Stx1a (syntaxin 1A) - Rat Genome Database

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Gene: Stx1a (syntaxin 1A) Rattus norvegicus
Analyze
Symbol: Stx1a
Name: syntaxin 1A
RGD ID: 69430
Description: Enables several functions, including ATP-dependent protein binding activity; calcium-dependent protein binding activity; and transmembrane transporter binding activity. Involved in several processes, including SNARE complex assembly; positive regulation of secretion by cell; and synaptic vesicle exocytosis. Located in several cellular components, including actomyosin; presynaptic active zone membrane; and secretory vesicle. Is integral component of presynaptic membrane and integral component of synaptic vesicle membrane. Part of synaptobrevin 2-SNAP-25-syntaxin-1a complex; synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex; and synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex. Is active in glutamatergic synapse. Human ortholog(s) of this gene implicated in Creutzfeldt-Jakob disease and Hirschsprung's disease. Orthologous to human STX1A (syntaxin 1A); PARTICIPATES IN insulin secretion pathway; INTERACTS WITH (S)-amphetamine; ammonium chloride; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: neuron-specific antigen HPC-1; P35A; synaptotagmin-associated 35 kDa protein; syntaxin 1 a; syntaxin 1 A (brain); syntaxin 1A (brain); syntaxin 1A (brain)-like; syntaxin-1A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   BB/OK  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21221,641,971 - 21,670,022 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1224,682,041 - 24,710,019 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01224,682,050 - 24,710,002 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01226,682,320 - 26,710,272 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41222,737,112 - 22,765,064 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1223,405,260 - 23,432,900 (-)NCBICelera
Cytogenetic Map12q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:7690687   PMID:7961655   PMID:8108429   PMID:9753330   PMID:10336434   PMID:10468580   PMID:10707983   PMID:10712642   PMID:10722844   PMID:10825299   PMID:10913252   PMID:11092755  
PMID:11118447   PMID:11533035   PMID:11707603   PMID:11832227   PMID:12115694   PMID:12130530   PMID:12145198   PMID:12145319   PMID:12175857   PMID:12221094   PMID:12730201   PMID:12761168  
PMID:12805290   PMID:12949219   PMID:14502428   PMID:14985338   PMID:15016962   PMID:15086514   PMID:15175344   PMID:15202772   PMID:15319413   PMID:15355307   PMID:15485808   PMID:15528447  
PMID:15721169   PMID:15872013   PMID:15935055   PMID:16540102   PMID:16672225   PMID:16720719   PMID:16861228   PMID:16888141   PMID:16959903   PMID:17002520   PMID:17027648   PMID:17447252  
PMID:17502420   PMID:17543282   PMID:17617378   PMID:17717182   PMID:17725325   PMID:18003982   PMID:18077557   PMID:18385322   PMID:18556353   PMID:18570918   PMID:18644890   PMID:18760330  
PMID:19039652   PMID:19364135   PMID:19546860   PMID:19716806   PMID:19748891   PMID:19793988   PMID:19843696   PMID:21040848   PMID:21076040   PMID:21173146   PMID:21209369   PMID:21266332  
PMID:21401123   PMID:21540180   PMID:21543213   PMID:21646859   PMID:21730064   PMID:21763275   PMID:21900493   PMID:21900502   PMID:22008253   PMID:22020284   PMID:22094010   PMID:22131420  
PMID:22411134   PMID:22871113   PMID:23315993   PMID:23341457   PMID:23403573   PMID:23641074   PMID:23643538   PMID:23665582   PMID:23761923   PMID:23801330   PMID:23821748   PMID:23962429  
PMID:24133272   PMID:24429282   PMID:24604356   PMID:24722188   PMID:24835618   PMID:24885604   PMID:25485479   PMID:25517944   PMID:26391271   PMID:26635000   PMID:26884341   PMID:27072493  
PMID:27466336   PMID:28137749   PMID:28483813   PMID:28515322   PMID:28596237   PMID:29133430   PMID:29476059   PMID:30156474   PMID:31308225   PMID:32086964   PMID:32669573  


Genomics

Comparative Map Data
Stx1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21221,641,971 - 21,670,022 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl1224,682,041 - 24,710,019 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01224,682,050 - 24,710,002 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01226,682,320 - 26,710,272 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41222,737,112 - 22,765,064 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1223,405,260 - 23,432,900 (-)NCBICelera
Cytogenetic Map12q12NCBI
STX1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl773,699,206 - 73,719,672 (-)EnsemblGRCh38hg38GRCh38
GRCh38773,699,210 - 73,719,673 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37773,113,540 - 73,133,999 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36772,751,476 - 72,771,924 (-)NCBINCBI36hg18NCBI36
Build 34772,558,190 - 72,578,613NCBI
Celera768,591,739 - 68,612,223 (-)NCBI
Cytogenetic Map7q11.23NCBI
HuRef768,995,950 - 69,016,432 (-)NCBIHuRef
CHM1_1773,259,272 - 73,279,754 (-)NCBICHM1_1
CRA_TCAGchr7v2772,446,607 - 72,467,089 (-)NCBI
Stx1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395135,051,473 - 135,079,954 (+)NCBIGRCm39mm39
GRCm39 Ensembl5135,052,336 - 135,079,954 (+)Ensembl
GRCm385135,023,482 - 135,051,100 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5135,023,482 - 135,051,100 (+)EnsemblGRCm38mm10GRCm38
MGSCv375135,499,442 - 135,526,969 (+)NCBIGRCm37mm9NCBIm37
MGSCv365135,308,199 - 135,335,726 (+)NCBImm8
Celera5132,033,901 - 132,061,428 (+)NCBICelera
Cytogenetic Map5G2NCBI
Stx1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545614,030,226 - 14,046,456 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545614,030,233 - 14,046,456 (+)NCBIChiLan1.0ChiLan1.0
STX1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1780,852,495 - 80,871,635 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl780,852,495 - 80,862,255 (-)Ensemblpanpan1.1panPan2
STX1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.166,574,616 - 6,583,002 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl66,574,631 - 6,581,833 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha68,263,577 - 8,280,400 (+)NCBI
ROS_Cfam_1.066,381,214 - 6,398,029 (+)NCBI
UMICH_Zoey_3.166,370,709 - 6,387,529 (+)NCBI
UNSW_CanFamBas_1.066,318,461 - 6,335,266 (+)NCBI
UU_Cfam_GSD_1.066,482,166 - 6,498,979 (+)NCBI
Stx1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344131,118,736 - 131,127,007 (+)NCBI
SpeTri2.0NW_0049365432,909,560 - 2,918,175 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
STX1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,347,495 - 9,367,948 (+)NCBI
ChlSab1.1 Ensembl289,347,532 - 9,368,585 (+)Ensembl
Vero_WHO_p1.0NW_0236660707,135,019 - 7,155,486 (-)NCBI
Stx1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474014,104,033 - 14,120,133 (+)NCBI

Position Markers
BF397463  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21221,656,433 - 21,656,907 (+)MAPPERmRatBN7.2
Rnor_6.01224,696,511 - 24,696,984NCBIRnor6.0
Rnor_5.01226,696,781 - 26,697,254UniSTSRnor5.0
RGSC_v3.41222,751,573 - 22,752,046UniSTSRGSC3.4
Celera1223,419,618 - 23,420,091UniSTS
RH 3.4 Map12327.3UniSTS
Cytogenetic Map12q12UniSTS
AU048378  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21221,650,148 - 21,650,283 (+)MAPPERmRatBN7.2
Rnor_6.01224,690,228 - 24,690,360NCBIRnor6.0
Rnor_5.01226,690,498 - 26,690,630UniSTSRnor5.0
RGSC_v3.41222,745,290 - 22,745,422UniSTSRGSC3.4
Celera1223,413,335 - 23,413,467UniSTS
Cytogenetic Map12q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12895459327911196Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121017588931975590Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)121025689031723732Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)121176499537522089Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121312721127285590Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721131723688Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721150320041Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121441977552716770Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121502198652716770Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121571460935964508Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121571460941291738Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121590890052716770Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121590890052716770Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121718558044098244Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121796086538409001Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121834247752716770Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121834247752716770Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121872904352716770Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121875259352716770Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101875259352716770Rat
2306789Ean6Experimental allergic neuritis QTL 64.9nervous system integrity trait (VT:0010566)experimental autoimmune neuritis severity score (CMO:0001528)122265070227190240Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)122265070245946937Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265070248598906Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)122265070252716770Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265072141291738Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)122287629743799153Rat
631521Pia12Pristane induced arthritis QTL 128.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122324124626710128Rat


Related Rat Strains
The following Strains have been annotated to Stx1a

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir24-1rno-miR-24-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir298rno-miR-298-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir497rno-miR-497-5pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830
Mir29arno-miR-29a-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830

Predicted Target Of
Summary Value
Count of predictions:222
Count of miRNA genes:140
Interacting mature miRNAs:173
Transcripts:ENSRNOT00000049601
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 68 2 10
Low 3 40 40 24 19 24 3 6 6 33 31 11 3
Below cutoff 3 17 17 17 5 5 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049601   ⟹   ENSRNOP00000040699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1224,682,041 - 24,710,019 (-)Ensembl
RefSeq Acc Id: NM_053788   ⟹   NP_446240
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21221,641,975 - 21,669,930 (-)NCBI
Rnor_6.01224,682,050 - 24,710,002 (-)NCBI
Rnor_5.01226,682,320 - 26,710,272 (-)NCBI
RGSC_v3.41222,737,112 - 22,765,064 (-)RGD
Celera1223,405,260 - 23,432,900 (-)RGD
Sequence:
RefSeq Acc Id: XR_005491588
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21221,641,971 - 21,670,022 (-)NCBI
RefSeq Acc Id: XR_005491589
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21221,643,247 - 21,670,022 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_446240   ⟸   NM_053788
- UniProtKB: P32851 (UniProtKB/Swiss-Prot),   A0A1E1ERK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000040699   ⟸   ENSRNOT00000049601
Transcriptome

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

Promoters
RGD ID:13698562
Promoter ID:EPDNEW_R9087
Type:initiation region
Name:Stx1a_1
Description:syntaxin 1A
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_6.01224,709,983 - 24,710,043EPDNEW

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69430 AgrOrtholog
BIND 130559
  130562
  130563
  130904
  133975
  134453
  134456
  134473
  134475
Ensembl Genes ENSRNOG00000029165 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000040699 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000049601 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STX1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syntaxin/epimorphin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syntaxin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  T_SNARE_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:116470 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 116470 ENTREZGENE
PANTHER PTHR19957:SF84 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syntaxin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Stx1a PhenoGen
PROSITE SYNTAXIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  T_SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SynN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  t_SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47661 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1E1ERK2 ENTREZGENE, UniProtKB/TrEMBL
  P32851 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Stx1a  syntaxin 1A  Stx1a  syntaxin 1A (brain)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Stx1a  syntaxin 1A (brain)    syntaxin 1a  Name updated 1299863 APPROVED
2002-06-10 Stx1a  syntaxin 1a      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization concentrated in 200 nm large, cholesterol-dependent clusters at which secretory vesicles preferentially dock and fuse 68723
gene_function participates with syntaxin 1 in locating cholesterol-dependent clusters in the plasmalemma, at which secretory vesicles preferentially dock and fuse 68723
gene_physical_interaction interacts with an omega-conotoxin-sensitive N-type calcium channel and with synaptotagmin 730159
gene_process main component of the exocytotic molecular machinery 625671
gene_process involved in membrane fusion and exocytosis 68723
gene_regulation phosphorylated by casien kinase I on Thr21 and casein kinase II on Ser14 of the N-ternimal domian 70601
gene_regulation during exocytosis calmodulin-activated protein kinase II (CaMKII)-alpha binds to syntaxin and can be released by EGTA or by phosphatase 625671
gene_transcript mRNA upregulated in frontal cortex of AA rat strain compared to ANA rat strain 1358772