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SETD5 SET domain containing 5 [ Homo sapiens (human) ]

Gene ID: 55209, updated on 5-Jan-2022

Summary

Official Symbol
SETD5provided by HGNC
Official Full Name
SET domain containing 5provided by HGNC
Primary source
HGNC:HGNC:25566
See related
Ensembl:ENSG00000168137 MIM:615743
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This function of this gene has yet to be determined but based on sequence similarity to other SET domain proteins it may function as a histone methyltransferase. Mutations in this gene have been associated with an autosomal dominant form of intellectual disability. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2017]
Expression
Ubiquitous expression in brain (RPKM 9.1), thyroid (RPKM 9.1) and 25 other tissues See more
Orthologs
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Genomic context

See SETD5 in Genome Data Viewer
Location:
3p25.3
Exon count:
36
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (9397615..9478154)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9439299..9519838)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SLIT-ROBO Rho GTPase activating protein 3 Neighboring gene phosphoglycerate mutase 1 pseudogene 4 Neighboring gene THUMPD3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 11896 Neighboring gene THUMP domain containing 3 Neighboring gene Sharpr-MPRA regulatory region 15302 Neighboring gene LHFPL tetraspan subfamily member 4 Neighboring gene uncharacterized LOC105376949

Genomic regions, transcripts, and products

Expression

  • Project title: 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?

Phenotypes

Associated conditions

Description Tests
Mental retardation, autosomal dominant 23
MedGen: C3810406 OMIM: 615761 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2014-11-06)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2014-11-06)

ClinGen Genome Curation PagePubMed

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10707, KIAA1757, DKFZp686J18276

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histone methyltransferase activity (H3-K36 specific) ISS
Inferred from Sequence or Structural Similarity
more info
 
enables histone methyltransferase activity (H3-K9 specific) ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in cognition ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in histone H3-K36 trimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in histone H3-K9 methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of DNA-templated transcription, elongation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of chromatin organization ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of histone acetylation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in euchromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
histone-lysine N-methyltransferase SETD5
Names
SET domain-containing protein 5
NP_001073986.1
NP_001278972.1
NP_001336380.1
XP_005265358.1
XP_005265360.1
XP_011532222.1
XP_011532223.1
XP_011532224.1
XP_011532229.1
XP_011532230.1
XP_011532232.1
XP_011532234.1
XP_011532235.1
XP_016862256.1
XP_016862257.1
XP_016862259.1
XP_016862260.1
XP_016862261.1
XP_016862262.1
XP_016862263.1
XP_016862264.1
XP_016862265.1
XP_016862266.1
XP_016862267.1
XP_016862268.1
XP_016862269.1
XP_016862271.1
XP_016862272.1
XP_016862273.1
XP_016862274.1
XP_016862275.1
XP_024309388.1
XP_024309389.1

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.

Genomic

  1. NG_034132.1 RefSeqGene

    Range
    4916..85455
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001080517.3NP_001073986.1  histone-lysine N-methyltransferase SETD5 isoform 1

    See identical proteins and their annotated locations for NP_001073986.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AB051544, AC018506, AI243838, AK092046, CR627408
    Consensus CDS
    CCDS46741.1
    UniProtKB/Swiss-Prot
    Q9C0A6
    Related
    ENSP00000385852.2, ENST00000402198.7
    Conserved Domains (1) summary
    smart00317
    Location:286395
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  2. NM_001292043.2NP_001278972.1  histone-lysine N-methyltransferase SETD5 isoform 2

    See identical proteins and their annotated locations for NP_001278972.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' exon structure and initiates translation at a downstream start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).
    Source sequence(s)
    AB051544, AC018506, AI243838, AK092046, AW021954, CR627408, DB275141
    Consensus CDS
    CCDS74892.1
    UniProtKB/Swiss-Prot
    Q9C0A6
    Conserved Domains (2) summary
    smart00317
    Location:188297
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cl27032
    Location:336556
    Utp14; Utp14 protein
  3. NM_001349451.2NP_001336380.1  histone-lysine N-methyltransferase SETD5 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' exon structure and initiates translation at a downstream start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus, compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).
    Source sequence(s)
    AC018506
    Consensus CDS
    CCDS74892.1
    Conserved Domains (2) summary
    smart00317
    Location:188297
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    cl27032
    Location:336556
    Utp14; Utp14 protein

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    9397615..9478154
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006770.1XP_016862259.1  histone-lysine N-methyltransferase SETD5 isoform X4

    Conserved Domains (3) summary
    PLN02217
    Location:13411448
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:473693
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:305454
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  2. XM_017006772.1XP_016862261.1  histone-lysine N-methyltransferase SETD5 isoform X8

    Conserved Domains (3) summary
    PLN02217
    Location:13281435
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:460680
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:292441
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  3. XM_017006773.1XP_016862262.1  histone-lysine N-methyltransferase SETD5 isoform X9

    Conserved Domains (3) summary
    PLN02217
    Location:13281435
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:441661
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:273422
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  4. XM_017006775.1XP_016862264.1  histone-lysine N-methyltransferase SETD5 isoform X13

    Conserved Domains (3) summary
    PLN02217
    Location:13091416
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:441661
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:273422
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  5. XM_017006767.1XP_016862256.1  histone-lysine N-methyltransferase SETD5 isoform X1

    Conserved Domains (3) summary
    PLN02217
    Location:13601467
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:473693
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:305454
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  6. XM_011533920.1XP_011532222.1  histone-lysine N-methyltransferase SETD5 isoform X1

    See identical proteins and their annotated locations for XP_011532222.1

    Conserved Domains (3) summary
    PLN02217
    Location:13601467
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:473693
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:305454
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  7. XM_024453620.1XP_024309388.1  histone-lysine N-methyltransferase SETD5 isoform X3

    Conserved Domains (3) summary
    PLN02217
    Location:13471454
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:460680
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:292441
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  8. XM_017006783.1XP_016862272.1  histone-lysine N-methyltransferase SETD5 isoform X19

    Conserved Domains (3) summary
    PLN02217
    Location:11341241
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:247467
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:79228
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  9. XM_011533927.1XP_011532229.1  histone-lysine N-methyltransferase SETD5 isoform X5

    Conserved Domains (3) summary
    PLN02217
    Location:13411448
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:454674
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:286435
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  10. XM_011533930.1XP_011532232.1  histone-lysine N-methyltransferase SETD5 isoform X12

    Conserved Domains (3) summary
    PLN02217
    Location:13151422
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:428648
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:260409
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  11. XM_005265303.1XP_005265360.1  histone-lysine N-methyltransferase SETD5 isoform X14

    Conserved Domains (3) summary
    PLN02217
    Location:13021409
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:415635
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:247396
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  12. XM_017006776.1XP_016862265.1  histone-lysine N-methyltransferase SETD5 isoform X16

    Conserved Domains (3) summary
    PLN02217
    Location:12231330
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:336556
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:168317
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  13. XM_017006779.1XP_016862268.1  histone-lysine N-methyltransferase SETD5 isoform X17

    Conserved Domains (3) summary
    PLN02217
    Location:12101317
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:323543
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:155304
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  14. XM_017006778.1XP_016862267.1  histone-lysine N-methyltransferase SETD5 isoform X16

    Conserved Domains (3) summary
    PLN02217
    Location:12231330
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:336556
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:168317
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  15. XM_017006780.1XP_016862269.1  histone-lysine N-methyltransferase SETD5 isoform X17

    Conserved Domains (3) summary
    PLN02217
    Location:12101317
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:323543
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:155304
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  16. XM_017006777.1XP_016862266.1  histone-lysine N-methyltransferase SETD5 isoform X16

    Conserved Domains (3) summary
    PLN02217
    Location:12231330
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:336556
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:168317
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  17. XM_011533932.1XP_011532234.1  histone-lysine N-methyltransferase SETD5 isoform X17

    See identical proteins and their annotated locations for XP_011532234.1

    Conserved Domains (3) summary
    PLN02217
    Location:12101317
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:323543
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:155304
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  18. XM_017006782.1XP_016862271.1  histone-lysine N-methyltransferase SETD5 isoform X18

    Conserved Domains (2) summary
    COG5644
    Location:473693
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:305454
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  19. XM_017006784.1XP_016862273.1  histone-lysine N-methyltransferase SETD5 isoform X20

    Related
    ENSP00000507953.1, ENST00000684055.1
    Conserved Domains (2) summary
    COG5644
    Location:473693
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:305454
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  20. XM_017006785.1XP_016862274.1  histone-lysine N-methyltransferase SETD5 isoform X21

    Conserved Domains (2) summary
    COG5644
    Location:473693
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:305454
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  21. XM_017006786.1XP_016862275.1  histone-lysine N-methyltransferase SETD5 isoform X22

    Conserved Domains (2) summary
    COG5644
    Location:473693
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:305454
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  22. XM_011533922.1XP_011532224.1  histone-lysine N-methyltransferase SETD5 isoform X2

    See identical proteins and their annotated locations for XP_011532224.1

    Conserved Domains (3) summary
    PLN02217
    Location:13531460
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:466686
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:298447
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  23. XM_017006771.1XP_016862260.1  histone-lysine N-methyltransferase SETD5 isoform X6

    Conserved Domains (3) summary
    PLN02217
    Location:13401447
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:453673
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:285434
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  24. XM_005265301.1XP_005265358.1  histone-lysine N-methyltransferase SETD5 isoform X10

    UniProtKB/TrEMBL
    E7EWN3
    Related
    ENSP00000384114.1, ENST00000407969.5
    Conserved Domains (3) summary
    PLN02217
    Location:13211428
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:453673
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:285434
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  25. XM_011533928.1XP_011532230.1  histone-lysine N-methyltransferase SETD5 isoform X7

    Conserved Domains (3) summary
    PLN02217
    Location:13341441
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:447667
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:279428
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  26. XM_017006774.1XP_016862263.1  histone-lysine N-methyltransferase SETD5 isoform X11

    Conserved Domains (3) summary
    PLN02217
    Location:13211428
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:434654
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:266415
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  27. XM_011533921.2XP_011532223.1  histone-lysine N-methyltransferase SETD5 isoform X1

    See identical proteins and their annotated locations for XP_011532223.1

    Conserved Domains (3) summary
    PLN02217
    Location:13601467
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:473693
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:305454
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  28. XM_017006768.2XP_016862257.1  histone-lysine N-methyltransferase SETD5 isoform X2

    Conserved Domains (3) summary
    PLN02217
    Location:13531460
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:466686
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:298447
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  29. XM_011533933.1XP_011532235.1  histone-lysine N-methyltransferase SETD5 isoform X17

    See identical proteins and their annotated locations for XP_011532235.1

    Conserved Domains (3) summary
    PLN02217
    Location:12101317
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:323543
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:155304
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins
  30. XM_024453621.1XP_024309389.1  histone-lysine N-methyltransferase SETD5 isoform X15

    Conserved Domains (3) summary
    PLN02217
    Location:12391346
    PLN02217; probable pectinesterase/pectinesterase inhibitor
    COG5644
    Location:352572
    COG5644; U3 small nucleolar RNA-associated protein 14 [Function unknown]
    cd19181
    Location:184333
    SET_SETD5; SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins

RNA

  1. XR_001740195.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_018187.2: Suppressed sequence

    Description
    NM_018187.2: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
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