Smyd2 (SET and MYND domain containing 2) - Rat Genome Database

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Gene: Smyd2 (SET and MYND domain containing 2) Rattus norvegicus
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Symbol: Smyd2
Name: SET and MYND domain containing 2
RGD ID: 727785
Description: Predicted to enable RNA polymerase II complex binding activity; histone H3K36 methyltransferase activity; and p53 binding activity. Involved in heart development. Predicted to be located in cytosol. Predicted to be active in nucleus. Orthologous to human SMYD2 (SET and MYND domain containing 2); PARTICIPATES IN histone modification pathway; methionine cycle/metabolic pathway; p53 signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: histone methyltransferase SMYD2; HSKM-B; N-lysine methyltransferase SMYD2; SET and MYND domain-containing protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813103,956,470 - 103,997,774 (-)NCBIGRCr8
mRatBN7.213101,425,270 - 101,466,576 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13101,425,273 - 101,466,576 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13103,940,656 - 103,981,564 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013105,329,429 - 105,370,669 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013102,534,981 - 102,578,302 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.013108,642,156 - 108,686,293 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13108,642,156 - 108,686,290 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013113,261,746 - 113,302,399 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413106,160,147 - 106,201,473 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.113106,349,462 - 106,390,567 (-)NCBI
Celera13100,910,865 - 100,950,701 (-)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO,ISS)
cytosol  (ISO,ISS)
nucleus  (IBA,ISO,ISS)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
2. Dysregulation of CREB binding protein triggers thrombin-induced proliferation of vascular smooth muscle cells. Chen J, etal., Mol Cell Biochem. 2008 Aug;315(1-2):123-30. Epub 2008 May 23.
3. Cardiac deletion of Smyd2 is dispensable for mouse heart development. Diehl F, etal., PLoS One. 2010 Mar 17;5(3):e9748. doi: 10.1371/journal.pone.0009748.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Targeting protein lysine methylation and demethylation in cancers. He Y, etal., Acta Biochim Biophys Sin (Shanghai). 2012 Jan;44(1):70-9. doi: 10.1093/abbs/gmr109.
6. Modes of p53 regulation. Kruse JP and Gu W, Cell. 2009 May 15;137(4):609-22. doi: 10.1016/j.cell.2009.04.050.
7. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
8. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
9. GOA pipeline RGD automated data pipeline
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Comprehensive gene review and curation RGD comprehensive gene curation
13. Lysine methyltransferase Smyd2 regulates Hsp90-mediated protection of the sarcomeric titin springs and cardiac function. Voelkel T, etal., Biochim Biophys Acta. 2013 Apr;1833(4):812-22. doi: 10.1016/j.bbamcr.2012.09.012. Epub 2012 Oct 6.
Additional References at PubMed
PMID:8889548   PMID:12783626   PMID:16805913   PMID:17108971   PMID:20870719   PMID:22862948   PMID:24880080   PMID:30337525   PMID:32096186  


Genomics

Comparative Map Data
Smyd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813103,956,470 - 103,997,774 (-)NCBIGRCr8
mRatBN7.213101,425,270 - 101,466,576 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13101,425,273 - 101,466,576 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13103,940,656 - 103,981,564 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013105,329,429 - 105,370,669 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013102,534,981 - 102,578,302 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.013108,642,156 - 108,686,293 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13108,642,156 - 108,686,290 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013113,261,746 - 113,302,399 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413106,160,147 - 106,201,473 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.113106,349,462 - 106,390,567 (-)NCBI
Celera13100,910,865 - 100,950,701 (-)NCBICelera
Cytogenetic Map13q26NCBI
SMYD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381214,281,159 - 214,337,131 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1214,281,102 - 214,337,131 (+)EnsemblGRCh38hg38GRCh38
GRCh371214,454,502 - 214,510,474 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361212,521,199 - 212,577,097 (+)NCBINCBI36Build 36hg18NCBI36
Build 341210,842,970 - 210,898,868NCBI
Celera1187,677,508 - 187,733,362 (+)NCBICelera
Cytogenetic Map1q32.3NCBI
HuRef1185,129,703 - 185,185,600 (+)NCBIHuRef
CHM1_11215,726,941 - 215,782,851 (+)NCBICHM1_1
T2T-CHM13v2.01213,520,680 - 213,576,627 (+)NCBIT2T-CHM13v2.0
Smyd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391189,612,689 - 189,654,758 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1189,612,689 - 189,654,560 (-)EnsemblGRCm39 Ensembl
GRCm381189,880,492 - 189,922,495 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1189,880,492 - 189,922,363 (-)EnsemblGRCm38mm10GRCm38
MGSCv371191,704,371 - 191,746,167 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361191,581,280 - 191,623,076 (-)NCBIMGSCv36mm8
Celera1196,790,858 - 196,832,656 (-)NCBICelera
Cytogenetic Map1H6NCBI
cM Map195.03NCBI
Smyd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554063,465,924 - 3,509,156 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554063,467,123 - 3,509,156 (-)NCBIChiLan1.0ChiLan1.0
SMYD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2135,065,100 - 35,121,132 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1135,029,402 - 35,085,432 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01189,849,167 - 189,905,193 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11194,729,116 - 194,761,043 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1194,729,116 - 194,761,045 (+)Ensemblpanpan1.1panPan2
SMYD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1712,281,581 - 12,331,294 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl712,281,710 - 12,331,164 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha711,855,760 - 11,905,351 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0711,991,481 - 12,041,301 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl711,991,446 - 12,044,237 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1711,915,043 - 11,964,795 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0712,019,583 - 12,068,986 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0712,143,792 - 12,193,251 (+)NCBIUU_Cfam_GSD_1.0
Smyd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934461,907,871 - 61,955,361 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366283,918,230 - 3,965,387 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366283,917,898 - 3,965,382 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMYD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9129,263,526 - 129,316,349 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19129,263,524 - 129,316,226 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29142,158,967 - 142,212,600 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMYD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12515,236,773 - 15,293,154 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2515,235,653 - 15,293,153 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605515,711,719 - 15,767,873 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smyd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477119,441,456 - 19,487,793 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477119,441,452 - 19,485,897 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smyd2
216 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:173
Count of miRNA genes:123
Interacting mature miRNAs:133
Transcripts:ENSRNOT00000004783
Prediction methods:Microtar, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

Markers in Region
RH130282  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.213101,425,352 - 101,425,540 (-)MAPPERmRatBN7.2
Rnor_6.013108,686,023 - 108,686,210NCBIRnor6.0
Rnor_5.013113,302,129 - 113,302,316UniSTSRnor5.0
RGSC_v3.413106,160,230 - 106,160,417UniSTSRGSC3.4
Celera13100,910,948 - 100,911,135UniSTS
RH 3.4 Map13697.9UniSTS
Cytogenetic Map13q27UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 49 33 19 33 8 11 74 35 41 11 8
Low 8 8 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000004783   ⟹   ENSRNOP00000004783
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl13101,425,273 - 101,466,576 (-)Ensembl
Rnor_6.0 Ensembl13108,642,156 - 108,686,290 (+)Ensembl
RefSeq Acc Id: NM_206851   ⟹   NP_996733
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813103,956,470 - 103,997,774 (-)NCBI
mRatBN7.213101,425,270 - 101,466,576 (-)NCBI
Rnor_6.013108,642,156 - 108,686,293 (+)NCBI
Rnor_5.013113,261,746 - 113,302,399 (+)NCBI
RGSC_v3.413106,160,147 - 106,201,473 (-)RGD
Celera13100,910,865 - 100,950,701 (-)RGD
Sequence:
RefSeq Acc Id: NP_996733   ⟸   NM_206851
- UniProtKB: Q7M6Z3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004783   ⟸   ENSRNOT00000004783
Protein Domains
MYND-type   SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7M6Z3-F1-model_v2 AlphaFold Q7M6Z3 1-433 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699106
Promoter ID:EPDNEW_R9631
Type:initiation region
Name:Smyd2_1
Description:SET and MYND domain containing 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.013108,642,172 - 108,642,232EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727785 AgrOrtholog
BioCyc Gene G2FUF-16899 BioCyc
Ensembl Genes ENSRNOG00000003583 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055011078 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004783 ENTREZGENE
  ENSRNOT00000004783.7 UniProtKB/Swiss-Prot
  ENSRNOT00055018776 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.220.160 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.25.40.10 UniProtKB/Swiss-Prot
  1.25.40.970 UniProtKB/TrEMBL
  2.170.270.10 UniProtKB/Swiss-Prot
  6.10.140.2220 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SET domain UniProtKB/TrEMBL
  Tetratricopeptide repeat domain UniProtKB/TrEMBL
InterPro SET_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SET_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMYD2_SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_MYND UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:289372 UniProtKB/Swiss-Prot
NCBI Gene 289372 ENTREZGENE
PANTHER HISTONE-LYSINE N-METHYLTRANSFERASE SMYD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  N-LYSINE METHYLTRANSFERASE SMYD2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-MYND UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Smyd2 PhenoGen
PROSITE SET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_MYND_1 UniProtKB/Swiss-Prot
  ZF_MYND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003583 RatGTEx
  ENSRNOG00055011078 RatGTEx
Superfamily-SCOP SET domain UniProtKB/TrEMBL
  SSF48452 UniProtKB/Swiss-Prot
  SSF82199 UniProtKB/Swiss-Prot
  TPR-like UniProtKB/TrEMBL
UniProt A6JGW2_RAT UniProtKB/TrEMBL
  A6JGW3_RAT UniProtKB/TrEMBL
  A6JGW4_RAT UniProtKB/TrEMBL
  A6JGW5_RAT UniProtKB/TrEMBL
  Q7M6Z3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Smyd2  SET and MYND domain containing 2      Symbol and Name status set to approved 1299863 APPROVED