Samd12 (sterile alpha motif domain containing 12) - Rat Genome Database
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Gene: Samd12 (sterile alpha motif domain containing 12) Rattus norvegicus
Analyze
Symbol: Samd12
Name: sterile alpha motif domain containing 12
RGD ID: 1561402
Description: Human ortholog(s) of this gene implicated in familial adult myoclonic epilepsy 1. Orthologous to human SAMD12 (sterile alpha motif domain containing 12); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC362910; RGD1561402; similar to sterile alpha motif domain containing 12; sterile alpha motif domain-containing protein 12
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
mRatBN7.2784,768,850 - 85,064,057 (-)NCBI
Rnor_6.0 Ensembl792,993,330 - 93,502,591 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0792,995,599 - 93,286,757 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0793,636,142 - 93,930,174 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4789,785,050 - 90,090,875 (-)NCBIRGSC3.4rn4RGSC3.4
Celera781,608,279 - 81,901,215 (-)NCBICelera
Cytogenetic Map7q31NCBI
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

Molecular Function

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Samd12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2784,768,850 - 85,064,057 (-)NCBI
Rnor_6.0 Ensembl792,993,330 - 93,502,591 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0792,995,599 - 93,286,757 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0793,636,142 - 93,930,174 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4789,785,050 - 90,090,875 (-)NCBIRGSC3.4rn4RGSC3.4
Celera781,608,279 - 81,901,215 (-)NCBICelera
Cytogenetic Map7q31NCBI
SAMD12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8118,189,455 - 118,622,112 (-)EnsemblGRCh38hg38GRCh38
GRCh388118,131,825 - 118,621,963 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378119,201,694 - 119,634,184 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh378119,144,064 - 119,634,202 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 368119,270,875 - 119,703,365 (-)NCBINCBI36hg18NCBI36
Build 348119,459,407 - 119,703,301NCBI
Celera8115,390,217 - 115,822,474 (-)NCBI
Cytogenetic Map8q24.11-q24.12NCBI
HuRef8114,528,469 - 114,960,887 (-)NCBIHuRef
CHM1_18119,242,770 - 119,675,254 (-)NCBICHM1_1
Samd12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391553,262,514 - 53,765,926 (-)NCBIGRCm39mm39
GRCm381553,399,113 - 53,902,535 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1553,453,810 - 53,902,537 (-)EnsemblGRCm38mm10GRCm38
MGSCv371553,293,356 - 53,733,991 (-)NCBIGRCm37mm9NCBIm37
MGSCv361553,291,884 - 53,732,519 (-)NCBImm8
Celera1555,020,883 - 55,465,415 (-)NCBICelera
Cytogenetic Map15C- D1NCBI
Samd12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541724,145,264 - 24,541,599 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541724,137,340 - 24,541,572 (-)NCBIChiLan1.0ChiLan1.0
SAMD12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.18117,345,231 - 117,832,607 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v08114,823,792 - 115,312,738 (-)NCBIMhudiblu_PPA_v0panPan3
SAMD12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1317,528,421 - 17,897,009 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11317,525,855 - 17,897,153 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Samd12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647027,858,661 - 28,230,543 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SAMD12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl420,143,864 - 20,569,129 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1420,143,614 - 20,570,780 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2421,342,600 - 21,379,800 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SAMD12
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18112,834,159 - 113,246,812 (-)NCBI
ChlSab1.1 Ensembl8112,877,688 - 113,246,824 (-)Ensembl
Samd12
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476316,475,162 - 16,867,444 (-)NCBI

