Smyd5 (SET and MYND domain containing 5) - Rat Genome Database
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Gene: Smyd5 (SET and MYND domain containing 5) Mus musculus
Analyze
Symbol: Smyd5
Name: SET and MYND domain containing 5
RGD ID: 1319336
MGI Page MGI
Description: Is expressed in several structures, including alimentary system; brain; heart; skeletal musculature; and spleen. Orthologous to human SMYD5 (SMYD family member 5); INTERACTS WITH 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AW536703; MGC29044; NN8-; NN8-4AG; Ra; Rai15; retinoic acid induced 15; retinoic acid responsive gene 1; retinoic acid-induced protein 15; Rr; Rrg1; SET and MYND domain-containing protein 5
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
GRCm39685,408,958 - 85,423,411 (+)NCBIGRCm39mm39
GRCm39 Ensembl685,408,971 - 85,423,417 (+)Ensembl
GRCm38685,431,976 - 85,446,429 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl685,431,989 - 85,446,435 (+)EnsemblGRCm38mm10GRCm38
MGSCv37685,381,970 - 85,396,423 (+)NCBIGRCm37mm9NCBIm37
MGSCv36685,397,647 - 85,411,441 (+)NCBImm8
Celera687,403,922 - 87,418,368 (+)NCBICelera
Cytogenetic Map6C3NCBI
cM Map637.44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. MGD data from the GO Consortium
2. RGD automated import pipeline
3. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8754834   PMID:8889548   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:15489334   PMID:15533813  
PMID:16141072   PMID:16141073   PMID:16602821   PMID:18799693   PMID:20305823   PMID:21267068   PMID:21677750   PMID:23912999   PMID:28250819   PMID:28981838  


Genomics

Comparative Map Data
Smyd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39685,408,958 - 85,423,411 (+)NCBIGRCm39mm39
GRCm39 Ensembl685,408,971 - 85,423,417 (+)Ensembl
GRCm38685,431,976 - 85,446,429 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl685,431,989 - 85,446,435 (+)EnsemblGRCm38mm10GRCm38
MGSCv37685,381,970 - 85,396,423 (+)NCBIGRCm37mm9NCBIm37
MGSCv36685,397,647 - 85,411,441 (+)NCBImm8
Celera687,403,922 - 87,418,368 (+)NCBICelera
Cytogenetic Map6C3NCBI
cM Map637.44NCBI
SMYD5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl273,214,222 - 73,227,221 (+)EnsemblGRCh38hg38GRCh38
GRCh38273,214,245 - 73,227,221 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37273,441,373 - 73,454,349 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36273,294,874 - 73,307,863 (+)NCBINCBI36hg18NCBI36
Build 34273,353,044 - 73,366,010NCBI
Celera273,292,193 - 73,305,182 (+)NCBI
Cytogenetic Map2p13.2NCBI
HuRef273,177,028 - 73,190,017 (+)NCBIHuRef
CHM1_1273,372,172 - 73,385,162 (+)NCBICHM1_1
Smyd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24117,969,615 - 117,984,082 (+)NCBI
Rnor_6.0 Ensembl4117,215,064 - 117,229,873 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04117,215,064 - 117,229,873 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04181,792,679 - 181,807,488 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44119,686,587 - 119,701,588 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14119,931,087 - 119,945,151 (+)NCBI
Celera4106,951,724 - 106,966,117 (+)NCBICelera
Cytogenetic Map4q34NCBI
Smyd5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542412,408,059 - 12,423,164 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542412,408,059 - 12,422,424 (-)NCBIChiLan1.0ChiLan1.0
SMYD5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A74,755,794 - 74,768,776 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A74,755,794 - 74,768,776 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A73,267,007 - 73,280,006 (+)NCBIMhudiblu_PPA_v0panPan3
SMYD5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1749,639,765 - 49,650,182 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11749,638,436 - 49,650,231 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Smyd5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493649116,997,962 - 17,011,470 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMYD5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl369,552,731 - 69,571,128 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1369,552,731 - 69,566,013 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2372,756,041 - 72,769,307 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMYD5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11433,946,154 - 33,959,571 (-)NCBI
ChlSab1.1 Ensembl1433,946,108 - 33,959,285 (-)Ensembl
Smyd5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624762416,229 - 429,763 (-)NCBI

Position Markers
AW536703  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38685,446,133 - 85,446,217UniSTSGRCm38
MGSCv37685,396,127 - 85,396,211UniSTSGRCm37
Celera687,418,072 - 87,418,156UniSTS
Cytogenetic Map6C3UniSTS
cM Map635.61UniSTS
Whitehead/MRC_RH6880.76UniSTS


