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    SUV39H2 SUV39H2 histone lysine methyltransferase [ Homo sapiens (human) ]

    Gene ID: 79723, updated on 2-May-2024

    Summary

    Official Symbol
    SUV39H2provided by HGNC
    Official Full Name
    SUV39H2 histone lysine methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:17287
    See related
    Ensembl:ENSG00000152455 MIM:606503; AllianceGenome:HGNC:17287
    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
    Summary
    Enables S-adenosyl-L-methionine binding activity; histone methyltransferase activity (H3-K9 specific); and zinc ion binding activity. Involved in chromatin assembly or disassembly and chromatin remodeling. Acts upstream of or within cellular response to hypoxia and negative regulation of transcription by RNA polymerase II. Located in chromatin. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 10.3), lymph node (RPKM 2.1) and 23 other tissues See more
    Orthologs
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    Genomic context

    Location:
    10p13
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (14878866..14904315)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (14892831..14918279)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (14920865..14946314)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3085 Neighboring gene Myb/SANT DNA binding domain containing 7 Neighboring gene heat shock protein family A (Hsp70) member 14 Neighboring gene SUV39H2 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2164 Neighboring gene NANOG hESC enhancer GRCh37_chr10:14946352-14947052 Neighboring gene DNA cross-link repair 1C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3087 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:14994732-14995460 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:14995461-14996188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2166 Neighboring gene meiosis/spermiogenesis associated 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:15033655-15034186 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:15034187-15034717 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 Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ23414

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables S-adenosyl-L-methionine binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3 methyltransferase activity TAS
    Traceable Author Statement
    more info
     
    enables histone H3K9 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K9 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K9 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription cis-regulatory region binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables ubiquitin-like ligase-substrate adaptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cellular response to hypoxia IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chromatin organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in circadian rhythm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in epigenetic programming in the zygotic pronuclei IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of gene expression, epigenetic ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    histone-lysine N-methyltransferase SUV39H2
    Names
    H3-K9-HMTase 2
    histone H3-K9 methyltransferase 2
    histone methyltransferase SUV39H2
    lysine N-methyltransferase 1B
    su(var)3-9 homolog 2
    suppressor of variegation 3-9 homolog 2
    NP_001180353.1
    NP_001180354.1
    NP_001180355.1
    NP_001180356.1
    NP_078946.1
    XP_011517964.1
    XP_047281697.1
    XP_054222708.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      D3DRT4, Q5JSS4, Q5JSS5, Q6I9Y3, Q8ND06, Q9H5I1
      Related
      ENSP00000346997.6, ENST00000354919.11
      Conserved Domains (2) summary
      cd18639
      Location:4795
      CD_SUV39H1_like; chromodomain of histone methyltransferase SUV39H1, and similar proteins
      cd10532
      Location:167409
      SET_SUV39H2; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins
    2. NM_001193425.2NP_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 (2) summary
      cd10532
      Location:107349
      SET_SUV39H2; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins
      cl28914
      Location:135
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
    3. NM_001193426.2NP_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
      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_001193427.2NP_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/TrEMBL
      Q5JSS2
      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_024670.4NP_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)
      AC069544, BC007754
      Consensus CDS
      CCDS7104.1
      UniProtKB/Swiss-Prot
      Q9H5I1
      Related
      ENSP00000319208.5, ENST00000313519.9
      Conserved Domains (2) summary
      cd10532
      Location:107349
      SET_SUV39H2; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins
      cl28914
      Location:135
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

    RNA

    1. NR_034181.2 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: 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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      14878866..14904315
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425741.1XP_047281697.1  histone-lysine N-methyltransferase SUV39H2 isoform X1

    2. XM_011519662.3XP_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 (2) summary
      cd10532
      Location:107349
      SET_SUV39H2; SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins
      cl28914
      Location:135
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      14892831..14918279
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366733.1XP_054222708.1  histone-lysine N-methyltransferase SUV39H2 isoform X1