U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    setd1a SET domain containing 1A, histone lysine methyltransferase [ Danio rerio (zebrafish) ]

    Gene ID: 556535, updated on 27-Mar-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    setd1aprovided by ZNC
    Official Full Name
    SET domain containing 1A, histone lysine methyltransferaseprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-080521-4
    See related
    Ensembl:ENSDARG00000060030 AllianceGenome:ZFIN:ZDB-GENE-080521-4
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Summary
    Predicted to enable RNA binding activity and histone methyltransferase activity (H3-K4 specific). Predicted to act upstream of or within chromatin organization and methylation. Predicted to be part of Set1C/COMPASS complex. Orthologous to human SETD1A (SET domain containing 1A, histone lysine methyltransferase). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    chromosome: 3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (32714083..32742578)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (32582379..32610861)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene si:dkey-16l2.17 Neighboring gene FUS RNA binding protein Neighboring gene hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase Neighboring gene TBC1 domain family, member 10b

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Ma Z, et al. Nature, 2019 Apr. PMID 30944473
    2. Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. Sun XJ, et al. PLoS One, 2008 Jan 30. PMID 18231586, Free PMC Article
    3. The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Fellous A, et al. Gene, 2019 Mar 1. PMID 30458291
    4. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
    5. Hematopoietic gene expression profile in zebrafish kidney marrow. Song HD, et al. Proc Natl Acad Sci U S A, 2004 Nov 16. PMID 15520368, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4 methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Set1C/COMPASS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Set1C/COMPASS complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    histone-lysine N-methyltransferase SETD1A
    XP_001920852.4
    XP_005164136.2
    XP_005164137.2
    XP_021329647.1
    XP_021329648.1
    XP_021329649.1
    XP_021329977.1
    XP_021329978.1
    XP_021329983.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007114.7 Reference GRCz11 Primary Assembly

      Range
      32714083..32742578
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021474302.1 → XP_021329977.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/TrEMBL
      A0A8M9PFJ8, E9QGQ0, F1QV90
      Related
      ENSDARP00000108328.2, ENSDART00000125022.4
      Conserved Domains (5) summary
      smart00317
      Location:2114 → 2237
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:2237 → 2253
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:89 → 183
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1969 → 2108
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      pfam12526
      Location:1504 → 1563
      DUF3729; Protein of unknown function (DUF3729)

    2. XM_021474308.1 → XP_021329983.1  histone-lysine N-methyltransferase SETD1A isoform X2

      UniProtKB/TrEMBL
      A0A8M9PSI4
      Conserved Domains (5) summary
      smart00317
      Location:2113 → 2236
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:2236 → 2252
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:89 → 183
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1968 → 2107
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      pfam12526
      Location:1503 → 1562
      DUF3729; Protein of unknown function (DUF3729)

    3. XM_021474303.1 → XP_021329978.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/TrEMBL
      A0A8M9PFJ8, E9QGQ0, F1QV90
      Related
      ENSDARP00000115396.2, ENSDART00000131774.4
      Conserved Domains (5) summary
      smart00317
      Location:2114 → 2237
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:2237 → 2253
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:89 → 183
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1969 → 2108
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      pfam12526
      Location:1504 → 1563
      DUF3729; Protein of unknown function (DUF3729)

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394535.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      202574..232842
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_001920817.7 → XP_001920852.4  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/TrEMBL
      A0A8M1QQT7
      Conserved Domains (5) summary
      smart00317
      Location:2114 → 2237
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:2237 → 2253
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:89 → 183
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1969 → 2108
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      pfam12526
      Location:1504 → 1563
      DUF3729; Protein of unknown function (DUF3729)

    2. XM_005164080.4 → XP_005164137.2  histone-lysine N-methyltransferase SETD1A isoform X2

      UniProtKB/TrEMBL
      A0A8M2BBI9
      Conserved Domains (5) summary
      smart00317
      Location:2113 → 2236
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:2236 → 2252
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:89 → 183
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1968 → 2107
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      pfam12526
      Location:1503 → 1562
      DUF3729; Protein of unknown function (DUF3729)

    3. XM_005164079.3 → XP_005164136.2  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/TrEMBL
      A0A8M1QQT7
      Conserved Domains (5) summary
      smart00317
      Location:2114 → 2237
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:2237 → 2253
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:89 → 183
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1969 → 2108
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      pfam12526
      Location:1504 → 1563
      DUF3729; Protein of unknown function (DUF3729)

    Reference GRCz11 ALT_DRER_TU_2

    Genomic

    1. NW_018395227.1 Reference GRCz11 ALT_DRER_TU_2

      Range
      76009..104504
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021473972.1 → XP_021329647.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/TrEMBL
      A0A8M9PFJ8, E9QGQ0, F1QV90
      Conserved Domains (5) summary
      smart00317
      Location:2114 → 2237
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:2237 → 2253
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:89 → 183
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1969 → 2108
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      pfam12526
      Location:1504 → 1563
      DUF3729; Protein of unknown function (DUF3729)

    2. XM_021473974.1 → XP_021329649.1  histone-lysine N-methyltransferase SETD1A isoform X2

      UniProtKB/TrEMBL
      A0A8M9PSI4
      Conserved Domains (5) summary
      smart00317
      Location:2113 → 2236
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:2236 → 2252
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:89 → 183
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1968 → 2107
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      pfam12526
      Location:1503 → 1562
      DUF3729; Protein of unknown function (DUF3729)

    3. XM_021473973.1 → XP_021329648.1  histone-lysine N-methyltransferase SETD1A isoform X1

      UniProtKB/TrEMBL
      A0A8M9PFJ8, E9QGQ0, F1QV90
      Conserved Domains (5) summary
      smart00317
      Location:2114 → 2237
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:2237 → 2253
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd12548
      Location:89 → 183
      RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
      pfam11764
      Location:1969 → 2108
      N-SET; COMPASS (Complex proteins associated with Set1p) component N
      pfam12526
      Location:1504 → 1563
      DUF3729; Protein of unknown function (DUF3729)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous