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    SETD3 SET domain containing 3, actin N3(tau)-histidine methyltransferase [ Homo sapiens (human) ]

    Gene ID: 84193, updated on 12-Nov-2024

    Summary

    Official Symbol
    SETD3provided by HGNC
    Official Full Name
    SET domain containing 3, actin N3(tau)-histidine methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:20493
    See related
    Ensembl:ENSG00000183576 MIM:615671; AllianceGenome:HGNC:20493
    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
    hSETD3; C14orf154
    Summary
    Enables protein-L-histidine N-tele-methyltransferase activity. Involved in actin modification and peptidyl-histidine methylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 33.6), kidney (RPKM 26.5) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SETD3 in Genome Data Viewer
    Location:
    14q32.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (99397748..99486458, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (93629309..93718026, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (99864085..99947196, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903412 Neighboring gene BCL11 transcription factor B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99677677-99678177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99695676-99696574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99703507-99704031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99713148-99714044 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99723824-99724098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99734631-99735236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99735237-99735841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9002 Neighboring gene uncharacterized LOC105370660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99750257-99750979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99784572-99785298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99786594-99787222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99787223-99787850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99788913-99789673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99798343-99799050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99799051-99799757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99814550-99815224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99815225-99815898 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99827260-99827481 Neighboring gene Sharpr-MPRA regulatory region 7827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99849405-99850263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99860795-99861575 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99874757-99875323 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:99878378-99879044 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99879711-99880376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99890523-99891386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99891387-99892249 Neighboring gene RNA, U6 small nuclear 91, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:99946327-99946828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99968944-99969444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99969445-99969945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99974643-99975198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99977641-99978142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99978143-99978642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99978643-99979643 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99988085-99988644 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99988645-99989206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99995945-99996467 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99996990-99997512 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99997513-99998033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99999970-100000571 Neighboring gene coiled-coil domain containing 85C Neighboring gene uncharacterized LOC105370661 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100003689-100004280 Neighboring gene cyclin K Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100004281-100004872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100006217-100006952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100011369-100012103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100017717-100018455 Neighboring gene HNF4 motif-containing MPRA enhancer 184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100029329-100030250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100030251-100031170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100033011-100033930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100035771-100036690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100036691-100037611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100037612-100038531 Neighboring gene VISTA enhancer hs1931 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:100045528-100046727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100054779-100055374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100057164-100057760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100064325-100065207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100068739-100069392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6067 Neighboring gene Sharpr-MPRA regulatory region 4550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100090366-100091068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9005 Neighboring gene HHIP like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100118444-100118944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100118945-100119445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100128755-100129256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100129257-100129756 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100130377-100130920 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100130921-100131465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100135414-100135955 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:100136897-100137496 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100137497-100138098 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100138099-100138698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100141430-100141993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100142557-100143120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100143121-100143683

    Genomic regions, transcripts, and products

    Expression

    • 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

    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

    • FLJ23027, MGC87236, DKFZp761E1415

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II-specific DNA-binding transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables actin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K36 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K36 methyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-L-histidine N-tele-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein-L-histidine N-tele-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT enables protein-lysine N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transcription coactivator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in actin modification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in actin modification IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in peptidyl-histidine methylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT involved_in peptidyl-lysine trimethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of uterine smooth muscle contraction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of uterine smooth muscle contraction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in chromatin IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    actin-histidine N-methyltransferase
    Names
    SET domain containing 3, actin histidine methyltransferase
    SET domain-containing protein 3
    histone-lysine N-methyltransferase setd3
    protein-L-histidine N-tele-methyltransferase
    NP_115609.2
    NP_954574.1
    XP_011535533.2
    XP_011535534.1
    XP_011535535.1
    XP_011535537.1
    XP_016877188.1
    XP_016877189.1
    XP_047287761.1
    XP_054232780.1
    XP_054232781.1
    XP_054232782.1
    XP_054232783.1

    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_032233.3NP_115609.2  actin-histidine N-methyltransferase isoform a

      See identical proteins and their annotated locations for NP_115609.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AK026680, BC037395, BX161471, CB988965
      Consensus CDS
      CCDS9951.1
      UniProtKB/Swiss-Prot
      A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
      Related
      ENSP00000327436.5, ENST00000331768.10
      Conserved Domains (2) summary
      cd19176
      Location:80329
      SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
      pfam09273
      Location:350475
      Rubis-subs-bind; Rubisco LSMT substrate-binding
    2. NM_199123.2NP_954574.1  actin-histidine N-methyltransferase isoform b

      See identical proteins and their annotated locations for NP_954574.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1, that causes a frameshift. The resulting isoform (b) is shorter and has a unique C-terminus compared to isoform a.
      Source sequence(s)
      BC009054, CB988965
      Consensus CDS
      CCDS9952.1
      UniProtKB/TrEMBL
      A6NJ55, Q6NXR6
      Related
      ENSP00000327910.3, ENST00000329331.7
      Conserved Domains (1) summary
      cd19176
      Location:80282
      SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      99397748..99486458 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017021699.2XP_016877188.1  actin-histidine N-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
      Conserved Domains (2) summary
      cd19176
      Location:80329
      SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
      pfam09273
      Location:350475
      Rubis-subs-bind; Rubisco LSMT substrate-binding
    2. XM_011537233.3XP_011535535.1  actin-histidine N-methyltransferase isoform X2

      Conserved Domains (2) summary
      pfam09273
      Location:292417
      Rubis-subs-bind; Rubisco LSMT substrate-binding
      cd19176
      Location:80271
      SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
    3. XM_011537231.3XP_011535533.2  actin-histidine N-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
      Conserved Domains (2) summary
      cd19176
      Location:80329
      SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
      pfam09273
      Location:350475
      Rubis-subs-bind; Rubisco LSMT substrate-binding
    4. XM_011537232.4XP_011535534.1  actin-histidine N-methyltransferase isoform X1

      See identical proteins and their annotated locations for XP_011535534.1

      UniProtKB/Swiss-Prot
      A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
      Conserved Domains (2) summary
      cd19176
      Location:80329
      SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
      pfam09273
      Location:350475
      Rubis-subs-bind; Rubisco LSMT substrate-binding
    5. XM_047431805.1XP_047287761.1  actin-histidine N-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
    6. XM_017021700.2XP_016877189.1  actin-histidine N-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
      Conserved Domains (2) summary
      cd19176
      Location:80329
      SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
      pfam09273
      Location:350475
      Rubis-subs-bind; Rubisco LSMT substrate-binding
    7. XM_011537235.1XP_011535537.1  actin-histidine N-methyltransferase isoform X3

      See identical proteins and their annotated locations for XP_011535537.1

      UniProtKB/TrEMBL
      A6NJ55, Q6NXR6
      Conserved Domains (1) summary
      cd19176
      Location:80282
      SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      93629309..93718026 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376806.1XP_054232781.1  actin-histidine N-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
    2. XM_054376807.1XP_054232782.1  actin-histidine N-methyltransferase isoform X2

    3. XM_054376805.1XP_054232780.1  actin-histidine N-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
    4. XM_054376808.1XP_054232783.1  actin-histidine N-methyltransferase isoform X3