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

Gene ID: 297514, updated on 2-Nov-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, Nov 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 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

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

  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

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

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

    UniProtKB/TrEMBL
    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

    Related
    ENSRNOP00000085738.2, ENSRNOT00000115284.2
Nucleotide Protein Strain
Heading Accession and Version

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