
About This Section
|
 Gene Network CentralTM Interacting Genes and Proteins Network for KDM1
5/45 Interacting proteins for KDM1 (ENSP000002461493 O603411, 2) via UniProtKB, MINT, and/or STRING (see all 45
)About this table
5/10 Gene Ontology (GO) biological process terms (links to tree view) (see all 10
): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0000122 | negative regulation of transcription from RNA polymerase II promoter |
IEA | -- | | GO:0001701 | in utero embryonic development |
IEA | -- | | GO:0006355 | regulation of transcription, DNA-dependent |
IEA | -- | | GO:0008283 | cell proliferation |
IEA | -- | | GO:0016568 | chromatin modification |
IEA | -- |
About this table
|
Drugs & Compounds
for KDM1(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
|
 Browse Tocris compounds for KDM1
6  Novoseek chemical compound relationships for KDM1 gene
| Compound |
Score |
Articles |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| lysine |
66.63 |
16 |
16567619 (1), 19208907 (1), 17392792 (1), 18581285 (1) (see all 11) |
| flavin-adenine dinucleotide |
53.77 |
6 |
17529991 (1), 17569509 (1) |
| flavin |
48.94 |
5 |
17511474 (2), 18039463 (1) |
| amine |
37.15 |
6 |
17511474 (2), 17367163 (1), 17529991 (1), 17569509 (1) |
| oxygen |
0.00 |
2 |
15811342 (1), 11595797 (1) |
| superoxide |
0.00 |
2 |
8791589 (1), 11595797 (1) |
About this table
|
Transcripts
for KDM1(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from Invitrogen,
Millipore, and/or
Abnova,
siRNAs from Applied Biosystems,
Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
Tagged/untagged cDNA clones from
OriGene,
Expression Assays from Applied Biosystems)
About This Section
| OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015013
Sigma-Aldrich siRNA and siRNA Panels for KDM1
Sigma-Aldrich shRNA for KDM1
Explore Sigma-Aldrich super-pooled esiRNAs
Applied Biosystems Silencer® siRNAs: NM_015013 REFSEQ mRNAs for KDM1 gene (2 alternative transcripts): NM_001009999.2 NM_015013.3
Applied Biosystems TaqMan ® Gene Expression Assays: NM_015013
OriGene GFP tagged cDNA clone in CMV expression vector: NM_015013
Myc/DDK tagged cDNA clone in CMV expression vector: NM_015013
untagged cDNA clones in CMV expression vector (see all 2): NM_001009999
Additional cDNA sequence: AK094536.1 21 DOTS entries: DT.445541 DT.75168215 DT.101965255 DT.100029753 DT.97807163 DT.100029754 DT.91810793 DT.91855964 DT.91864063 DT.100792121 DT.208132 DT.100792124 DT.102833397 DT.95305991 DT.92409945 DT.95118653 DT.95305995 DT.100029751 DT.95326557 DT.92398041 DT.95219935 24/350 AceView cDNA sequences (see all 350
):BE886699 AW337957 BM477281 BE251405 BQ083143 AA429058 AW138979 BQ938129 BQ434897 CB131888 BU184343 CN484497 BU521265 CN482870 BM772768 CF135181 BQ214471 BQ636096 BQ948080 BQ898499 BF931010 AA337953 CA489878 BM698411 Unigene Clusters for KDM1: Lysine (K)-specific demethylase 1 Hs.591518 [show with all ESTs], Hs.656420 [show with all ESTs]Unigene Representative Sequences: BC040194, AK094536
GeneLoc Exon Structure
5/6 Alternative Splicing Database (ASD) splice patterns (SP) for KDM1 (see all 6
)
| ExUns: | 1 | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14a | · | 14b | ^ | 15 | ^ | 16a | · | 16b | · | 16c | ^ | 17a | · | 17b | · | 17c | ^ | 18 | ^ | 19a | · | 19b | ^ | 20 | ^ |
|---|
|
| SP1: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | - | | | | | | | | - | | | | | | | | - | | |
| SP2: | | | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | - | | | | | | | | - | | | | | | | | - | | |
| SP3: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | - | | | | - | | | | - | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | | | | | | | | | - | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
About this scheme
ECgene alternative splicing isoforms for KDM1
