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Aliases for SETD5 Gene

Aliases for SETD5 Gene

  • SET Domain Containing 5 2 3 5
  • SET Domain-Containing Protein 5 3
  • KIAA1757 4

External Ids for SETD5 Gene

Previous GeneCards Identifiers for SETD5 Gene

  • GC03P009414
  • GC03P009439
  • GC03P009376

Summaries for SETD5 Gene

Entrez Gene Summary for SETD5 Gene

  • 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]

GeneCards Summary for SETD5 Gene

SETD5 (SET Domain Containing 5) is a Protein Coding gene. Diseases associated with SETD5 include Mental Retardation, Autosomal Dominant 23 and Cornelia De Lange Syndrome. Among its related pathways are PKMTs methylate histone lysines. An important paralog of this gene is KMT2E.

UniProtKB/Swiss-Prot for SETD5 Gene

  • Probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. Acts as a regulator of histone acetylation during gene transcription.

Additional gene information for SETD5 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETD5 Gene

Genomics for SETD5 Gene

GeneHancer (GH) Regulatory Elements for SETD5 Gene

Promoters and enhancers for SETD5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J009394 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 746.9 +1.4 1376 9.8 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SETD5 THUMPD3-AS1 GC03P009403 BRPF1 RAD18 TTLL3 GHRLOS FANCD2 SRGAP3-AS3 JAGN1
GH03J009430 Promoter 0.5 EPDnew 650.3 +32.8 32759 0.1 SETD5 GC03M009409 GC03P009403
GH03J009889 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 71.4 +493.2 493203 2.4 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B JAGN1 CIDEC BRPF1 RAD18 SETD5 FANCD2 LINC00852 TTLL3 GHRLOS SEC13
GH03J010188 Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 84.2 +797.2 797230 12.1 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A ZNF2 ZBTB7B YY1 POLR2B BRPF1 SETD5 IRAK2 GHRLOS LINC00852 TATDN2 FANCD2 GHRL TTLL3 SEC13
GH03J009730 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 61.8 +334.4 334419 3 CLOCK FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 NFYC BRPF1 SETD5 SRGAP3-AS3 THUMPD3-AS1 CYCSP10 SRGAP3-AS1 ENSG00000269886 RAD18 EMC3-AS1 ENSG00000269894
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SETD5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SETD5 gene promoter:
  • AP-2alphaA
  • c-Ets-1
  • AP-2alpha
  • STAT5A
  • AP-2beta
  • AP-2gamma
  • Sp1
  • Egr-3
  • Egr-2
  • CBF-C

Genomic Locations for SETD5 Gene

Genomic Locations for SETD5 Gene
chr3:9,397,615-9,479,240
(GRCh38/hg38)
Size:
81,626 bases
Orientation:
Plus strand
chr3:9,439,299-9,520,924
(GRCh37/hg19)
Size:
81,626 bases
Orientation:
Plus strand

Genomic View for SETD5 Gene

Genes around SETD5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETD5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETD5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETD5 Gene

Proteins for SETD5 Gene

  • Protein details for SETD5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9C0A6-SETD5_HUMAN
    Recommended name:
    SET domain-containing protein 5
    Protein Accession:
    Q9C0A6
    Secondary Accessions:
    • Q6AI17
    • Q8WUB6
    • Q9H3X4
    • Q9H6V7
    • Q9H7S3
    • Q9NVI9

    Protein attributes for SETD5 Gene

    Size:
    1442 amino acids
    Molecular mass:
    157515 Da
    Quaternary structure:
    • Interacts with components of the PAF1 complex (PAF1C) such as LEO1, CTR9 and CDC73. Interacts with NCOR1.
    SequenceCaution:
    • Sequence=AAH20956.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA91762.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB14903.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15144.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB21848.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for SETD5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETD5 Gene

Post-translational modifications for SETD5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Boster Bio Antibodies for SETD5
  • Santa Cruz Biotechnology (SCBT) Antibodies for SETD5

No data available for DME Specific Peptides for SETD5 Gene

Domains & Families for SETD5 Gene

Gene Families for SETD5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SETD5 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SETD5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SETD5: view

No data available for UniProtKB/Swiss-Prot for SETD5 Gene

Function for SETD5 Gene

Molecular function for SETD5 Gene

UniProtKB/Swiss-Prot Function:
Probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. Acts as a regulator of histone acetylation during gene transcription.

Phenotypes From GWAS Catalog for SETD5 Gene

genes like me logo Genes that share phenotypes with SETD5: view

Human Phenotype Ontology for SETD5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SETD5 Gene

MGI Knock Outs for SETD5:
  • Setd5 Setd5<tm1a(EUCOMM)Wtsi>

Animal Model Products

miRNA for SETD5 Gene

miRTarBase miRNAs that target SETD5

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for SETD5 Gene

Localization for SETD5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETD5 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SETD5 gene
Compartment Confidence
nucleus 5
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Nucleus (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SETD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm IDA --
GO:0016593 colocalizes_with Cdc73/Paf1 complex ISS,IEA --
genes like me logo Genes that share ontologies with SETD5: view

Pathways & Interactions for SETD5 Gene

SuperPathways for SETD5 Gene

SuperPathway Contained pathways
1 PKMTs methylate histone lysines
genes like me logo Genes that share pathways with SETD5: view

Pathways by source for SETD5 Gene

1 BioSystems pathway for SETD5 Gene

Gene Ontology (GO) - Biological Process for SETD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016569 covalent chromatin modification IEA,ISS --
GO:0035065 regulation of histone acetylation ISS,IEA --
genes like me logo Genes that share ontologies with SETD5: view

No data available for SIGNOR curated interactions for SETD5 Gene

Drugs & Compounds for SETD5 Gene

No Compound Related Data Available

Transcripts for SETD5 Gene

Unigene Clusters for SETD5 Gene

SET domain containing 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SETD5 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b · 14c ^ 15 ^ 16a · 16b ^
SP1: - -
SP2: - - -
SP3: - - - -
SP4: - - - -
SP5:
SP6: - - - - -
SP7: - - - -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

ExUns: 17 ^ 18 ^ 19a · 19b · 19c · 19d ^ 20 ^ 21 ^ 22 ^ 23 ^ 24a · 24b · 24c ^ 25a · 25b ^ 26a · 26b ^ 27
SP1: - - - -
SP2: - - - -
SP3:
SP4:
SP5: -
SP6:
SP7:
SP8:
SP9: -
SP10: -
SP11: - -
SP12:
SP13: -

Relevant External Links for SETD5 Gene

GeneLoc Exon Structure for
SETD5
ECgene alternative splicing isoforms for
SETD5

Expression for SETD5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SETD5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SETD5 Gene

This gene is overexpressed in Cervix (39.4) and Breast (29.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SETD5 Gene



Protein tissue co-expression partners for SETD5 Gene

NURSA nuclear receptor signaling pathways regulating expression of SETD5 Gene:

SETD5

SOURCE GeneReport for Unigene cluster for SETD5 Gene:

Hs.288164

Evidence on tissue expression from TISSUES for SETD5 Gene

  • Nervous system(4.8)
  • Intestine(4.4)
  • Lung(3.1)
  • Eye(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SETD5 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • chin
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • salivary gland
  • skull
  • tooth
Thorax:
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
  • penis
  • testicle
  • urethra
General:
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SETD5: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SETD5 Gene

Orthologs for SETD5 Gene

This gene was present in the common ancestor of animals.

Orthologs for SETD5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SETD5 34 33
  • 98.75 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SETD5 34 33
  • 94.42 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SETD5 34 33
  • 94.29 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Setd5 33
  • 92.13 (n)
mouse
(Mus musculus)
Mammalia Setd5 16 34 33
  • 91.97 (n)
oppossum
(Monodelphis domestica)
Mammalia SETD5 34
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETD5 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves SETD5 34 33
  • 73.16 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SETD5 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia setd5 33
  • 65.29 (n)
Str.11463 33
zebrafish
(Danio rerio)
Actinopterygii setd5 34 33
  • 58.9 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG9007 34
  • 4 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-24 34
  • 19 (a)
ManyToMany
Y73B3A.1 34
  • 12 (a)
ManyToMany
set-9 34
  • 7 (a)
ManyToMany
set-26 34
  • 7 (a)
ManyToMany
Species where no ortholog for SETD5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SETD5 Gene

ENSEMBL:
Gene Tree for SETD5 (if available)
TreeFam:
Gene Tree for SETD5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SETD5: view image

Paralogs for SETD5 Gene

Paralogs for SETD5 Gene

(3) SIMAP similar genes for SETD5 Gene using alignment to 9 proteins:

  • SETD5_HUMAN
  • C9JLA7_HUMAN
  • C9JLM1_HUMAN
  • E7EWN3_HUMAN
  • F2Z2J0_HUMAN
  • F8WD12_HUMAN
  • H0Y3R4_HUMAN
  • H7C1F2_HUMAN
  • H7C1Q2_HUMAN
genes like me logo Genes that share paralogs with SETD5: view

Variants for SETD5 Gene

Sequence variations from dbSNP and Humsavar for SETD5 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs587777325 pathogenic, Mental retardation, autosomal dominant 23 9,445,055(+) A/T coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs587777326 pathogenic, Mental retardation, autosomal dominant 23 9,448,459(+) CACA/CA coding_sequence_variant, frameshift, non_coding_transcript_variant
rs587777327 pathogenic, Mental retardation, autosomal dominant 23 9,470,735(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, stop_gained
rs587777328 pathogenic, Mental retardation, autosomal dominant 23 9,475,533(+) G/GG coding_sequence_variant, downstream_transcript_variant, frameshift, genic_downstream_transcript_variant, non_coding_transcript_variant
rs587777329 pathogenic, Mental retardation, autosomal dominant 23 9,475,618(+) T/ coding_sequence_variant, downstream_transcript_variant, frameshift, genic_downstream_transcript_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SETD5 Gene

Variant ID Type Subtype PubMed ID
dgv277n21 CNV loss 19592680
esv2675276 CNV deletion 23128226
esv3595237 CNV loss 21293372
nsv237037 CNV deletion 16902084
nsv3692 CNV insertion 18451855
nsv527954 CNV loss 19592680
nsv821981 CNV loss 20364138

Variation tolerance for SETD5 Gene

Residual Variation Intolerance Score: 3.71% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.59; 65.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SETD5 Gene

Human Gene Mutation Database (HGMD)
SETD5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SETD5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETD5 Gene

Disorders for SETD5 Gene

MalaCards: The human disease database

(5) MalaCards diseases for SETD5 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SETD5 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SETD5_HUMAN
  • Mental retardation, autosomal dominant 23 (MRD23) [MIM:615761]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD23 patients manifest moderate to severe intellectual disability with additional variable features of brachycephaly, a low hairline, depressed nasal bridge, prominent high nasal root, tubular nose, upslanting palpebral fissures, long and smooth philtrum, micrognathia, thin upper lip, and crowded teeth. Behavioral problems, including obsessive-compulsive disorder, hand flapping with ritualized behavior, and autism, are prominent features. {ECO:0000269 PubMed:24680889, ECO:0000269 PubMed:25138099, ECO:0000269 PubMed:27375234, ECO:0000269 PubMed:28549204}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SETD5

genes like me logo Genes that share disorders with SETD5: view

No data available for Genatlas for SETD5 Gene

Publications for SETD5 Gene

  1. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11214970) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  2. SETD5 gene variant associated with mild intellectual disability - a case report. (PMID: 28549204) Stur E … Louro ID (Genetics and molecular research : GMR 2017) 3 4 58
  3. Setd5 is essential for mammalian development and the co-transcriptional regulation of histone acetylation. (PMID: 27864380) Osipovich AB … Magnuson MA (Development (Cambridge, England) 2016) 2 3 58
  4. SETD5 loss-of-function mutation as a likely cause of a familial syndromic intellectual disability with variable phenotypic expression. (PMID: 27375234) Szczałuba K … Płoski R (American journal of medical genetics. Part A 2016) 3 4 58
  5. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. (PMID: 25138099) Kuechler A … Engels H (European journal of human genetics : EJHG 2015) 3 4 58

Products for SETD5 Gene

Sources for SETD5 Gene

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