Format

Send to:

Choose Destination

SETD1A SET domain containing 1A, histone lysine methyltransferase [ Homo sapiens (human) ]

Gene ID: 9739, updated on 27-Nov-2021

Summary

Official Symbol
SETD1Aprovided by HGNC
Official Full Name
SET domain containing 1A, histone lysine methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:29010
See related
Ensembl:ENSG00000099381 MIM:611052
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
Also known as
Set1; EPEDD; KMT2F; Set1A; NEDSID
Summary
The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a member of the class V-like SAM-binding methyltransferase superfamily. [provided by RefSeq, Dec 2016]
Expression
Ubiquitous expression in testis (RPKM 10.6), bone marrow (RPKM 6.2) and 25 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See SETD1A in Genome Data Viewer
Location:
16p11.2
Exon count:
22
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (30956618..30984664)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30969075..30995985)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene F-box and leucine rich repeat protein 19 Neighboring gene Sharpr-MPRA regulatory region 7559 Neighboring gene ORAI calcium release-activated calcium modulator 3 Neighboring gene hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7 Neighboring gene syntaxin 1B

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
Epilepsy, early-onset, with or without developmental delay
MedGen: C5394228 OMIM: 618832 GeneReviews: Not available
not available
Neurodevelopmental disorder with speech impairment and dysmorphic facies
MedGen: C5436699 OMIM: 619056 GeneReviews: Not available
not available

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2018-02-28)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2018-02-28)

ClinGen Genome Curation PagePubMed

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat Three components (Setd1A, CXXC1, WDR5) of the Set1 histone methyltransferase complex are identified to interact with HIV-1 Tat in Jurkat cell PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0339

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables beta-catenin binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables histone methyltransferase activity (H3-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
part_of Set1C/COMPASS complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of Set1C/COMPASS complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of Set1C/COMPASS complex TAS
Traceable Author Statement
more info
PubMed 
located_in chromatin IDA
Inferred from Direct Assay
more info
PubMed 
part_of histone methyltransferase complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase SETD1A
Names
SET domain-containing protein 1A
hSET1A
lysine N-methyltransferase 2F
set1/Ash2 histone methyltransferase complex subunit SET1
NP_055527.1
XP_005255780.1
XP_006721169.1
XP_016879398.1
XP_024306267.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_052948.1 RefSeqGene

    Range
    5461..32371
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014712.3NP_055527.1  histone-lysine N-methyltransferase SETD1A

    See identical proteins and their annotated locations for NP_055527.1

    Status: REVIEWED

    Source sequence(s)
    AB002337, BC027450
    Consensus CDS
    CCDS32435.1
    UniProtKB/Swiss-Prot
    O15047
    Related
    ENSP00000262519.8, ENST00000262519.14
    Conserved Domains (5) summary
    smart00317
    Location:15681691
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16911707
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12548
    Location:92186
    RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
    pfam11764
    Location:14251562
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl26247
    Location:10701130
    DNA_pol3_delta2; DNA polymerase III, delta subunit

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_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    30956618..30984664
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023909.1XP_016879398.1  histone-lysine N-methyltransferase SETD1A isoform X1

    UniProtKB/Swiss-Prot
    O15047
    Conserved Domains (5) summary
    smart00317
    Location:15681691
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16911707
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12548
    Location:92186
    RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
    pfam11764
    Location:14251562
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl26247
    Location:10701130
    DNA_pol3_delta2; DNA polymerase III, delta subunit
  2. XM_005255723.1XP_005255780.1  histone-lysine N-methyltransferase SETD1A isoform X1

    See identical proteins and their annotated locations for XP_005255780.1

    UniProtKB/Swiss-Prot
    O15047
    Related
    ENSP00000507683.1, ENST00000684162.1
    Conserved Domains (5) summary
    smart00317
    Location:15681691
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16911707
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12548
    Location:92186
    RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
    pfam11764
    Location:14251562
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl26247
    Location:10701130
    DNA_pol3_delta2; DNA polymerase III, delta subunit
  3. XM_006721106.3XP_006721169.1  histone-lysine N-methyltransferase SETD1A isoform X1

    See identical proteins and their annotated locations for XP_006721169.1

    UniProtKB/Swiss-Prot
    O15047
    Conserved Domains (5) summary
    smart00317
    Location:15681691
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16911707
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12548
    Location:92186
    RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
    pfam11764
    Location:14251562
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl26247
    Location:10701130
    DNA_pol3_delta2; DNA polymerase III, delta subunit
  4. XM_024450499.1XP_024306267.1  histone-lysine N-methyltransferase SETD1A isoform X1

    Conserved Domains (5) summary
    smart00317
    Location:15681691
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00508
    Location:16911707
    PostSET; Cysteine-rich motif following a subset of SET domains
    cd12548
    Location:92186
    RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)
    pfam11764
    Location:14251562
    N-SET; COMPASS (Complex proteins associated with Set1p) component N
    cl26247
    Location:10701130
    DNA_pol3_delta2; DNA polymerase III, delta subunit
Support Center