Smyd3 (SET and MYND domain containing 3) - Rat Genome Database

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Gene: Smyd3 (SET and MYND domain containing 3) Rattus norvegicus
Analyze
Symbol: Smyd3
Name: SET and MYND domain containing 3
RGD ID: 1562635
Description: Predicted to enable RNA polymerase II complex binding activity; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and histone-lysine N-methyltransferase activity. Predicted to act upstream of or within several processes, including cellular response to dexamethasone stimulus; nucleosome assembly; and regulation of protein phosphorylation. Predicted to be located in cytosol and nucleoplasm. Orthologous to human SMYD3 (SET and MYND domain containing 3); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: histone-lysine N-methyltransferase SMYD3; LOC498295; MGC114517; SET and MYND domain-containing protein 3; similar to SET and MYND domain containing 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21390,709,263 - 91,266,209 (-)NCBI
Rnor_6.01397,330,120 - 97,807,813 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013102,581,420 - 102,588,971 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.013102,350,012 - 102,473,942 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41394,643,716 - 95,108,789 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1390,265,163 - 90,818,620 (-)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:16805913   PMID:23752591   PMID:25738358   PMID:33144524  


Genomics

Comparative Map Data
Smyd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21390,709,263 - 91,266,209 (-)NCBI
Rnor_6.01397,330,120 - 97,807,813 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013102,581,420 - 102,588,971 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.013102,350,012 - 102,473,942 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41394,643,716 - 95,108,789 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1390,265,163 - 90,818,620 (-)NCBICelera
Cytogenetic Map13q26NCBI
SMYD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1245,749,342 - 246,507,312 (-)EnsemblGRCh38hg38GRCh38
GRCh381245,749,342 - 246,507,279 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371245,912,649 - 246,670,581 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361243,979,267 - 244,647,334 (-)NCBINCBI36hg18NCBI36
Build 341242,238,685 - 242,906,752NCBI
Celera1219,204,089 - 219,959,418 (-)NCBI
Cytogenetic Map1q44NCBI
HuRef1216,300,241 - 217,057,123 (-)NCBIHuRef
CHM1_11247,184,928 - 247,943,100 (-)NCBICHM1_1
Smyd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391178,779,525 - 179,345,618 (-)NCBIGRCm39mm39
GRCm39 Ensembl1178,779,525 - 179,345,606 (-)Ensembl
GRCm381178,951,960 - 179,518,053 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1178,951,960 - 179,518,041 (-)EnsemblGRCm38mm10GRCm38
MGSCv371180,885,162 - 181,448,134 (-)NCBIGRCm37mm9NCBIm37
MGSCv361180,791,706 - 181,354,678 (-)NCBImm8
Celera1186,017,554 - 186,588,962 (-)NCBICelera
Cytogenetic Map1H4NCBI
cM Map183.48NCBI
Smyd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554068,768,588 - 9,417,525 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554068,768,365 - 9,417,612 (-)NCBIChiLan1.0ChiLan1.0
SMYD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11226,737,739 - 227,481,309 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1226,737,960 - 227,481,191 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01221,371,348 - 222,125,774 (-)NCBIMhudiblu_PPA_v0panPan3
SMYD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1736,561,080 - 37,250,336 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl736,565,901 - 37,250,578 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha736,041,500 - 36,732,806 (-)NCBI
ROS_Cfam_1.0736,391,898 - 37,082,573 (-)NCBI
UMICH_Zoey_3.1736,231,858 - 36,922,858 (-)NCBI
UNSW_CanFamBas_1.0736,245,479 - 36,930,875 (-)NCBI
UU_Cfam_GSD_1.0736,513,397 - 37,199,813 (-)NCBI
Smyd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934449,528,419 - 50,211,118 (-)NCBI
SpeTri2.0NW_0049365264,536,157 - 5,218,883 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMYD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1018,267,603 - 19,019,537 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11018,267,598 - 19,019,520 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21020,923,785 - 21,568,712 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103230910
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12582,794,748 - 83,531,942 (-)NCBI
Vero_WHO_p1.0NW_02366605585,053,359 - 85,234,932 (-)NCBI
Smyd3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477113,149,547 - 13,943,352 (+)NCBI

