Sfmbt2 (Scm-like with four mbt domains 2) - Rat Genome Database
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Gene: Sfmbt2 (Scm-like with four mbt domains 2) Rattus norvegicus
Analyze
Symbol: Sfmbt2
Name: Scm-like with four mbt domains 2
RGD ID: 1305027
Description: Predicted to have histone binding activity. Predicted to be involved in negative regulation of gene expression. Predicted to localize to aggresome; cytosol; and nuclear speck. Orthologous to human SFMBT2 (Scm like with four mbt domains 2); INTERACTS WITH bisphenol A; copper atom; copper(0).
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC307106; scm-like with four MBT domains protein 2
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
mRatBN7.21767,934,296 - 68,128,905 (-)NCBI
Rnor_6.0 Ensembl1771,723,620 - 71,897,972 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01771,719,012 - 71,904,303 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01773,408,697 - 73,595,867 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41779,200,904 - 79,378,766 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11779,211,736 - 79,377,708 (-)NCBI
Celera1767,433,594 - 67,609,582 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
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

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:21605348   PMID:23385818  


Genomics

Comparative Map Data
Sfmbt2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21767,934,296 - 68,128,905 (-)NCBI
Rnor_6.0 Ensembl1771,723,620 - 71,897,972 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01771,719,012 - 71,904,303 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01773,408,697 - 73,595,867 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41779,200,904 - 79,378,766 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11779,211,736 - 79,377,708 (-)NCBI
Celera1767,433,594 - 67,609,582 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
SFMBT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl107,158,624 - 7,411,486 (-)EnsemblGRCh38hg38GRCh38
GRCh38107,158,624 - 7,411,490 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37107,200,586 - 7,453,452 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36107,244,255 - 7,493,456 (-)NCBINCBI36hg18NCBI36
Celera107,129,950 - 7,379,087 (-)NCBI
Cytogenetic Map10p14NCBI
HuRef107,118,749 - 7,371,946 (-)NCBIHuRef
CHM1_1107,200,896 - 7,453,725 (-)NCBICHM1_1
Sfmbt2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39210,375,251 - 10,600,064 (+)NCBIGRCm39mm39
GRCm39 Ensembl210,375,321 - 10,600,064 (+)Ensembl
GRCm38210,370,440 - 10,595,253 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl210,370,510 - 10,595,253 (+)EnsemblGRCm38mm10GRCm38
MGSCv37210,294,209 - 10,516,787 (+)NCBIGRCm37mm9NCBIm37
MGSCv36210,288,288 - 10,513,106 (+)NCBImm8
Celera210,320,248 - 10,520,053 (+)NCBICelera
Cytogenetic Map2A1NCBI
cM Map27.81NCBI
Sfmbt2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542123,691,648 - 23,913,781 (-)NCBIChiLan1.0ChiLan1.0
SFMBT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1107,167,086 - 7,419,939 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl107,172,229 - 7,419,939 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0107,184,075 - 7,439,100 (-)NCBIMhudiblu_PPA_v0panPan3
SFMBT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl228,661,058 - 28,853,364 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1228,637,365 - 28,856,505 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sfmbt2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364847,344,144 - 7,558,341 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SFMBT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1063,877,025 - 64,070,772 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11063,877,033 - 64,070,867 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21070,147,465 - 70,194,176 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SFMBT2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.197,219,723 - 7,474,928 (-)NCBI
ChlSab1.1 Ensembl97,226,295 - 7,445,892 (-)Ensembl
Sfmbt2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247752,151,927 - 2,386,949 (-)NCBI

Position Markers
D17Mgh9  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01771,892,469 - 71,892,616NCBIRnor6.0
Rnor_5.01773,584,141 - 73,584,288UniSTSRnor5.0
RGSC_v3.41779,373,262 - 79,373,410RGDRGSC3.4
RGSC_v3.41779,373,263 - 79,373,410UniSTSRGSC3.4
RGSC_v3.11779,384,095 - 79,384,243RGD
Celera1767,604,079 - 67,604,226UniSTS
RH 3.4 Map17635.7RGD
RH 3.4 Map17635.7UniSTS
RH 2.0 Map17595.2RGD
Cytogenetic Map17q12.3UniSTS
D17Got82  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01771,733,481 - 71,733,770NCBIRnor6.0
Rnor_5.01773,423,166 - 73,423,455UniSTSRnor5.0
RGSC_v3.41779,210,764 - 79,211,054RGDRGSC3.4
RGSC_v3.41779,210,765 - 79,211,054UniSTSRGSC3.4
RGSC_v3.11779,221,598 - 79,221,887RGD
Celera1767,443,455 - 67,443,744UniSTS
RH 3.4 Map17658.8RGD
RH 3.4 Map17658.8UniSTS
RH 2.0 Map17581.6RGD
Cytogenetic Map17q12.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17173413148Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17173413148Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17333697273413148Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17333697273413148Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17333697273413148Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172149095074823273Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172841314873413148Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)173097522875975228Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)173097522875975228Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173205588277922655Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173330362778303627Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173628324577922655Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173779030673413148Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)174117605786176057Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)174117605786176057Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174173108086731080Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174254187285446768Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174435615789356157Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)174866025273413148Rat
1354635Bp245Blood pressure QTL 2456arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)174866025273413148Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)175241095790843779Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175347518090690466Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)175387148890843779Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175399194790843779Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175622429686731080Rat
70210Cm15Cardiac mass QTL 156.5heart right ventricle mass (VT:0007033)heart right ventricle wet weight (CMO:0000072)176219570373981731Rat
1600398Edcs5Endometrial carcinoma susceptibility QTL 52.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)176219570374702206Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)176219582286194199Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176549735982019219Rat
1300131Bp193Blood pressure QTL 1933.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176700421277922655Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176751265790843779Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176933327285183543Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:253
Count of miRNA genes:164
Interacting mature miRNAs:186
Transcripts:ENSRNOT00000065942
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 4
Low 28 51 40 18 40 1 1 70 23 37 6 1
Below cutoff 2 14 6 1 1 1 7 8 4 11 5 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065942   ⟹   ENSRNOP00000061879
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1771,723,620 - 71,897,972 (-)Ensembl
RefSeq Acc Id: NM_001107364   ⟹   NP_001100834
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21767,938,904 - 68,122,571 (-)NCBI
Rnor_6.01771,723,620 - 71,897,972 (-)NCBI
Rnor_5.01773,408,697 - 73,595,867 (-)NCBI
RGSC_v3.41779,200,904 - 79,378,766 (-)RGD
Celera1767,433,594 - 67,609,582 (-)RGD
Sequence:
RefSeq Acc Id: XM_006254210   ⟹   XP_006254272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21767,934,296 - 68,128,905 (-)NCBI
Rnor_6.01771,719,012 - 71,904,303 (-)NCBI
Rnor_5.01773,408,697 - 73,595,867 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006254211   ⟹   XP_006254273
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01771,719,012 - 71,901,245 (-)NCBI
Rnor_5.01773,408,697 - 73,595,867 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006254212   ⟹   XP_006254274
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21767,934,296 - 68,126,722 (-)NCBI
Rnor_6.01771,719,012 - 71,901,660 (-)NCBI
Rnor_5.01773,408,697 - 73,595,867 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006254213   ⟹   XP_006254275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21767,934,296 - 68,127,961 (-)NCBI
Rnor_6.01771,719,012 - 71,903,098 (-)NCBI
Rnor_5.01773,408,697 - 73,595,867 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006254214   ⟹   XP_006254276
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01771,719,012 - 71,900,975 (-)NCBI
Rnor_5.01773,408,697 - 73,595,867 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006254215   ⟹   XP_006254277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21767,934,296 - 68,128,388 (-)NCBI
Rnor_6.01771,719,012 - 71,903,790 (-)NCBI
Rnor_5.01773,408,697 - 73,595,867 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006254216   ⟹   XP_006254278
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21767,934,296 - 68,128,904 (-)NCBI
Rnor_6.01771,719,012 - 71,904,303 (-)NCBI
Rnor_5.01773,408,697 - 73,595,867 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039095776   ⟹   XP_038951704
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21767,934,296 - 68,069,358 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100834   ⟸   NM_001107364
- UniProtKB: D4A643 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006254278   ⟸   XM_006254216
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006254272   ⟸   XM_006254210
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006254277   ⟸   XM_006254215
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006254275   ⟸   XM_006254213
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006254274   ⟸   XM_006254212
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006254273   ⟸   XM_006254211
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006254276   ⟸   XM_006254214
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000061879   ⟸   ENSRNOT00000065942
RefSeq Acc Id: XP_038951704   ⟸   XM_039095776
- Peptide Label: isoform X3
Protein Domains
SLED

Transcriptome

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


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)
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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
LE/Stm (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
LEW/Crl (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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 73537263 73537264 C T snv F344/NRrrc (Illumina) (KNAW), F344/NHsd (KNAW), F344/NCrl (KNAW), F344/NRrrc (SOLiD) (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 71845591 71845592 C T snv F344/NCrl (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 79325204 79325205 C T snv F344/NCrl (ICL), HCR/1Mco (UMich), F344/NHsd (ICAHN), HCR/2Mco (UMich), LCR/2Mco (UMich), LCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305027 AgrOrtholog
Ensembl Genes ENSRNOG00000029235 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061879 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065942 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.1380.20 UniProtKB/TrEMBL
InterPro DUF3588 UniProtKB/TrEMBL
  Mbt UniProtKB/TrEMBL
  SLED_sf UniProtKB/TrEMBL
KEGG Report rno:307106 UniProtKB/TrEMBL
NCBI Gene 307106 ENTREZGENE
Pfam DUF3588 UniProtKB/TrEMBL
  MBT UniProtKB/TrEMBL
PhenoGen Sfmbt2 PhenoGen
PROSITE MBT UniProtKB/TrEMBL
SMART MBT UniProtKB/TrEMBL
UniProt D4A643 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Sfmbt2  Scm-like with four mbt domains 2   Sfmbt2_predicted  Scm-like with four mbt domains 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sfmbt2_predicted  Scm-like with four mbt domains 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED