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    kmt2ca lysine (K)-specific methyltransferase 2Ca [ Danio rerio (zebrafish) ]

    Gene ID: 560793, updated on 11-Apr-2024

    Summary

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    Official Symbol
    kmt2caprovided by ZNC
    Official Full Name
    lysine (K)-specific methyltransferase 2Caprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-080520-3
    See related
    Ensembl:ENSDARG00000079312 AllianceGenome:ZFIN:ZDB-GENE-080520-3
    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
    Also known as
    mll3a; si:ch211-244o18.1; si:ch211-244o18.2
    Summary
    Predicted to enable histone binding activity; histone methyltransferase activity (H3-K4 specific); and transcription coactivator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within chromatin organization and methylation. Predicted to be located in nucleus. Predicted to be part of MLL3/4 complex. Human ortholog(s) of this gene implicated in Klatskin's tumor; Kleefstra syndrome 2; esophagus squamous cell carcinoma; and squamous cell carcinoma. Orthologous to human KMT2C (lysine methyltransferase 2C). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See kmt2ca in Genome Data Viewer
    Location:
    chromosome: 24
    Exon count:
    61
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 24 NC_007135.7 (7336866..7549578)
    105 previous assembly GRCz10 (GCF_000002035.5) 24 NC_007135.6 (7307683..7520242)

    Chromosome 24 - NC_007135.7Genomic Context describing neighboring genes Neighboring gene actin related protein 3B Neighboring gene X-ray repair complementing defective repair in Chinese hamster cells 2 Neighboring gene uncharacterized LOC560947 Neighboring gene UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Genome-wide association study of kidney function decline in individuals of European descent. Gorski M, et al. Kidney Int, 2015 May. PMID 25493955, Free PMC Article
    2. The DEAD-box RNA helicase Ddx39ab is essential for myocyte and lens development in zebrafish. Zhang L, et al. Development, 2018 Apr 23. PMID 29636379
    3. 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
    4. 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
    5. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4 monomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    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
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of MLL3/4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase MLL3; histone-lysine N-methyltransferase 2C
    Names
    myeloid/lymphoid or mixed-lineage leukemia 3
    myeloid/lymphoid or mixed-lineage leukemia 3a
    XP_005162602.1
    XP_005162603.1
    XP_005162604.1
    XP_005162605.1
    XP_017209413.1
    XP_017209414.1
    XP_021325943.1

    NCBI Reference Sequences (RefSeq)

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    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_007135.7 Reference GRCz11 Primary Assembly

      Range
      7336866..7549578
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005162545.4 → XP_005162602.1  histone-lysine N-methyltransferase 2C isoform X1

      UniProtKB/TrEMBL
      A0A8M2B9E0
      Conserved Domains (13) summary
      smart00398
      Location:1707 → 1760
      HMG; high mobility group
      smart00317
      Location:4819 → 4940
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:4942 → 4958
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:4820 → 4958
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      cd15509
      Location:360 → 404
      PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
      cd15513
      Location:1030 → 1076
      PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
      cd15594
      Location:406 → 451
      PHD2_KMT2C; PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15596
      Location:973 → 1029
      PHD4_KMT2C; PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15697
      Location:4440 → 4544
      ePHD2_KMT2C; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C)
      pfam04487
      Location:2586 → 2683
      CITED; CITED
      pfam05964
      Location:4599 → 4649
      FYRN; F/Y-rich N-terminus
      pfam05965
      Location:4656 → 4736
      FYRC; F/Y rich C-terminus
      cl22851
      Location:263 → 346
      PHD_SF; PHD finger superfamily

    2. XM_017353925.2 → XP_017209414.1  histone-lysine N-methyltransferase 2C isoform X3

      UniProtKB/TrEMBL
      A0A8M6YY65

    3. XM_017353924.2 → XP_017209413.1  histone-lysine N-methyltransferase 2C isoform X2

      UniProtKB/TrEMBL
      A0A8M6YWB8

    4. XM_005162547.4 → XP_005162604.1  histone-lysine N-methyltransferase 2C isoform X5

      UniProtKB/TrEMBL
      A0A8M2B9E8
      Related
      ENSDARP00000115827.2, ENSDART00000137010.4
      Conserved Domains (13) summary
      smart00398
      Location:1691 → 1744
      HMG; high mobility group
      smart00317
      Location:4803 → 4924
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:4926 → 4942
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:4804 → 4942
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      cd15509
      Location:360 → 404
      PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
      cd15513
      Location:1030 → 1076
      PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
      cd15594
      Location:406 → 451
      PHD2_KMT2C; PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15596
      Location:973 → 1029
      PHD4_KMT2C; PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15697
      Location:4424 → 4528
      ePHD2_KMT2C; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C)
      pfam04487
      Location:2570 → 2667
      CITED; CITED
      pfam05964
      Location:4583 → 4633
      FYRN; F/Y-rich N-terminus
      pfam05965
      Location:4640 → 4720
      FYRC; F/Y rich C-terminus
      cl22851
      Location:263 → 346
      PHD_SF; PHD finger superfamily

    5. XM_021470268.1 → XP_021325943.1  histone-lysine N-methyltransferase 2C isoform X7

      UniProtKB/TrEMBL
      A0A8M9PG96
      Conserved Domains (17) summary
      smart00398
      Location:1658 → 1711
      HMG; high mobility group
      smart00317
      Location:4770 → 4891
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:4893 → 4909
      PostSET; Cysteine-rich motif following a subset of SET domains
      cd15509
      Location:360 → 404
      PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
      cd15513
      Location:1030 → 1076
      PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
      cd15594
      Location:406 → 451
      PHD2_KMT2C; PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15596
      Location:973 → 1029
      PHD4_KMT2C; PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15697
      Location:4391 → 4495
      ePHD2_KMT2C; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C)
      pfam07271
      Location:3397 → 3554
      Cytadhesin_P30; Cytadhesin P30/P32
      pfam04487
      Location:2537 → 2634
      CITED
      pfam05964
      Location:4549 → 4600
      FYRN; F/Y-rich N-terminus
      pfam05965
      Location:4607 → 4690
      FYRC; F/Y rich C-terminus
      pfam09606
      Location:3094 → 3352
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      cl22851
      Location:263 → 346
      PHD_SF; PHD finger superfamily
      cl25732
      Location:3143 → 3241
      SMC_N; RecF/RecN/SMC N terminal domain
      cl26464
      Location:1850 → 2305
      Atrophin-1; Atrophin-1 family
      cl28246
      Location:515 → 759
      DnaJ; DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]

    6. XM_005162548.4 → XP_005162605.1  histone-lysine N-methyltransferase 2C isoform X6

      UniProtKB/TrEMBL
      A0A8M2B9D3
      Conserved Domains (13) summary
      smart00398
      Location:1667 → 1720
      HMG; high mobility group
      smart00317
      Location:4779 → 4900
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:4902 → 4918
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:4780 → 4918
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      cd15509
      Location:360 → 404
      PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
      cd15513
      Location:990 → 1036
      PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
      cd15594
      Location:406 → 451
      PHD2_KMT2C; PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15596
      Location:933 → 989
      PHD4_KMT2C; PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15697
      Location:4400 → 4504
      ePHD2_KMT2C; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C)
      pfam04487
      Location:2546 → 2643
      CITED; CITED
      pfam05964
      Location:4559 → 4609
      FYRN; F/Y-rich N-terminus
      pfam05965
      Location:4616 → 4696
      FYRC; F/Y rich C-terminus
      cl22851
      Location:263 → 346
      PHD_SF; PHD finger superfamily

    7. XM_005162546.4 → XP_005162603.1  histone-lysine N-methyltransferase 2C isoform X4

      UniProtKB/TrEMBL
      A0A8M2B9Q2
      Conserved Domains (13) summary
      smart00398
      Location:1707 → 1760
      HMG; high mobility group
      smart00317
      Location:4815 → 4936
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      smart00508
      Location:4938 → 4954
      PostSET; Cysteine-rich motif following a subset of SET domains
      COG2940
      Location:4747 → 4954
      SET; SET domain-containing protein (function unknown) [General function prediction only]
      cd15509
      Location:360 → 404
      PHD1_KMT2C_like; PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)
      cd15513
      Location:1030 → 1076
      PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D
      cd15594
      Location:406 → 451
      PHD2_KMT2C; PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15596
      Location:973 → 1029
      PHD4_KMT2C; PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C)
      cd15697
      Location:4440 → 4544
      ePHD2_KMT2C; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C)
      pfam04487
      Location:2586 → 2683
      CITED; CITED
      pfam05964
      Location:4599 → 4649
      FYRN; F/Y-rich N-terminus
      pfam05965
      Location:4656 → 4736
      FYRC; F/Y rich C-terminus
      cl22851
      Location:263 → 346
      PHD_SF; PHD finger superfamily

    RNA

    1. XR_002456618.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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