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SUV39H2 suppressor of variegation 3-9 homolog 2 [ Homo sapiens (human) ]

Gene ID: 79723, updated on 17-Jun-2019

Summary

Official Symbol
SUV39H2provided by HGNC
Official Full Name
suppressor of variegation 3-9 homolog 2provided by HGNC
Primary source
HGNC:HGNC:17287
See related
Ensembl:ENSG00000152455 MIM:606503
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
KMT1B
Expression
Broad expression in testis (RPKM 10.3), lymph node (RPKM 2.1) and 23 other tissues See more
Orthologs

Genomic context

See SUV39H2 in Genome Data Viewer
Location:
10p13
Exon count:
8
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (14878783..14904315)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (14920782..14946314)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene cerebral dopamine neurotrophic factor Neighboring gene zinc finger and SCAN domain containing 29 pseudogene Neighboring gene heat shock protein family A (Hsp70) member 14 Neighboring gene DNA cross-link repair 1C Neighboring gene meiosis/spermiogenesis associated 1 Neighboring gene olfactory receptor family 7 subfamily E member 110 pseudogene Neighboring gene olfactory receptor family 7 subfamily E member 26 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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Histone Modifications, organism-specific biosystem (from WikiPathways)
    Histone Modifications, organism-specific biosystemHistones can undergo many post-translational modifications that are involved in transcription regulation. This pathway provides an overview of various modifications for histones H3 and H4 and the en...
  • Lysine degradation, organism-specific biosystem (from KEGG)
    Lysine degradation, organism-specific biosystem
    Lysine degradation
  • Lysine degradation, conserved biosystem (from KEGG)
    Lysine degradation, conserved biosystem
    Lysine degradation
  • PKMTs methylate histone lysines, organism-specific biosystem (from REACTOME)
    PKMTs methylate histone lysines, organism-specific biosystemLysine methyltransferases (KMTs) and arginine methyltransferases (RMTs) have a common mechanism of catalysis. Both families transfer a methyl group from a common donor, S-adenosyl-L-methionine (SAM),...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ23414

Gene Ontology Provided by GOA

Function Evidence Code Pubs
S-adenosyl-L-methionine binding IDA
Inferred from Direct Assay
more info
PubMed 
histone methyltransferase activity (H3-K9 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase activity (H3-K9 specific) IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
cellular response to hypoxia IDA
Inferred from Direct Assay
more info
PubMed 
chromatin assembly or disassembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K9 dimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K9 trimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone lysine methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chromatin IDA
Inferred from Direct Assay
more info
PubMed 
chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase SUV39H2
Names
H3-K9-HMTase 2
histone H3-K9 methyltransferase 2
lysine N-methyltransferase 1B
su(var)3-9 homolog 2
NP_001180353.1
NP_001180354.1
NP_001180355.1
NP_001180356.1
NP_078946.1
XP_006717566.1
XP_011517964.1
XP_016872126.1

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.

mRNA and Protein(s)

  1. NM_001193424.2NP_001180353.1  histone-lysine N-methyltransferase SUV39H2 isoform 1

    See identical proteins and their annotated locations for NP_001180353.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (1).
    Source sequence(s)
    BC007754, DB040298
    Consensus CDS
    CCDS53494.1
    UniProtKB/Swiss-Prot
    Q9H5I1
    Related
    ENSP00000346997.6, ENST00000354919.10
    Conserved Domains (3) summary
    smart00317
    Location:250373
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:4893
    Chromo; Chromo (CHRromatin Organization MOdifier) domain
    pfam05033
    Location:154242
    Pre-SET; Pre-SET motif
  2. NM_001193425.1NP_001180354.1  histone-lysine N-methyltransferase SUV39H2 isoform 2

    See identical proteins and their annotated locations for NP_001180354.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon compared to variant 1. This results in translation initiation from an in-frame, downstream AUG, and a shorter isoform (2) compared to isoform 1. Variants 2 and 3 encode the same isoform.
    Source sequence(s)
    AC069544, AL360083, BC007754, BU928392
    Consensus CDS
    CCDS7104.1
    UniProtKB/Swiss-Prot
    Q9H5I1
    Conserved Domains (3) summary
    smart00317
    Location:190313
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:233
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam05033
    Location:87182
    Pre-SET; Pre-SET motif
  3. NM_001193426.1NP_001180355.1  histone-lysine N-methyltransferase SUV39H2 isoform 3

    See identical proteins and their annotated locations for NP_001180355.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate donor splice site at an internal coding exon compared to variant 1, maintaining the reading frame, and resulting in a shorter isoform (3) missing an internal protein segment compared compared to isoform 1.
    Source sequence(s)
    BC007754, BC029360, DB040298
    Consensus CDS
    CCDS53493.1
    UniProtKB/Swiss-Prot
    Q9H5I1
    Related
    ENSP00000367576.3, ENST00000378325.7
    Conserved Domains (2) summary
    smart00317
    Location:100193
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:4793
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
  4. NM_001193427.1NP_001180356.1  histone-lysine N-methyltransferase SUV39H2 isoform 4

    See identical proteins and their annotated locations for NP_001180356.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' terminal exon, and uses an alternate donor splice site at an internal coding exon compared to variant 1. This results in translation initiation from an in-frame, downstream AUG, and a shorter isoform (4) missing an internal protein segment compared compared to isoform 1.
    Source sequence(s)
    BC007754, BU928392
    UniProtKB/Swiss-Prot
    Q9H5I1
    Related
    ENSP00000388968.1, ENST00000433779.5
    Conserved Domains (2) summary
    smart00317
    Location:40133
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:233
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
  5. NM_024670.3NP_078946.1  histone-lysine N-methyltransferase SUV39H2 isoform 2

    See identical proteins and their annotated locations for NP_078946.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and is missing the subsequent exon compared to variant 1. This results in translation initiation from an in-frame, downstream AUG, and a shorter isoform (2) compared to isoform 1. Variants 2 and 3 encode the same isoform.
    Source sequence(s)
    BC007754
    Consensus CDS
    CCDS7104.1
    UniProtKB/Swiss-Prot
    Q9H5I1
    Related
    ENSP00000319208.5, ENST00000313519.9
    Conserved Domains (3) summary
    smart00317
    Location:190313
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:233
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam05033
    Location:87182
    Pre-SET; Pre-SET motif

RNA

  1. NR_034181.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) is missing an internal exon compared to variant 1. It is represented as non-coding because the use of the 5'-most supported translational start codon as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK225369, BC007754, DB040298
    Related
    ENST00000378331.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    14878783..14904315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017016637.1XP_016872126.1  histone-lysine N-methyltransferase SUV39H2 isoform X1

    UniProtKB/Swiss-Prot
    Q9H5I1
    Conserved Domains (3) summary
    smart00317
    Location:190313
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:233
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam05033
    Location:87182
    Pre-SET; Pre-SET motif
  2. XM_011519662.2XP_011517964.1  histone-lysine N-methyltransferase SUV39H2 isoform X1

    See identical proteins and their annotated locations for XP_011517964.1

    UniProtKB/Swiss-Prot
    Q9H5I1
    Conserved Domains (3) summary
    smart00317
    Location:190313
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:233
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam05033
    Location:87182
    Pre-SET; Pre-SET motif
  3. XM_006717503.3XP_006717566.1  histone-lysine N-methyltransferase SUV39H2 isoform X1

    See identical proteins and their annotated locations for XP_006717566.1

    UniProtKB/Swiss-Prot
    Q9H5I1
    Conserved Domains (3) summary
    smart00317
    Location:190313
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam00385
    Location:233
    Chromo; Chromo (CHRromatin Organisation MOdifier) domain
    pfam05033
    Location:87182
    Pre-SET; Pre-SET motif
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