Snta1 (syntrophin, alpha 1) - Rat Genome Database

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Gene: Snta1 (syntrophin, alpha 1) Rattus norvegicus
Analyze
Symbol: Snta1
Name: syntrophin, alpha 1
RGD ID: 1307068
Description: Exhibits PDZ domain binding activity. Predicted to be involved in several processes, including negative regulation of peptidyl-cysteine S-nitrosylation; regulation of blood circulation; and regulation of ion transmembrane transport. Localizes to neuromuscular junction and sarcolemma. Biomarker of status epilepticus. Human ortholog(s) of this gene implicated in long QT syndrome; long QT syndrome 12; and sudden infant death syndrome. Orthologous to human SNTA1 (syntrophin alpha 1); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH (+)-pilocarpine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: alpha-1-syntrophin; LOC362242; syntrophin, acidic 1
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
mRatBN7.23142,876,285 - 142,906,737 (-)NCBI
Rnor_6.0 Ensembl3149,874,030 - 149,905,944 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03149,874,023 - 149,905,980 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03156,245,190 - 156,278,486 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43144,843,678 - 144,874,238 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13144,749,301 - 144,779,860 (-)NCBI
Celera3141,611,616 - 141,641,783 (-)NCBICelera
Cytogenetic Map3q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
atenolol pharmacodynamics pathway  (ISO)
betaxolol pharmacodynamics pathway  (ISO)
bisoprolol pharmacodynamics pathway  (ISO)
bupranolol drug pathway  (ISO)
bupranolol pharmacodynamics pathway  (ISO)
carvedilol pharmacodynamics pathway  (ISO)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
esmolol pharmacodynamics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
fosphenytoin pharmacokinetics pathway  (ISO)
ibutilide pharmacodynamics pathway  (ISO)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
metoprolol pharmacodynamics pathway  (ISO)
mexiletine pharmacodynamics pathway  (ISO)
nadolol pharmacodynamics pathway  (ISO)
nebivolol pharmacodynamics pathway  (ISO)
nifedipine pharmacodynamics pathway  (ISO)
nimodipine pharmacodynamics pathway  (ISO)
nisoldipine pharmacodynamics pathway  (ISO)
nitrendipine pharmacodynamics pathway  (ISO)
penbutolol pharmacodynamics pathway  (ISO)
phenytoin pharmacodynamics pathway  (ISO)
pindolol pharmacodynamics pathway  (ISO)
procainamide pharmacodynamics pathway  (ISO)
propranolol pharmacodynamics pathway  (ISO)
quinidine pharmacodynamics pathway  (ISO)
sotalol pharmacodynamics pathway  (ISO)
timolol pharmacodynamics pathway  (ISO)
verapamil pharmacodynamics pathway  (ISO)

References

Additional References at PubMed
PMID:10995443   PMID:11043403   PMID:11115849   PMID:11717465   PMID:12477932   PMID:12600881   PMID:16935300   PMID:17628813   PMID:18591664   PMID:25931508  


Genomics

Comparative Map Data
Snta1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23142,876,285 - 142,906,737 (-)NCBI
Rnor_6.0 Ensembl3149,874,030 - 149,905,944 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03149,874,023 - 149,905,980 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03156,245,190 - 156,278,486 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43144,843,678 - 144,874,238 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13144,749,301 - 144,779,860 (-)NCBI
Celera3141,611,616 - 141,641,783 (-)NCBICelera
Cytogenetic Map3q41NCBI
SNTA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2033,407,955 - 33,443,892 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2033,407,957 - 33,443,763 (-)EnsemblGRCh38hg38GRCh38
GRCh382033,407,957 - 33,443,853 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372031,995,763 - 32,031,569 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362031,459,424 - 31,495,359 (-)NCBINCBI36hg18NCBI36
Build 342031,459,423 - 31,495,359NCBI
Celera2028,749,527 - 28,785,451 (-)NCBI
Cytogenetic Map20q11.21NCBI
HuRef2028,783,561 - 28,819,451 (-)NCBIHuRef
CHM1_12031,896,842 - 31,932,765 (-)NCBICHM1_1
Snta1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392154,218,234 - 154,250,004 (-)NCBIGRCm39mm39
GRCm39 Ensembl2154,218,233 - 154,250,019 (-)Ensembl
GRCm382154,376,313 - 154,408,107 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2154,376,313 - 154,408,099 (-)EnsemblGRCm38mm10GRCm38
MGSCv372154,202,050 - 154,233,820 (-)NCBIGRCm37mm9NCBIm37
MGSCv362154,067,769 - 154,099,522 (-)NCBImm8
Celera2160,280,592 - 160,313,658 (-)NCBICelera
Cytogenetic Map2H1NCBI
cM Map276.52NCBI
Snta1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542227,844,853 - 27,871,547 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542227,844,699 - 27,872,104 (+)NCBIChiLan1.0ChiLan1.0
SNTA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12030,810,787 - 30,844,472 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2030,810,787 - 30,844,476 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02029,696,137 - 29,732,258 (-)NCBIMhudiblu_PPA_v0panPan3
SNTA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12422,636,716 - 22,665,828 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2422,636,756 - 22,665,741 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2422,281,583 - 22,313,637 (-)NCBI
ROS_Cfam_1.02423,322,134 - 23,354,134 (-)NCBI
UMICH_Zoey_3.12422,597,383 - 22,628,609 (-)NCBI
UNSW_CanFamBas_1.02422,708,067 - 22,740,033 (-)NCBI
UU_Cfam_GSD_1.02423,139,650 - 23,170,903 (-)NCBI
Snta1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640171,615,021 - 171,653,713 (-)NCBI
SpeTri2.0NW_0049365617,101,654 - 7,134,529 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNTA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11736,917,276 - 36,946,232 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21741,867,614 - 41,896,571 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SNTA1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1237,703,002 - 37,737,529 (-)NCBI
ChlSab1.1 Ensembl237,702,971 - 37,737,423 (-)Ensembl
Snta1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248425,805,409 - 5,834,553 (+)NCBI

