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    Setd5 SET domain containing 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 297514, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Setd5provided by RGD
    Official Full Name
    SET domain containing 5provided by RGD
    Primary source
    RGD:1310433
    See related
    EnsemblRapid:ENSRNOG00000007472 AllianceGenome:RGD:1310433
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1310433
    Summary
    Predicted to enable methylated histone binding activity; protein-lysine N-methyltransferase activity; and transcription corepressor activity. Predicted to be involved in several processes, including regulation of DNA-templated transcription; regulation of chromatin organization; and regulation of synapse assembly. Predicted to be located in euchromatin and nucleoplasm. Predicted to be part of Rpd3L-Expanded complex and Set3 complex. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 23. Orthologous to human SETD5 (SET domain containing 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 174.1), Thymus (RPKM 155.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Setd5 in Genome Data Viewer
    Location:
    4q42
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (147772955..147850669)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (146217172..146294896)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (145017549..145095247)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene THUMP domain containing 3 Neighboring gene U6 spliceosomal RNA Neighboring gene THUMPD3 antisense RNA 1 Neighboring gene transfer RNA proline (anticodon AGG) 26 Neighboring gene LHFPL tetraspan subfamily member 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Integrated Analysis of Genetic Abnormalities of the Histone Lysine Methyltransferases in Prostate Cancer. Zhang Y, et al. Med Sci Monit, 2019 Jan 7. PMID 30616239, Free PMC Article
    2. SETD5 Regulates Glycolysis in Breast Cancer Stem-Like Cells and Fuels Tumor Growth. Yang Z, et al. Am J Pathol, 2022 Apr. PMID 35063407
    3. SET domain-containing 5 is a potential prognostic biomarker that promotes esophageal squamous cell carcinoma stemness. Piao L, et al. Exp Cell Res, 2020 Apr 1. PMID 31981592
    4. Setd5 haploinsufficiency alters neuronal network connectivity and leads to autistic-like behaviors in mice. Moore SM, et al. Transl Psychiatry, 2019 Jan 17. PMID 30655503, Free PMC Article
    5. Setd5 is required in cardiopharyngeal mesoderm for heart development and its haploinsufficiency is associated with outflow tract defects in mouse. Cheung MY, et al. Genesis, 2021 Aug. PMID 34050709, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    NOT enables histone H3 methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K36 methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K9 methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables methylated histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cognition ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase III ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA-templated transcription elongation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of chromatin organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of Rpd3L-Expanded complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Set3 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in euchromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase SETD5
    Names
    SET domain-containing protein 5
    NP_001100084.1
    XP_006237074.1
    XP_006237077.1
    XP_006237078.1
    XP_006237080.1
    XP_017448059.1
    XP_038963325.1
    XP_038963326.1
    XP_038963329.1
    XP_063141934.1
    XP_063141935.1
    XP_063141936.1
    XP_063141937.1
    XP_063141938.1
    XP_063141939.1
    XP_063141940.1

    NCBI Reference Sequences (RefSeq)

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    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_001106614.2 → NP_001100084.1  histone-lysine N-methyltransferase SETD5

      See identical proteins and their annotated locations for NP_001100084.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A0A8I6A251, A6IBP2
      Conserved Domains (1) summary
      smart00317
      Location:293 → 402
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      147772955..147850669
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006237012.5 → XP_006237074.1  histone-lysine N-methyltransferase SETD5 isoform X2

      UniProtKB/TrEMBL
      A0A8I6A251
      Conserved Domains (1) summary
      smart00317
      Location:318 → 427
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

    2. XM_006237016.4 → XP_006237078.1  histone-lysine N-methyltransferase SETD5 isoform X5

      UniProtKB/TrEMBL
      A0A8I6A251
      Related
      ENSRNOP00000110266.1, ENSRNOT00000168940.1
      Conserved Domains (1) summary
      smart00317
      Location:305 → 414
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

    3. XM_039107397.1 → XP_038963325.1  histone-lysine N-methyltransferase SETD5 isoform X6

      UniProtKB/TrEMBL
      A0A8I6A251
      Conserved Domains (1) summary
      cd19181
      Location:279 → 428
      SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins

    4. XM_006237018.5 → XP_006237080.1  histone-lysine N-methyltransferase SETD5 isoform X7

      UniProtKB/TrEMBL
      A0A8I6A251
      Conserved Domains (1) summary
      smart00317
      Location:286 → 395
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

    5. XM_017592570.3 → XP_017448059.1  histone-lysine N-methyltransferase SETD5 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A251
      Conserved Domains (1) summary
      cd19181
      Location:305 → 454
      SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins

    6. XM_063285864.1 → XP_063141934.1  histone-lysine N-methyltransferase SETD5 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A251

    7. XM_063285865.1 → XP_063141935.1  histone-lysine N-methyltransferase SETD5 isoform X1

      UniProtKB/TrEMBL
      A0A8I6A251

    8. XM_039107398.2 → XP_038963326.1  histone-lysine N-methyltransferase SETD5 isoform X8

      UniProtKB/TrEMBL
      A0A8I5ZVR7
      Related
      ENSRNOP00000083274.1, ENSRNOT00000110888.2
      Conserved Domains (1) summary
      cd19181
      Location:260 → 409
      SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins

    9. XM_063285868.1 → XP_063141938.1  histone-lysine N-methyltransferase SETD5 isoform X10

      UniProtKB/TrEMBL
      A6IBP3

    10. XM_063285869.1 → XP_063141939.1  histone-lysine N-methyltransferase SETD5 isoform X10

      UniProtKB/TrEMBL
      A6IBP3

    11. XM_063285866.1 → XP_063141936.1  histone-lysine N-methyltransferase SETD5 isoform X3

      UniProtKB/TrEMBL
      A0A8I6A251, D4A2W7
      Related
      ENSRNOP00000059211.2, ENSRNOT00000066723.4

    12. XM_006237015.4 → XP_006237077.1  histone-lysine N-methyltransferase SETD5 isoform X4

      See identical proteins and their annotated locations for XP_006237077.1

      UniProtKB/TrEMBL
      A0A8I6A251
      Conserved Domains (1) summary
      cd19181
      Location:286 → 435
      SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins

    13. XM_039107401.2 → XP_038963329.1  histone-lysine N-methyltransferase SETD5 isoform X12

      Conserved Domains (1) summary
      cd19181
      Location:305 → 454
      SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins

    14. XM_063285870.1 → XP_063141940.1  histone-lysine N-methyltransferase SETD5 isoform X11

    15. XM_063285867.1 → XP_063141937.1  histone-lysine N-methyltransferase SETD5 isoform X9

      UniProtKB/TrEMBL
      A6IBP3
      Related
      ENSRNOP00000085738.2, ENSRNOT00000115284.2
    Nucleotide Protein Strain
    Heading Accession and Version

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