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Setd4 SET domain containing 4 [ Mus musculus (house mouse) ]

Gene ID: 224440, updated on 18-Apr-2024

Summary

Official Symbol
Setd4provided by MGI
Official Full Name
SET domain containing 4provided by MGI
Primary source
MGI:MGI:2136890
See related
Ensembl:ENSMUSG00000022948 AllianceGenome:MGI:2136890
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
ORF21; C21orf18
Summary
Enables histone methyltransferase activity (H3-K4 specific). Involved in several processes, including histone H3-K4 methylation; positive regulation of cytokine production; and regulation of cell proliferation in bone marrow. Predicted to be located in cytosol and nucleus. Is expressed in several structures, including alimentary system; genitourinary system; heart; nervous system; and sensory organ. Orthologous to human SETD4 (SET domain containing 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E18 (RPKM 1.7), CNS E14 (RPKM 1.5) and 28 other tissues See more
Orthologs
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Genomic context

Location:
16 C4; 16 54.52 cM
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (93380345..93401693, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (93583457..93604791, complement)

Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1700029J03 gene Neighboring gene STARR-seq mESC enhancer starr_41529 Neighboring gene STARR-seq mESC enhancer starr_41530 Neighboring gene STARR-seq mESC enhancer starr_41531 Neighboring gene predicted gene, 30695 Neighboring gene STARR-seq mESC enhancer starr_41532 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:93572605-93572851 Neighboring gene STARR-seq mESC enhancer starr_41534 Neighboring gene STARR-positive B cell enhancer mm9_chr16:93607761-93608062 Neighboring gene carbonyl reductase 1 Neighboring gene carbonyl reductase 1B

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables histone H3K36 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone H3K4 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone H3K4 methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3K4 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H4K20 methyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein-lysine N-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
SET domain-containing protein 4
NP_001404050.1
NP_001404051.1
NP_001404052.1
NP_001404053.1
NP_001404054.1
NP_001404055.1
NP_001404056.1
NP_001404057.1
NP_001404058.1
NP_001404059.1
NP_001404060.1
NP_663457.2
XP_011244423.1
XP_017172462.1
XP_017172466.1
XP_030104955.1
XP_030104957.1
XP_030104958.1
XP_036015803.1

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_001417121.1NP_001404050.1  SET domain-containing protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC160993
    UniProtKB/Swiss-Prot
    G3X9W6, P58467
  2. NM_001417122.1NP_001404051.1  SET domain-containing protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC160993
    UniProtKB/Swiss-Prot
    G3X9W6, P58467
  3. NM_001417123.1NP_001404052.1  SET domain-containing protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC160993
    UniProtKB/Swiss-Prot
    G3X9W6, P58467
  4. NM_001417124.1NP_001404053.1  SET domain-containing protein 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC160993
    UniProtKB/Swiss-Prot
    G3X9W6, P58467
  5. NM_001417125.1NP_001404054.1  SET domain-containing protein 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC160993
  6. NM_001417126.1NP_001404055.1  SET domain-containing protein 4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC160993
  7. NM_001417127.1NP_001404056.1  SET domain-containing protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC160993
    Related
    ENSMUSP00000156698.2, ENSMUST00000232870.2
  8. NM_001417128.1NP_001404057.1  SET domain-containing protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC160993
  9. NM_001417129.1NP_001404058.1  SET domain-containing protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC160993
  10. NM_001417130.1NP_001404059.1  SET domain-containing protein 4 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC160993
  11. NM_001417131.1NP_001404060.1  SET domain-containing protein 4 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC160993
  12. NM_145482.4NP_663457.2  SET domain-containing protein 4 isoform 1

    See identical proteins and their annotated locations for NP_663457.2

    Status: VALIDATED

    Source sequence(s)
    AC160993
    Consensus CDS
    CCDS28340.1
    UniProtKB/Swiss-Prot
    G3X9W6, P58467
    UniProtKB/TrEMBL
    A0A3B2WB63
    Related
    ENSMUSP00000156723.2, ENSMUST00000233931.2
    Conserved Domains (2) summary
    pfam09273
    Location:313424
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19177
    Location:49286
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins

RNA

  1. NR_184423.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC160993
  2. NR_184424.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC160993

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000082.7 Reference GRCm39 C57BL/6J

    Range
    93380345..93401693 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030249098.2XP_030104958.1  SET domain-containing protein 4 isoform X4

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    cd19177
    Location:1225
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
    pfam09273
    Location:252363
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  2. XM_017316973.3XP_017172462.1  SET domain-containing protein 4 isoform X2

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    cd19177
    Location:49286
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
    pfam09273
    Location:313395
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  3. XM_030249095.2XP_030104955.1  SET domain-containing protein 4 isoform X3

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    pfam09273
    Location:262373
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19177
    Location:3235
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
  4. XM_030249097.2XP_030104957.1  SET domain-containing protein 4 isoform X4

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    cd19177
    Location:1225
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
    pfam09273
    Location:252363
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  5. XM_011246121.4XP_011244423.1  SET domain-containing protein 4 isoform X3

    See identical proteins and their annotated locations for XP_011244423.1

    UniProtKB/TrEMBL
    A0A3B2WB63
    Conserved Domains (2) summary
    pfam09273
    Location:262373
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19177
    Location:3235
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
  6. XM_036159910.1XP_036015803.1  SET domain-containing protein 4 isoform X5

    Conserved Domains (1) summary
    cd19177
    Location:49286
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins
  7. XM_017316977.3XP_017172466.1  SET domain-containing protein 4 isoform X6

    UniProtKB/TrEMBL
    A0A3B2WCJ7
    Related
    ENSMUSP00000156553.2, ENSMUST00000154355.3
    Conserved Domains (1) summary
    cd19177
    Location:49241
    SET_SETD4; SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins

RNA

  1. XR_004939189.1 RNA Sequence

  2. XR_001781817.3 RNA Sequence

  3. XR_003951789.2 RNA Sequence

  4. XR_003951787.2 RNA Sequence

  5. XR_001781818.3 RNA Sequence