Position Markers
U00677  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23142,876,653 - 142,876,733 (+)MAPPER
Rnor_6.03149,874,388 - 149,874,467NCBIRnor6.0
Rnor_5.03156,245,559 - 156,245,638UniSTSRnor5.0
RGSC_v3.43144,844,039 - 144,844,118UniSTSRGSC3.4
Celera3141,611,977 - 141,612,056UniSTS
Cytogenetic Map3q41UniSTS
RH134532  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23142,876,382 - 142,876,576 (+)MAPPER
Rnor_6.03149,874,117 - 149,874,310NCBIRnor6.0
Rnor_5.03156,245,288 - 156,245,481UniSTSRnor5.0
RGSC_v3.43144,843,768 - 144,843,961UniSTSRGSC3.4
Celera3141,611,706 - 141,611,899UniSTS
RH 3.4 Map31294.8UniSTS
Cytogenetic Map3q41UniSTS
AU048638  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23142,879,770 - 142,880,170 (+)MAPPER
mRatBN7.23142,879,945 - 142,880,170 (+)MAPPER
Rnor_6.03149,877,682 - 149,877,906NCBIRnor6.0
Rnor_6.03149,877,505 - 149,877,906NCBIRnor6.0
Rnor_5.03156,248,676 - 156,249,077UniSTSRnor5.0
Rnor_5.03156,248,853 - 156,249,077UniSTSRnor5.0
RGSC_v3.43144,847,156 - 144,847,557UniSTSRGSC3.4
RGSC_v3.43144,847,333 - 144,847,557UniSTSRGSC3.4
Celera3141,615,104 - 141,615,330UniSTS
Cytogenetic Map3q41UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3126575595153412619Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3136876155170935007Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3147072047154807958Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3148348517171467264Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3148348739163640325Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:62
Count of miRNA genes:56
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000021715
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


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 43 11 3 3 8 11 37 29 23 7 8
Low 3 46 38 19 38 37 6 18 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021715   ⟹   ENSRNOP00000021715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3149,874,030 - 149,905,944 (-)Ensembl
RefSeq Acc Id: NM_001100901   ⟹   NP_001094371
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23142,876,293 - 142,906,709 (-)NCBI
Rnor_6.03149,874,027 - 149,905,944 (-)NCBI
Rnor_5.03156,245,190 - 156,278,486 (-)NCBI
RGSC_v3.43144,843,678 - 144,874,238 (-)RGD
Celera3141,611,616 - 141,641,783 (-)RGD
Sequence:
RefSeq Acc Id: XM_006235326   ⟹   XP_006235388
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23142,876,285 - 142,906,737 (-)NCBI
Rnor_6.03149,874,023 - 149,905,980 (-)NCBI
Rnor_5.03156,245,190 - 156,278,486 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001094371 (Get FASTA)   NCBI Sequence Viewer  
  XP_006235388 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI00087 (Get FASTA)   NCBI Sequence Viewer  
  AAI69101 (Get FASTA)   NCBI Sequence Viewer  
  EDL85970 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001094371   ⟸   NM_001100901
- UniProtKB: B5DFL0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235388   ⟸   XM_006235326
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000021715   ⟸   ENSRNOT00000021715
Protein Domains
PDZ   PH

Transcriptome

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

Promoters
RGD ID:13692572
Promoter ID:EPDNEW_R3097
Type:initiation region
Name:Snta1_1
Description:syntrophin, alpha 1
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_6.03149,905,921 - 149,905,981EPDNEW

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)
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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:1307068 AgrOrtholog
Ensembl Genes ENSRNOG00000016062 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021715 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021715 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
  2.30.42.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7370211 IMAGE-MGC_LOAD
InterPro PDZ UniProtKB/TrEMBL
  PDZ_sf UniProtKB/TrEMBL
  PH_dom-like UniProtKB/TrEMBL
  PHsplit_syntrophin UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  SNTA1 UniProtKB/TrEMBL
  Syntrophin UniProtKB/TrEMBL
KEGG Report rno:362242 UniProtKB/TrEMBL
MGC_CLONE MGC:112776 IMAGE-MGC_LOAD
NCBI Gene 362242 ENTREZGENE
PANTHER PTHR10554:SF6 UniProtKB/TrEMBL
  Syntrophin UniProtKB/TrEMBL
Pfam PDZ UniProtKB/TrEMBL
  PF00169 UniProtKB/TrEMBL
  PH_17 UniProtKB/TrEMBL
PhenoGen Snta1 PhenoGen
PROSITE PDZ UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
SMART PDZ UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP PDZ UniProtKB/TrEMBL
UniProt B5DFL0 ENTREZGENE, UniProtKB/TrEMBL
  Q498T0_RAT UniProtKB/TrEMBL
UniProt Secondary F1MA17 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-02-04 Snta1  syntrophin, alpha 1  Snta1  syntrophin, acidic 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Snta1  syntrophin, acidic 1  Snta1_predicted  syntrophin, acidic 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Snta1_predicted  syntrophin, acidic 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED