Smyd1 (SET and MYND domain containing 1) - Rat Genome Database
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Gene: Smyd1 (SET and MYND domain containing 1) Mus musculus
Analyze
Symbol: Smyd1
Name: SET and MYND domain containing 1
RGD ID: 1552115
MGI Page MGI
Description: Is expressed in several structures, including 1st branchial arch; embryo mesenchyme; heart; maxillary process; and spleen. Orthologous to human SMYD1 (SET and MYND domain containing 1); PARTICIPATES IN histone modification pathway; INTERACTS WITH 1,2-dichloroethane; 1,2-dimethylhydrazine; 2,2',4,4',5,5'-hexachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 4632404M21Rik; B; Bop; C78565; CD8b-opposite; CD8beta opposite strand; histone-lysine N-methyltransferase Smyd1; m-BOP; SET and MYND domain-containing protein 1; zinc finger protein BOP; Zmynd18
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39671,190,924 - 71,239,265 (-)NCBIGRCm39mm39
GRCm39 Ensembl671,190,924 - 71,299,217 (-)Ensembl
GRCm38671,213,940 - 71,262,281 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl671,213,940 - 71,322,233 (-)EnsemblGRCm38mm10GRCm38
MGSCv37671,163,934 - 71,212,275 (-)NCBIGRCm37mm9NCBIm37
MGSCv36671,144,757 - 71,191,832 (-)NCBImm8
Celera673,293,207 - 73,341,506 (-)NCBICelera
Cytogenetic Map6C1NCBI
cM Map632.14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA)
nucleus  (IBA,IDA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:7590968   PMID:9013956   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11489994   PMID:11923873   PMID:12011100   PMID:12477932   PMID:14610273  
PMID:15890826   PMID:16141072   PMID:16141073   PMID:16477022   PMID:16638982   PMID:16805913   PMID:17875930   PMID:18424556   PMID:18799693   PMID:19162039   PMID:19620969   PMID:20059953  
PMID:20305823   PMID:20943667   PMID:21071677   PMID:21267068   PMID:21382375   PMID:21873635   PMID:22147266   PMID:24039817   PMID:24105743   PMID:24146773   PMID:25002400   PMID:25336743  
PMID:25803368   PMID:26162853   PMID:26410624   PMID:26688546   PMID:26935107   PMID:27663768   PMID:29499397   PMID:29866044   PMID:30061404   PMID:32325033   PMID:32574189  


Genomics

Comparative Map Data
Smyd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39671,190,924 - 71,239,265 (-)NCBIGRCm39mm39
GRCm39 Ensembl671,190,924 - 71,299,217 (-)Ensembl
GRCm38671,213,940 - 71,262,281 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl671,213,940 - 71,322,233 (-)EnsemblGRCm38mm10GRCm38
MGSCv37671,163,934 - 71,212,275 (-)NCBIGRCm37mm9NCBIm37
MGSCv36671,144,757 - 71,191,832 (-)NCBImm8
Celera673,293,207 - 73,341,506 (-)NCBICelera
Cytogenetic Map6C1NCBI
cM Map632.14NCBI
SMYD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl288,067,825 - 88,113,384 (+)EnsemblGRCh38hg38GRCh38
GRCh38288,067,825 - 88,113,384 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37288,367,344 - 88,412,903 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36288,148,497 - 88,194,018 (+)NCBINCBI36hg18NCBI36
Celera288,373,097 - 88,418,568 (-)NCBI
Cytogenetic Map2p11.2NCBI
HuRef287,289,577 - 87,335,154 (+)NCBIHuRef
CHM1_1288,296,599 - 88,342,189 (+)NCBICHM1_1
Smyd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24103,195,330 - 103,252,989 (-)NCBI
Rnor_6.0 Ensembl499,074,535 - 99,125,111 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0499,071,122 - 99,125,143 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04163,848,270 - 163,904,185 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44104,423,556 - 104,475,134 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14104,664,623 - 104,728,216 (-)NCBI
Celera492,378,302 - 92,428,867 (-)NCBICelera
Cytogenetic Map4q31NCBI
Smyd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955424769,287 - 800,885 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955424769,287 - 800,646 (-)NCBIChiLan1.0ChiLan1.0
SMYD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A89,109,444 - 89,155,797 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A89,108,642 - 89,155,797 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A87,201,207 - 87,246,416 (+)NCBIMhudiblu_PPA_v0panPan3
SMYD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1738,259,624 - 38,298,183 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11738,260,897 - 38,298,248 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Smyd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936712747,060 - 781,142 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMYD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl357,867,223 - 57,945,953 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1357,866,078 - 57,918,576 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2360,559,524 - 60,607,410 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMYD1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11418,676,396 - 18,721,532 (-)NCBI
ChlSab1.1 Ensembl1418,676,394 - 18,720,903 (-)Ensembl
Smyd1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474916,400,037 - 16,432,956 (-)NCBI

Position Markers
C78565  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38671,214,054 - 71,214,216UniSTSGRCm38
MGSCv37671,164,048 - 71,164,210UniSTSGRCm37
Celera673,293,321 - 73,293,483UniSTS
Cytogenetic Map6C1UniSTS
cM Map630.5UniSTS
Whitehead/MRC_RH6713.88UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25440480Moaq2_mmodifier of alien QTL 2 (mouse)61117500000Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139100000Mouse
1300556Cia6_mcollagen induced arthritis QTL 6 (mouse)Not determined6446488487426034Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396656149Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396656149Mouse
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396656149Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396656149Mouse
26884441Sklq3_mskull length QTL 3, 5 week (mouse)6760000080600000Mouse
1357442Dbts1_mdiabetes 1 (mouse)Not determined61823414873387692Mouse
10412213Sxbq2_mSGC/Knj cross B6 QTL 2 (mouse)Not determined61991268671322775Mouse
13208564Bmiq7_mbody mass index QTL 7 (mouse)62500000080000000Mouse
4141782Mrdq5_mmodifier of retinal degeneration QTL 5 (mouse)Not determined3285065078238974Mouse
14746995Manh60_mmandible shape 60 (mouse)63722567771225677Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63866962592607450Mouse
1301326Trbv4c2_mT cell receptor beta variable 4 (mouse)Not determined64089129671379171Mouse
12880424V25Dq4_mvitamin D inactive form serum level QTL 4 (mouse)64160000075600000Mouse
1301266Lmr4_mleishmaniasis resistance 4 (mouse)Not determined64211637376116515Mouse
11040600Lmr4c_mleishmaniasis resistance 4c (mouse)64211637376116515Mouse
11040601Lmr4a_mleishmaniasis resistance 4a (mouse)64211637376116515Mouse
11533915Mts4_mmammary tumor susceptibility 4 (mouse)64211637376116515Mouse
12910785Pwgrq16_mpost-weaning growth rate QTL 16 (mouse)64382681377811523Mouse
12910798Pwgrq5_mpre-weaning growth rate QTL 5 (mouse)64382681377811523Mouse
12910802Pwbwq12_mpost-weaning body weight QTL 12 (mouse)64382681377811523Mouse
12910807Pwbwq11_mpost-weaning body weight QTL 11 (mouse)64382681377811523Mouse
12910809Pwbwq10_mpost-weaning body weight QTL 10 (mouse)64382681377811523Mouse
12910820Ogrq3_moverall growth rate QTL 3 (mouse)64382681377811523Mouse
1300618Pgia19_mproteoglycan induced arthritis 19 (mouse)Not determined64531405987426034Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645314059128835032Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46935985136423692Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648720000125360000Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648720000148450000Mouse
4140983Srilp_msleep response to influenza, light phase (mouse)Not determined4872655675447710Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648726556125356785Mouse
1301254Skts11_mskin tumor susceptibility 11 (mouse)Not determined65117915085179300Mouse
1357683Igf1sl1_mIGF-1 serum levels 1 (mouse)Not determined652161713116155267Mouse
4141028Mclr_mmethylcholanthrene lymphoma resistance (mouse)Not determined5437342788379171Mouse
15039373Adip28_madiposity 28 (mouse)65630821190308211Mouse
15039375Bw41_mbody weight QTL 41 (mouse)65630821190308211Mouse
1558977Skmw10_mskeletal muscle weight 10 (mouse)Not determined65844758392447710Mouse
10043972Obq28_mobesity QTL 28 (mouse)Not determined65854043392540433Mouse
1301740Bwq2_mbody weight QTL 2 (mouse)Not determined66005768094057799Mouse
1301369Im4_mimmunoregulatory 4 (mouse)Not determined66348473897484905Mouse
1300650Bw18_mbody weight QTL 18 (mouse)Not determined666713869100714031Mouse
1301876Bits2_mbitterness sensitivity 2 (mouse)Not determined670425898104426034Mouse
1301813Skl3_mskeletal size (tail length) 3 (mouse)Not determined670425898104426034Mouse
1301034Egrm2_mearly growth rate (mouse)Not determined670425898104426034Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1952
Count of miRNA genes:601
Interacting mature miRNAs:735
Transcripts:ENSMUST00000074301, ENSMUST00000114186, ENSMUST00000114188, ENSMUST00000129630, ENSMUST00000173297, ENSMUST00000173730
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000074301   ⟹   ENSMUSP00000073911
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl671,213,940 - 71,262,281 (-)Ensembl
RefSeq Acc Id: ENSMUST00000114186   ⟹   ENSMUSP00000109824
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl671,213,942 - 71,262,253 (-)Ensembl
RefSeq Acc Id: ENSMUST00000114188   ⟹   ENSMUSP00000109826
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl671,215,342 - 71,322,233 (-)Ensembl
RefSeq Acc Id: ENSMUST00000129630   ⟹   ENSMUSP00000133300
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl671,259,605 - 71,262,232 (-)Ensembl
RefSeq Acc Id: ENSMUST00000173297   ⟹   ENSMUSP00000133878
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl671,312,054 - 71,322,206 (-)Ensembl
RefSeq Acc Id: ENSMUST00000173730   ⟹   ENSMUSP00000134399
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl671,215,500 - 71,216,874 (-)Ensembl
RefSeq Acc Id: NM_001160127   ⟹   NP_001153599
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39671,190,924 - 71,239,265 (-)NCBI
GRCm38671,213,940 - 71,262,281 (-)ENTREZGENE
MGSCv37671,163,934 - 71,212,275 (-)RGD
Celera673,293,207 - 73,341,506 (-)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_009762   ⟹   NP_033892
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39671,190,924 - 71,239,265 (-)NCBI
GRCm38671,213,940 - 71,262,281 (-)ENTREZGENE
MGSCv37671,163,934 - 71,212,275 (-)RGD
Celera673,293,207 - 73,341,506 (-)RGD
cM Map6 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_033892   ⟸   NM_009762
- Peptide Label: isoform 2
- UniProtKB: P97443 (UniProtKB/Swiss-Prot),   Q3UQT9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001153599   ⟸   NM_001160127
- Peptide Label: isoform 1
- UniProtKB: P97443 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000073911   ⟸   ENSMUST00000074301
RefSeq Acc Id: ENSMUSP00000133300   ⟸   ENSMUST00000129630
RefSeq Acc Id: ENSMUSP00000133878   ⟸   ENSMUST00000173297
RefSeq Acc Id: ENSMUSP00000134399   ⟸   ENSMUST00000173730
RefSeq Acc Id: ENSMUSP00000109826   ⟸   ENSMUST00000114188
RefSeq Acc Id: ENSMUSP00000109824   ⟸   ENSMUST00000114186
Protein Domains
MYND-type   SET

Promoters
RGD ID:6889952
Promoter ID:EPDNEW_M8427
Type:multiple initiation site
Name:Smyd1_1
Description:Mus musculus SET and MYND domain containing 1 , transcript variant2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38671,262,244 - 71,262,304EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:104790 AgrOrtholog
Ensembl Genes ENSMUSG00000055027 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000073911 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000109824 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000109826 UniProtKB/TrEMBL
  ENSMUSP00000133300 UniProtKB/TrEMBL
  ENSMUSP00000133878 UniProtKB/TrEMBL
  ENSMUSP00000134399 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000074301 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000114186 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000114188 UniProtKB/TrEMBL
  ENSMUST00000129630 UniProtKB/TrEMBL
  ENSMUST00000173297 UniProtKB/TrEMBL
  ENSMUST00000173730 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro SET_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_MYND UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:12180 UniProtKB/Swiss-Prot
MGD MGI:104790 ENTREZGENE
NCBI Gene 12180 ENTREZGENE
Pfam SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-MYND UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Smyd1 PhenoGen
PROSITE SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_MYND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_MYND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3UXZ0_MOUSE UniProtKB/TrEMBL
  G3UZ94_MOUSE UniProtKB/TrEMBL
  G5E8R7_MOUSE UniProtKB/TrEMBL
  P97443 ENTREZGENE
  Q3UQT9 ENTREZGENE, UniProtKB/TrEMBL
  Q8BMV4_MOUSE UniProtKB/TrEMBL
  SMYD1_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary P97442 UniProtKB/Swiss-Prot
  P97444 UniProtKB/Swiss-Prot
  Q6DFW7 UniProtKB/Swiss-Prot