Position Markers
D13Got79  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21390,972,702 - 90,972,828 (-)MAPPER
Rnor_6.01396,627,501 - 96,627,626NCBIRnor6.0
Rnor_5.013101,654,006 - 101,654,131UniSTSRnor5.0
RGSC_v3.41394,926,164 - 94,926,290RGDRGSC3.4
RGSC_v3.41394,926,165 - 94,926,290UniSTSRGSC3.4
RGSC_v3.11395,115,101 - 95,115,226RGD
Celera1390,525,340 - 90,525,464UniSTS
RH 3.4 Map13615.3UniSTS
RH 3.4 Map13615.3RGD
RH 2.0 Map13661.7RGD
Cytogenetic Map13q26UniSTS
D13Got81  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21391,029,626 - 91,029,766 (-)MAPPER
Rnor_6.01396,571,632 - 96,571,768NCBIRnor6.0
Rnor_5.013101,598,377 - 101,598,513UniSTSRnor5.0
RGSC_v3.41394,983,543 - 94,983,681RGDRGSC3.4
RGSC_v3.41394,983,544 - 94,983,681UniSTSRGSC3.4
RGSC_v3.11395,172,482 - 95,172,617RGD
Celera1390,582,253 - 90,582,390UniSTS
RH 2.0 Map13664.9RGD
Cytogenetic Map13q26UniSTS
RH141956  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21390,989,928 - 90,990,115 (-)MAPPER
Rnor_6.01396,611,294 - 96,611,480NCBIRnor6.0
Rnor_5.013101,637,799 - 101,637,985UniSTSRnor5.0
RGSC_v3.41394,943,931 - 94,944,117UniSTSRGSC3.4
Celera1390,542,559 - 90,542,745UniSTS
RH 3.4 Map13605.7UniSTS
Cytogenetic Map13q26UniSTS
BE117945  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21391,264,328 - 91,264,497 (+)MAPPER
Rnor_6.01397,805,933 - 97,806,101NCBIRnor6.0
Rnor_5.013102,815,737 - 102,815,905UniSTSRnor5.0
RGSC_v3.41395,213,960 - 95,214,128UniSTSRGSC3.4
Celera1390,816,740 - 90,816,908UniSTS
RH 3.4 Map13609.5UniSTS
Cytogenetic Map13q26UniSTS
BE118607  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21390,808,093 - 90,808,302 (+)MAPPER
Rnor_6.01397,429,211 - 97,429,419NCBIRnor6.0
Rnor_5.013102,449,103 - 102,449,311UniSTSRnor5.0
RGSC_v3.41394,742,574 - 94,742,782UniSTSRGSC3.4
Celera1390,363,852 - 90,364,060UniSTS
RH 3.4 Map13608.5UniSTS
Cytogenetic Map13q26UniSTS
RH132992  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21390,709,310 - 90,709,490 (+)MAPPER
Rnor_6.01397,330,166 - 97,330,345NCBIRnor6.0
Rnor_5.013102,350,058 - 102,350,237UniSTSRnor5.0
RGSC_v3.41394,643,762 - 94,643,941UniSTSRGSC3.4
Celera1390,265,209 - 90,265,388UniSTS
RH 3.4 Map13607.5UniSTS
Cytogenetic Map13q26UniSTS
BE102203  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21391,127,453 - 91,127,619 (+)MAPPER
Rnor_6.01397,538,052 - 97,538,217NCBIRnor6.0
Rnor_5.013102,558,863 - 102,559,028UniSTSRnor5.0
RGSC_v3.41395,084,791 - 95,084,956UniSTSRGSC3.4
Celera1390,680,011 - 90,680,176UniSTS
RH 3.4 Map13609.4UniSTS
Cytogenetic Map13q26UniSTS
AU047954  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21390,867,243 - 90,867,413 (-)MAPPER
Rnor_6.01396,731,528 - 96,731,697NCBIRnor6.0
Rnor_5.013101,757,626 - 101,757,795UniSTSRnor5.0
RGSC_v3.41394,820,650 - 94,820,819UniSTSRGSC3.4
Celera1390,420,957 - 90,421,128UniSTS
Cytogenetic Map13q26UniSTS
BE107361  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21390,915,758 - 90,915,917 (-)MAPPER
Rnor_6.01396,683,175 - 96,683,333NCBIRnor6.0
Rnor_5.013101,709,273 - 101,709,431UniSTSRnor5.0
RGSC_v3.41394,869,299 - 94,869,457UniSTSRGSC3.4
Celera1390,469,334 - 90,469,492UniSTS
RH 3.4 Map13608.5UniSTS
Cytogenetic Map13q26UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:32
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000040829
Prediction methods:Miranda, Rnahybrid
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: NM_001025762   ⟹   NP_001020933
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21390,709,265 - 91,266,209 (-)NCBI
Rnor_6.01397,330,120 - 97,807,813 (-)NCBI
Rnor_5.013102,350,012 - 102,473,942 (-)NCBI
Rnor_5.013102,581,420 - 102,588,971 (-)NCBI
RGSC_v3.41394,643,716 - 95,108,789 (-)RGD
Celera1390,265,163 - 90,818,620 (-)RGD
Sequence:
RefSeq Acc Id: XM_039090987   ⟹   XP_038946915
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21390,709,263 - 91,171,384 (-)NCBI
RefSeq Acc Id: XM_039090988   ⟹   XP_038946916
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21390,709,263 - 91,170,101 (-)NCBI
RefSeq Acc Id: XM_039090989   ⟹   XP_038946917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21390,709,263 - 91,154,588 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001020933   ⟸   NM_001025762
- UniProtKB: Q4V8B9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038946915   ⟸   XM_039090987
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038946916   ⟸   XM_039090988
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038946917   ⟸   XM_039090989
- Peptide Label: isoform X3
Protein Domains
MYND-type   SET


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562635 AgrOrtholog
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7457098 IMAGE-MGC_LOAD
InterPro Hist-Lys_N-MeTrfase_Smyd3 UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  SMYD3_SET UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/TrEMBL
  Znf_MYND UniProtKB/TrEMBL
KEGG Report rno:498295 UniProtKB/TrEMBL
MGC_CLONE MGC:114517 IMAGE-MGC_LOAD
NCBI Gene 498295 ENTREZGENE
Pfam SET UniProtKB/TrEMBL
  zf-MYND UniProtKB/TrEMBL
PhenoGen Smyd3 PhenoGen
PROSITE SAM_MT43_2 UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
  ZF_MYND_1 UniProtKB/TrEMBL
  ZF_MYND_2 UniProtKB/TrEMBL
SMART SET UniProtKB/TrEMBL
UniProt Q4V8B9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Smyd3  SET and MYND domain containing 3  LOC498295  similar to SET and MYND domain containing 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC498295  similar to SET and MYND domain containing 3      Symbol and Name status set to provisional 70820 PROVISIONAL