Position Markers
D7Rat112  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0793,417,642 - 93,417,887NCBIRnor6.0
Rnor_5.0794,061,716 - 94,061,961UniSTSRnor5.0
Celera782,019,130 - 82,019,375UniSTS
RH 3.4 Map7586.8UniSTS
RH 3.4 Map7586.8RGD
RH 2.0 Map7497.5RGD
SHRSP x BN Map751.19RGD
Cytogenetic Map7q31UniSTS
D7Rat139  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0793,155,229 - 93,155,402NCBIRnor6.0
Rnor_5.0793,795,643 - 93,795,816UniSTSRnor5.0
RGSC_v3.4789,944,922 - 89,945,095UniSTSRGSC3.4
RGSC_v3.4789,944,921 - 89,945,095RGDRGSC3.4
RGSC_v3.1789,979,152 - 89,979,325RGD
Celera781,765,848 - 81,766,021UniSTS
RH 3.4 Map7581.0RGD
RH 3.4 Map7581.0UniSTS
RH 2.0 Map7494.8RGD
SHRSP x BN Map752.31RGD
Cytogenetic Map7q31UniSTS
BE105380  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0792,995,830 - 92,996,007NCBIRnor6.0
Rnor_5.0793,636,373 - 93,636,550UniSTSRnor5.0
RGSC_v3.4789,785,281 - 89,785,458UniSTSRGSC3.4
Celera781,608,510 - 81,608,687UniSTS
RH 3.4 Map7583.2UniSTS
Cytogenetic Map7q31UniSTS
BF405999  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0793,172,140 - 93,172,387NCBIRnor6.0
Rnor_5.0793,812,554 - 93,812,801UniSTSRnor5.0
RGSC_v3.4789,961,833 - 89,962,080UniSTSRGSC3.4
Celera781,782,767 - 81,783,014UniSTS
RH 3.4 Map7583.2UniSTS
Cytogenetic Map7q31UniSTS
BF415978  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0793,385,026 - 93,385,152NCBIRnor6.0
Rnor_5.0794,029,078 - 94,029,204UniSTSRnor5.0
RGSC_v3.4790,193,183 - 90,193,309UniSTSRGSC3.4
Celera781,987,798 - 81,987,924UniSTS
RH 3.4 Map7587.5UniSTS
Cytogenetic Map7q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)73586772993155402Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)75025210395252103Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)75079381895793818Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)751252005111589099Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)75320034498200344Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)75425951299259512Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)755495689100495689Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)755495689100495689Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)755495689100495689Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)755495689100495689Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)755495689100495689Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)755495689100495689Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)755495689100495689Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)761047589113228378Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)768518460113518460Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)769399586111043530Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)769399586111043530Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)770421228115421228Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)777428105127748511Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)777428234122421148Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
724537Niddm52Non-insulin dependent diabetes mellitus QTL 520.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)788365265102588450Rat
1641908Teswt1Testicular weight QTL 13.28testis mass (VT:1000644)both testes wet weight (CMO:0000175)788365265103867802Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)788365265119318087Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)788365265121986709Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:52
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000064877
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


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 48 2 5
Low 37 24 10 8 10 8 8 26 34 25 6 8
Below cutoff 3 6 30 28 11 28 3 1 14

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064877   ⟹   ENSRNOP00000063213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl792,995,599 - 93,280,009 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076080   ⟹   ENSRNOP00000068009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl793,193,233 - 93,502,591 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076327   ⟹   ENSRNOP00000068320
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl792,993,330 - 92,996,025 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077033   ⟹   ENSRNOP00000068526
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl793,192,354 - 93,502,571 (-)Ensembl
RefSeq Acc Id: NM_001130562   ⟹   NP_001124034
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2784,768,850 - 85,064,057 (-)NCBI
Rnor_6.0792,995,599 - 93,286,757 (-)NCBI
Rnor_5.0793,636,142 - 93,930,174 (-)NCBI
RGSC_v3.4789,785,050 - 90,090,875 (-)RGD
Celera781,608,279 - 81,901,215 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001124034 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM16267 (Get FASTA)   NCBI Sequence Viewer  
  EDM16268 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001124034   ⟸   NM_001130562
- Sequence:
RefSeq Acc Id: ENSRNOP00000068526   ⟸   ENSRNOT00000077033
RefSeq Acc Id: ENSRNOP00000063213   ⟸   ENSRNOT00000064877
RefSeq Acc Id: ENSRNOP00000068320   ⟸   ENSRNOT00000076327
RefSeq Acc Id: ENSRNOP00000068009   ⟸   ENSRNOT00000076080
Protein Domains
SAM

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)
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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
GH/OmrMcwi (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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561402 AgrOrtholog
Ensembl Genes ENSRNOG00000043390 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063213 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068009 UniProtKB/TrEMBL
  ENSRNOP00000068320 UniProtKB/TrEMBL
  ENSRNOP00000068526 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064877 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076080 UniProtKB/TrEMBL
  ENSRNOT00000076327 UniProtKB/TrEMBL
  ENSRNOT00000077033 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
InterPro Aveugle-like_SAM_dom UniProtKB/TrEMBL
  SAM UniProtKB/TrEMBL
  SAM/pointed UniProtKB/TrEMBL
NCBI Gene 362910 ENTREZGENE
Pfam SAM_2 UniProtKB/TrEMBL
PhenoGen Samd12 PhenoGen
PROSITE SAM_DOMAIN UniProtKB/TrEMBL
SMART SAM UniProtKB/TrEMBL
Superfamily-SCOP SAM_homology UniProtKB/TrEMBL
UniProt A0A096MJ65_RAT UniProtKB/TrEMBL
  A0A096MKI3_RAT UniProtKB/TrEMBL
  A0A1Y8KXX4_RAT UniProtKB/TrEMBL
  M0R3J7_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-29 Samd12  sterile alpha motif domain containing 12  RGD1561402_predicted  similar to sterile alpha motif domain containing 12 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561402_predicted  similar to sterile alpha motif domain containing 12 (predicted)  LOC362910  similar to sterile alpha motif domain containing 12  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC362910  similar to sterile alpha motif domain containing 12      Symbol and Name status set to provisional 70820 PROVISIONAL