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
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63866962592607450Mouse
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
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648726556125356785Mouse
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
4141990Etax6_methanol induced ataxia 6 (mouse)Not determined7132262186275719Mouse
1302020Bbaa20_mB.burgdorferi-associated arthritis 20 (mouse)Not determined67132262193464093Mouse
1300869Stheal5_msoft tissue heal 5 (mouse)Not determined671575060105575178Mouse
1300954Fcsa1_mfemoral cross-sectional area 1 (mouse)Not determined671981024105981170Mouse
1301521Pas1c_mpulmonary adenoma susceptibility 1c (mouse)Not determined671981024105981170Mouse
13506930Recrq9_mrecombination rate in male meiosis QTL 9 (mouse)673500000134700000Mouse
1301320Ots1_movarian teratoma susceptibility 1 (mouse)Not determined675447583104503555Mouse
1301571Arrd1_mage-related retinal degeneration 1 (mouse)Not determined67554435692607450Mouse
1300674Nidd3n_mnon-insulin-dependent diabetes mellitus 3 in NSY (mouse)Not determined67554435694225955Mouse
10412195Efw_mepididymal fat weight (mouse)Not determined67554435694225955Mouse
10043901Pfat5_mpredicted fat percentage 5 (mouse)Not determined675607306109607450Mouse
10412208Cypr4_mcytokine production 4 (mouse)Not determined675716503109716697Mouse
1357875Pfat2_mpredicted fat percentage 2 (mouse)Not determined676463949110464093Mouse
14697704Stsl4_mSalmonella typhimurium susceptibility locus 4 (mouse)67710000090000000Mouse
13824985Alh1_mamplitude of lateral head displacement 1 (mouse)67800000097000000Mouse
4141376Dbm1_mdiabetes modifier 1 (mouse)Not determined678629504121115387Mouse
14696731Pairq1_mP. aeruginosa infection resistance QTL 1 (mouse)681500000102200000Mouse
10043864T2dm4sa_mtype 2 diabetes mellitus 4 in SMXA RI mice (mouse)Not determined683713869147052561Mouse
11251720Ewc4_methanol withdrawal and consumption 4 (mouse)684122513118122513Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1342
Count of miRNA genes:561
Interacting mature miRNAs:671
Transcripts:ENSMUST00000045693, ENSMUST00000130928, ENSMUST00000134405, ENSMUST00000152218, ENSMUST00000153749, ENSMUST00000156322
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: ENSMUST00000045693   ⟹   ENSMUSP00000048537
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,431,989 - 85,446,435 (+)Ensembl
RefSeq Acc Id: ENSMUST00000130928
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,441,740 - 85,445,197 (+)Ensembl
RefSeq Acc Id: ENSMUST00000134405
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,441,630 - 85,445,443 (+)Ensembl
RefSeq Acc Id: ENSMUST00000152218
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,432,002 - 85,440,342 (+)Ensembl
RefSeq Acc Id: ENSMUST00000153749
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,442,573 - 85,445,432 (+)Ensembl
RefSeq Acc Id: ENSMUST00000156322
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,441,725 - 85,444,960 (+)Ensembl
RefSeq Acc Id: ENSMUST00000204428
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,439,144 - 85,441,955 (+)Ensembl
RefSeq Acc Id: ENSMUST00000204615
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl685,432,073 - 85,432,818 (+)Ensembl
RefSeq Acc Id: NM_144918   ⟹   NP_659167
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39685,408,958 - 85,423,411 (+)NCBI
GRCm38685,431,976 - 85,446,429 (+)ENTREZGENE
MGSCv37685,381,970 - 85,396,423 (+)RGD
Celera687,403,922 - 87,418,368 (+)RGD
cM Map6 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_659167   ⟸   NM_144918
- UniProtKB: Q3TYX3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000048537   ⟸   ENSMUST00000045693
Protein Domains
SET

Promoters
RGD ID:6840006
Promoter ID:MM_KWN:46681
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day2,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6
Transcripts:OTTMUST00000042294,   OTTMUST00000042295
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36685,381,774 - 85,382,274 (+)MPROMDB
RGD ID:6890224
Promoter ID:EPDNEW_M8563
Type:initiation region
Name:Smyd5_1
Description:Mus musculus SET and MYND domain containing 5 , 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
GRCm38685,431,983 - 85,432,043EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:108048 AgrOrtholog
Ensembl Genes ENSMUSG00000033706 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000048537 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000045693 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro SET_dom UniProtKB/Swiss-Prot
KEGG Report mmu:232187 UniProtKB/Swiss-Prot
MGD MGI:108048 ENTREZGENE
NCBI Gene 232187 ENTREZGENE
Pfam SET UniProtKB/Swiss-Prot
PhenoGen Smyd5 PhenoGen
PROSITE SET UniProtKB/Swiss-Prot
SMART SET UniProtKB/Swiss-Prot
UniProt Q3TYX3 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q3TRB2 UniProtKB/Swiss-Prot
  Q91YL6 UniProtKB/Swiss-Prot