Format

Send to:

Choose Destination

SETD4 SET domain containing 4 [ Homo sapiens (human) ]

Gene ID: 54093, updated on 7-Jun-2020

Summary

Official Symbol
SETD4provided by HGNC
Official Full Name
SET domain containing 4provided by HGNC
Primary source
HGNC:HGNC:1258
See related
Ensembl:ENSG00000185917
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
C21orf18; C21orf27
Expression
Ubiquitous expression in testis (RPKM 7.1), skin (RPKM 4.7) and 25 other tissues See more
Orthologs

Genomic context

See SETD4 in Genome Data Viewer
Location:
21q22.12
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (36034541..36061037, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (37406839..37432869, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1436 Neighboring gene ribosomal protein L23a pseudogene 3 Neighboring gene ribosomal modification protein rimK like family member B pseudogene 1 Neighboring gene SETD4 antisense RNA 1 Neighboring gene uncharacterized LOC100133286 Neighboring gene RNA, U6 small nuclear 992, pseudogene Neighboring gene carbonyl reductase 1

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

Phenotypes

NHGRI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein-lysine N-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
peptidyl-lysine monomethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
peptidyl-lysine trimethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
SET domain-containing protein 4

NCBI Reference Sequences (RefSeq)

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_001007259.2NP_001007260.1  SET domain-containing protein 4 isoform 2

    See identical proteins and their annotated locations for NP_001007260.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and has alternatively spliced 3' terminal exon, which causes a frame-shift compared to variant 1. The resulting shorter isoform (2) has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC002898, BF195582
    Consensus CDS
    CCDS42923.1
    UniProtKB/Swiss-Prot
    Q9NVD3
    Related
    ENSP00000382159.2, ENST00000399208.6
    Conserved Domains (2) summary
    pfam00856
    Location:210273
    SET; SET domain
    cl21457
    Location:145272
    TIM_phosphate_binding; TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate ...
  2. NM_001007261.2NP_001007262.1  SET domain-containing protein 4 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs at the 5' and 3' ends, contains an additional exon in the 5' region, and initiates translation from an alternate start codon compared to variant 1. The resulting isoform (4) has a shorter N-terminus and a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AB004853, BC002898, BF195582
    Consensus CDS
    CCDS74791.1
    UniProtKB/Swiss-Prot
    Q9NVD3
    UniProtKB/TrEMBL
    A8MTS1
    Related
    ENSP00000382156.1, ENST00000399205.5
    Conserved Domains (2) summary
    pfam00856
    Location:186249
    SET; SET domain
    cl21457
    Location:121248
    TIM_phosphate_binding; TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate ...
  3. NM_001286752.2NP_001273681.1  SET domain-containing protein 4 isoform 3

    See identical proteins and their annotated locations for NP_001273681.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs at the 5' and 3' ends, contains an additional exon in the 5' region, and initiates translation from an alternate start codon compared to variant 1. The resulting isoform (3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AI636385, AK095215, BC036556, DC394539
    Consensus CDS
    CCDS74792.1
    UniProtKB/Swiss-Prot
    Q9NVD3
    Related
    ENSP00000382161.1, ENST00000399212.5
    Conserved Domains (2) summary
    pfam00856
    Location:186249
    SET; SET domain
    pfam09273
    Location:293401
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  4. NM_017438.5NP_059134.1  SET domain-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_059134.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AI636385, AK001660, DC394539
    Consensus CDS
    CCDS13640.1
    UniProtKB/Swiss-Prot
    Q9NVD3
    Related
    ENSP00000329189.4, ENST00000332131.8
    Conserved Domains (2) summary
    pfam00856
    Location:210273
    SET; SET domain
    pfam09273
    Location:317425
    Rubis-subs-bind; Rubisco LSMT substrate-binding

RNA

  1. NR_040087.3 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an exon in the mid-region compared to variant 1. It is represented as non-coding because the use of the translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF391112, AI636385, DC394539
    Related
    ENST00000481477.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    36034541..36061037 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011529642.2XP_011527944.1  SET domain-containing protein 4 isoform X2