3 Ensembl transcripts including schematic representations: ENST00000246149
ENST00000400181
ENST00000356634
|
Expression
for KDM1
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 219 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Expression Assays from
Applied Biosystems
)
About This Section
| KDM1 expression in normal and diseased human tissues
Applied Biosystems TaqMan ® Gene Expression Assays for KDM1
1 / 2 5 probe-sets matching KDM1 gene Data from
(Publications) and GNF BioGPS
About these images
About these images
CGAP SAGE TAG: TTTCACATAA
SOURCE GeneReport for Unigene clusters: Hs.591518 Hs.656420
UniProtKB/Swiss-Prot: KDM1_HUMAN, O60341Tissue specificity: Ubiquitously expressed |
Orthologs
for KDM1
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for KDM1 gene from 5/18 species (see all 18
)
About this table Species with no ortholog for KDM1
ENSEMBL Gene Tree for KDM1 | Paralogs
for KDM1(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
| Paralogs for KDM1 gene
- PAOX2 SMOX2 AOF12
|
SNPs/Variants
for KDM1(According to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Genotyping Reagents from
Applied Biosystems)
About This Section
|
HapMap Linkage Disequilibrium images for KDM1 (up to first 250kb)
|
Disorders & Mutations
for KDM1
(in which this Gene is Involved, According to
OMIM, UniProtKB,
Novoseek, PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
HGMD, GAD,
HuGE Navigator,
BCGD,
and/or TGDB.)
About This Section
|
OMIM: 609132
2 Novoseek disease relationships for KDM1 gene
About this table
|
Medical News
for KDM1(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications
for KDM1 (in
PubMed.
Associations of this gene to articles via
1Novoseek,
2HGNC,
3Entrez Gene,
4UniProtKB/Swiss-Prot,
5UniProtKB/TrEMBL,
6GAD, and/or
7PharmGKB)
About This Section
| 10/78 PubMed articles for KDM1 gene (see all 78
):- A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. (PubMed id 12493763)1, 2, 3, 4 Hakimi M.A....Shiekhattar R. (2003)
- Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PubMed id 9628581)2, 3, 4 Nagase T....Ohara O. (1998)
- Crystal structure of human histone lysine-specific demethylase 1 (LSD1). (PubMed id 16956976)1, 3, 4 Chen Y.... Lei M. (2006)
- LSD1 demethylates repressive histone marks to promote androgen- receptor-dependent transcription. (PubMed id 16079795)1, 3, 4 Metzger E.... Schuele R. (2005)
- Regulation of LSD1 histone demethylase activity by its associated factors. (PubMed id 16140033)1, 3, 4 Shi Y.-J.... Shi Y. (2005)
- Histone demethylation catalysed by LSD1 is a flavin-dependent oxidative process. (PubMed id 15811342)1, 3, 4 Forneris F.... Battaglioli E. (2005)
- Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase. (PubMed id 16885027)1, 3, 4 Yang M.... Yu H. (2006)
- An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. (PubMed id 16079794)1, 3, 4 Lee M.G.... Shiekhattar R. (2005)
- p53 is regulated by the lysine demethylase LSD1. (PubMed id 17805299)1, 3, 4 Huang J....Berger S.L. (2007)
- Solution structure of the SWIRM domain of human histone demethylase LSD1. (PubMed id 16531230)1, 3, 4 Tochio N....Yokoyama S. (2006)
|
Search for KDM1
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing KDM1
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
and/or
H-InvDB)
About This Section
|
| Other Databases showing KDM1
(According to HUGE)
About This Section
| |
Specialized Databases showing KDM1(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| About This Section
| --
| Services
for KDM1(Reagents available from Applied Biosystems, Antibodies and assays by Cell
Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section
| 
Products for KDM1:
 | |
 | | | | |
 |
 |  |  | |
 | Antibodies & Assays for KDM1 (LSD1) |
| | | | | Search Tocris compounds for KDM1 |
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