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

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Gene: Smyd2 (SET and MYND domain containing 2) Rattus norvegicus
Analyze
Symbol: Smyd2
Name: SET and MYND domain containing 2
RGD ID: 727785
Description: Predicted to enable RNA polymerase II complex binding activity; histone methyltransferase activity (H3-K36 specific); and p53 binding activity. Involved in heart development. Located in cytosol and 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; benzo[a]pyrene.
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 Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.213101,425,270 - 101,466,576 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl13101,425,273 - 101,466,576 (-)Ensembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113106,349,462 - 106,390,567 (-)NCBI
Celera13100,910,865 - 100,950,701 (-)NCBICelera
Cytogenetic Map13q27NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA,ISO,ISS)
cytosol  (IDA,ISO,ISS)
nucleus  (IBA,IDA,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
mRatBN7.213101,425,270 - 101,466,576 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl13101,425,273 - 101,466,576 (-)Ensembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.113106,349,462 - 106,390,567 (-)NCBI
Celera13100,910,865 - 100,950,701 (-)NCBICelera
Cytogenetic Map13q27NCBI
SMYD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381214,281,159 - 214,337,131 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1214,281,102 - 214,337,131 (+)EnsemblGRCh38hg38GRCh38
GRCh371214,454,502 - 214,510,474 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361212,521,199 - 212,577,097 (+)NCBINCBI36hg18NCBI36
Build 341210,842,970 - 210,898,868NCBI
Celera1187,677,508 - 187,733,362 (+)NCBI
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 (+)NCBI
Smyd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391189,612,689 - 189,654,758 (-)NCBIGRCm39mm39
GRCm39 Ensembl1189,612,689 - 189,654,560 (-)Ensembl
GRCm381189,880,492 - 189,922,495 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1189,880,492 - 189,922,363 (-)EnsemblGRCm38mm10GRCm38
MGSCv371191,704,371 - 191,746,167 (-)NCBIGRCm37mm9NCBIm37
MGSCv361191,581,280 - 191,623,076 (-)NCBImm8
Celera1196,790,858 - 196,832,656 (-)NCBICelera
Cytogenetic Map1H6NCBI
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
PanPan1.11194,729,116 - 194,761,043 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1194,729,116 - 194,761,045 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01189,849,167 - 189,905,193 (+)NCBIMhudiblu_PPA_v0panPan3
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 (+)NCBI
ROS_Cfam_1.0711,991,481 - 12,041,301 (+)NCBI
ROS_Cfam_1.0 Ensembl711,991,446 - 12,044,237 (+)Ensembl
UMICH_Zoey_3.1711,915,043 - 11,964,795 (+)NCBI
UNSW_CanFamBas_1.0712,019,583 - 12,068,986 (+)NCBI
UU_Cfam_GSD_1.0712,143,792 - 12,193,251 (+)NCBI
Smyd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934461,907,871 - 61,955,361 (-)NCBI
SpeTri2.0NW_0049366283,917,898 - 3,965,382 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMYD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9129,263,520 - 129,317,325 (-)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 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2515,235,653 - 15,293,153 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605515,711,719 - 15,767,873 (-)NCBIVero_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_1.0hetGla2
HetGla 1.0NW_00462477119,441,452 - 19,485,897 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
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


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

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.


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004783   ⟹   ENSRNOP00000004783
RefSeq Status:
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
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:
Reference Sequences
RefSeq Acc Id: NP_996733   ⟸   NM_206851
- UniProtKB: Q7M6Z3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004783   ⟸   ENSRNOT00000004783
Protein Domains
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

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 108666238 108666239 C T snv MR/N (MCW), ACI/N (MCW)
13 108681638 108681639 A T snv ACI/N (MCW), WN/N (MCW), MR/N (MCW)
13 108685987 108685988 T C snv WN/N (MCW)
13 108685993 108685994 C T snv WN/N (2020), FHH/EurMcwi (2019), FHL/EurMcwi (RGD), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), FHH/EurMcwi (RGD)
13 108685995 108685996 A G snv WN/N (MCW)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 113302099 113302100 C T snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), FHL/EurMcwi (KNAW), FHH/EurMcwi (KNAW), WN/N (KNAW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 106160447 106160448 G A snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), LCR/1Mco (UMich), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), WN/N (KNAW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
13 101425570 101425571 G A snv WN/N (2020), FHH/EurMcwi (2019)


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
Ensembl Protein ENSRNOP00000004783 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004783 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot
  2.170.270.10 UniProtKB/Swiss-Prot
InterPro SET_dom UniProtKB/Swiss-Prot
  SET_dom_sf UniProtKB/Swiss-Prot
  SMYD2_SET UniProtKB/Swiss-Prot
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot
  Znf_MYND UniProtKB/Swiss-Prot
KEGG Report rno:289372 UniProtKB/Swiss-Prot
NCBI Gene 289372 ENTREZGENE
Pfam SET UniProtKB/Swiss-Prot
  zf-MYND UniProtKB/Swiss-Prot
PhenoGen Smyd2 PhenoGen
PROSITE SET UniProtKB/Swiss-Prot
  ZF_MYND_1 UniProtKB/Swiss-Prot
  ZF_MYND_2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48452 UniProtKB/Swiss-Prot
  SSF82199 UniProtKB/Swiss-Prot
UniProt 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