    See identical proteins and their annotated locations for XP_011527944.1

    UniProtKB/Swiss-Prot
    Q9NVD3
    Conserved Domains (2) summary
    pfam00856
    Location:186249
    SET; SET domain
    pfam09273
    Location:293401
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  2. XM_011529637.2XP_011527939.1  SET domain-containing protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011527939.1

    UniProtKB/Swiss-Prot
    Q9NVD3
    Conserved Domains (2) summary
    pfam00856
    Location:210273
    SET; SET domain
    pfam09273
    Location:317425
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  3. XM_011529643.1XP_011527945.1  SET domain-containing protein 4 isoform X2

    See identical proteins and their annotated locations for XP_011527945.1

    UniProtKB/Swiss-Prot
    Q9NVD3
    Conserved Domains (2) summary
    pfam00856
    Location:186249
    SET; SET domain
    pfam09273
    Location:293401
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  4. XM_011529636.2XP_011527938.1  SET domain-containing protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011527938.1

    UniProtKB/Swiss-Prot
    Q9NVD3
    Conserved Domains (2) summary
    pfam00856
    Location:210273
    SET; SET domain
    pfam09273
    Location:317425
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  5. XM_011529640.3XP_011527942.1  SET domain-containing protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011527942.1

    UniProtKB/Swiss-Prot
    Q9NVD3
    Conserved Domains (2) summary
    pfam00856
    Location:210273
    SET; SET domain
    pfam09273
    Location:317425
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  6. XM_011529644.1XP_011527946.1  SET domain-containing protein 4 isoform X2

    See identical proteins and their annotated locations for XP_011527946.1

    UniProtKB/Swiss-Prot
    Q9NVD3
    Conserved Domains (2) summary
    pfam00856
    Location:186249
    SET; SET domain
    pfam09273
    Location:293401
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  7. XM_017028404.1XP_016883893.1  SET domain-containing protein 4 isoform X2

    UniProtKB/Swiss-Prot
    Q9NVD3
    Conserved Domains (2) summary
    pfam00856
    Location:186249
    SET; SET domain
    pfam09273
    Location:293401
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  8. XM_011529639.1XP_011527941.1  SET domain-containing protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011527941.1

    UniProtKB/Swiss-Prot
    Q9NVD3
    Conserved Domains (2) summary
    pfam00856
    Location:210273
    SET; SET domain
    pfam09273
    Location:317425
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  9. XM_011529638.2XP_011527940.1  SET domain-containing protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011527940.1

    UniProtKB/Swiss-Prot
    Q9NVD3
    Related
    ENSP00000382163.1, ENST00000399215.5
    Conserved Domains (2) summary
    pfam00856
    Location:210273
    SET; SET domain
    pfam09273
    Location:317425
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  10. XM_024452122.1XP_024307890.1  SET domain-containing protein 4 isoform X4

    Related
    ENSP00000396837.1, ENST00000429161.5
  11. XM_024452121.1XP_024307889.1  SET domain-containing protein 4 isoform X4

    Related
    ENSP00000399998.1, ENST00000424303.5
  12. XM_017028405.2XP_016883894.1  SET domain-containing protein 4 isoform X3

    UniProtKB/Swiss-Prot
    Q9NVD3
    Related
    ENSP00000382158.1, ENST00000399207.5
    Conserved Domains (2) summary
    pfam00856
    Location:210273
    SET; SET domain
    cl21457
    Location:145272
    TIM_phosphate_binding; TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate ...

RNA

  1. XR_001754878.2 RNA Sequence

  2. XR_937525.3 RNA Sequence

  3. XR_001754877.2 RNA Sequence

  4. XR_001754879.2 RNA Sequence

  5. XR_002958620.1 RNA Sequence

  6. XR_001754881.1 RNA Sequence

  7. XR_001754880.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001007258.1: Suppressed sequence

    Description
    NM_001007258.1: This RefSeq was permanently suppressed because it contains the wrong CDS. If the correct CDS was annotated, it would be a nonsense-mediated mRNA decay (NMD) candidate.
  2. NM_001007260.1: Suppressed sequence

    Description
    NM_001007260.1: This RefSeq was permanently suppressed because it contains the wrong CDS. If the correct CDS was annotated, it would be a nonsense-mediated mRNA decay (NMD) candidate.
  3. NM_001007262.1: Suppressed sequence

    Description
    NM_001007262.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Support Center