Spata13 (spermatogenesis associated 13) - Rat Genome Database

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Gene: Spata13 (spermatogenesis associated 13) Rattus norvegicus
Analyze
Symbol: Spata13
Name: spermatogenesis associated 13
RGD ID: 1307364
Description: Predicted to enable guanyl-nucleotide exchange factor activity and identical protein binding activity. Predicted to be involved in cell migration; plasma membrane bounded cell projection assembly; and regulation of cell migration. Predicted to be located in several cellular components, including filopodium; lamellipodium; and ruffle membrane. Orthologous to human SPATA13 (spermatogenesis associated 13); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC305938; spermatogenesis-associated protein 13
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Spata13Tn(sb-T2/Bart3)2.267Mcwi  
Genetic Models: F344-Spata13Tn(sb-T2/Bart3)2.267Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21534,778,479 - 34,907,645 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1534,778,473 - 34,905,114 (+)Ensembl
Rnor_6.01540,937,652 - 41,066,645 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1540,937,708 - 41,066,769 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01544,749,770 - 44,878,760 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41539,722,469 - 39,849,214 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11539,806,342 - 39,864,914 (+)NCBI
Celera1534,478,795 - 34,605,121 (+)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
aristolochic acid  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
chlordecone  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenthion  (ISO)
fenvalerate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gentamycin  (EXP)
hydrogen cyanide  (ISO)
hydroquinone O-beta-D-glucopyranoside  (ISO)
indometacin  (ISO)
lipopolysaccharide  (ISO)
methapyrilene  (ISO)
methidathion  (ISO)
paracetamol  (EXP)
PCB138  (ISO)
pirinixic acid  (ISO)
potassium cyanide  (ISO)
propiconazole  (ISO)
raloxifene  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:17145773   PMID:17599059   PMID:19151759   PMID:19934221   PMID:25750125  


Genomics

Comparative Map Data
Spata13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21534,778,479 - 34,907,645 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1534,778,473 - 34,905,114 (+)Ensembl
Rnor_6.01540,937,652 - 41,066,645 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1540,937,708 - 41,066,769 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01544,749,770 - 44,878,760 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41539,722,469 - 39,849,214 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11539,806,342 - 39,864,914 (+)NCBI
Celera1534,478,795 - 34,605,121 (+)NCBICelera
Cytogenetic Map15p12NCBI
SPATA13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381323,979,802 - 24,307,069 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1323,979,805 - 24,307,074 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1323,979,810 - 24,035,027 (+)EnsemblGRCh38hg38GRCh38
GRCh371324,553,941 - 24,881,207 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361323,632,887 - 23,776,048 (+)NCBINCBI36hg18NCBI36
Build 341323,632,886 - 23,776,048NCBI
Celera135,797,087 - 5,943,877 (+)NCBI
Cytogenetic Map13q12.12NCBI
HuRef135,546,585 - 5,692,908 (+)NCBIHuRef
CHM1_11324,702,689 - 24,849,248 (+)NCBICHM1_1
T2T-CHM13v2.01323,186,689 - 23,514,163 (+)NCBI
Spata13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391460,722,617 - 61,002,005 (+)NCBIGRCm39mm39
GRCm39 Ensembl1460,871,450 - 61,002,005 (+)Ensembl
GRCm381460,485,168 - 60,764,556 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1460,634,001 - 60,764,556 (+)EnsemblGRCm38mm10GRCm38
MGSCv371461,253,566 - 61,383,393 (+)NCBIGRCm37mm9NCBIm37
MGSCv361459,588,150 - 59,718,666 (+)NCBImm8
Celera1458,411,392 - 58,543,017 (+)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1431.77NCBI
Spata13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554974,224,374 - 4,307,335 (-)NCBIChiLan1.0ChiLan1.0
SPATA13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11323,772,869 - 23,921,025 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0135,298,466 - 5,626,162 (+)NCBIMhudiblu_PPA_v0panPan3
SPATA13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12514,389,174 - 14,732,665 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2514,667,527 - 14,811,327 (+)NCBI
ROS_Cfam_1.02514,720,317 - 14,864,381 (+)NCBI
UMICH_Zoey_3.12514,665,576 - 14,745,923 (+)NCBI
UNSW_CanFamBas_1.02514,686,844 - 14,748,577 (+)NCBI
UU_Cfam_GSD_1.02514,652,735 - 14,796,901 (+)NCBI
Spata13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945116,635,240 - 116,957,681 (+)NCBI
SpeTri2.0NW_0049366881,433,231 - 1,569,954 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPATA13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1112,806,674 - 3,161,372 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2112,160,029 - 2,281,822 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SPATA13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.133,767,078 - 4,085,379 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605740,409,981 - 40,742,603 (-)NCBIVero_WHO_p1.0
Spata13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477613,703,451 - 13,852,924 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D15Got33  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21534,803,505 - 34,803,622 (+)MAPPERmRatBN7.2
Rnor_6.01540,962,709 - 40,962,825NCBIRnor6.0
Rnor_5.01544,774,824 - 44,774,940UniSTSRnor5.0
RGSC_v3.41539,748,613 - 39,748,730RGDRGSC3.4
RGSC_v3.41539,748,614 - 39,748,730UniSTSRGSC3.4
RGSC_v3.11539,764,314 - 39,764,430RGD
Celera1534,504,124 - 34,504,240UniSTS
RH 3.4 Map15226.2UniSTS
RH 3.4 Map15226.2RGD
RH 2.0 Map15123.9RGD
Cytogenetic Map15p12UniSTS
D15Mco14  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21534,875,844 - 34,876,020 (+)MAPPERmRatBN7.2
Rnor_6.01541,035,266 - 41,035,441NCBIRnor6.0
Rnor_5.01544,847,381 - 44,847,556UniSTSRnor5.0
RGSC_v3.41539,820,949 - 39,821,125RGDRGSC3.4
RGSC_v3.41539,820,950 - 39,821,125UniSTSRGSC3.4
RGSC_v3.11539,836,649 - 39,836,825RGD
Celera1534,576,404 - 34,576,567UniSTS
Cytogenetic Map15p12UniSTS
BE119336  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21534,852,330 - 34,852,514 (+)MAPPERmRatBN7.2
Rnor_6.01541,011,678 - 41,011,861NCBIRnor6.0
Rnor_5.01544,823,793 - 44,823,976UniSTSRnor5.0
RGSC_v3.41539,797,436 - 39,797,619UniSTSRGSC3.4
Celera1534,552,982 - 34,553,165UniSTS
RH 3.4 Map15227.7UniSTS
Cytogenetic Map15p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat


Genetic Models
This gene Spata13 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:169
Count of miRNA genes:138
Interacting mature miRNAs:155
Transcripts:ENSRNOT00000018407
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 8 30 14 19 14 31 34 18 11
Low 1 35 27 27 27 8 11 43 1 23 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018407   ⟹   ENSRNOP00000018406
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1534,778,473 - 34,905,114 (+)Ensembl
Rnor_6.0 Ensembl1540,937,708 - 41,066,769 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114572   ⟹   ENSRNOP00000090978
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1534,778,473 - 34,905,114 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115440   ⟹   ENSRNOP00000087721
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1534,876,801 - 34,905,114 (+)Ensembl
RefSeq Acc Id: NM_001191686   ⟹   NP_001178615
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21534,778,536 - 34,904,114 (+)NCBI
Rnor_6.01540,937,731 - 41,063,117 (+)NCBI
Rnor_5.01544,749,770 - 44,878,760 (+)NCBI
Celera1534,478,795 - 34,605,121 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252113   ⟹   XP_006252175
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21534,778,479 - 34,907,645 (+)NCBI
Rnor_6.01540,937,652 - 41,066,645 (+)NCBI
Rnor_5.01544,749,770 - 44,878,760 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252114   ⟹   XP_006252176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21534,844,156 - 34,907,645 (+)NCBI
Rnor_6.01541,002,904 - 41,066,645 (+)NCBI
Rnor_5.01544,749,770 - 44,878,760 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252115   ⟹   XP_006252177
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21534,876,067 - 34,907,645 (+)NCBI
Rnor_6.01541,035,379 - 41,066,645 (+)NCBI
Rnor_5.01544,749,770 - 44,878,760 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039093322   ⟹   XP_038949250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21534,832,951 - 34,907,645 (+)NCBI
RefSeq Acc Id: XM_039093323   ⟹   XP_038949251
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21534,867,449 - 34,907,645 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001178615   ⟸   NM_001191686
- Sequence:
RefSeq Acc Id: XP_006252175   ⟸   XM_006252113
- Peptide Label: isoform X1
- UniProtKB: D3ZWB4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252176   ⟸   XM_006252114
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006252177   ⟸   XM_006252115
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000018406   ⟸   ENSRNOT00000018407
RefSeq Acc Id: XP_038949250   ⟸   XM_039093322
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949251   ⟸   XM_039093323
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000087721   ⟸   ENSRNOT00000115440
RefSeq Acc Id: ENSRNOP00000090978   ⟸   ENSRNOT00000114572
Protein Domains
DH   PH   SH3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZWB4-F1-model_v2 AlphaFold D3ZWB4 1-1245 view protein structure

Transcriptome

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

Promoters
RGD ID:13699736
Promoter ID:EPDNEW_R10260
Type:initiation region
Name:Spata13_1
Description:spermatogenesis associated 13
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_6.01540,937,698 - 40,937,758EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307364 AgrOrtholog
BioCyc Gene G2FUF-13519 BioCyc
Ensembl Genes ENSRNOG00000013707 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018406 ENTREZGENE
  ENSRNOP00000018406.7 UniProtKB/TrEMBL
  ENSRNOP00000087721 ENTREZGENE
  ENSRNOP00000087721.1 UniProtKB/TrEMBL
  ENSRNOP00000090978 ENTREZGENE
  ENSRNOP00000090978.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018407 ENTREZGENE
  ENSRNOT00000018407.8 UniProtKB/TrEMBL
  ENSRNOT00000114572 ENTREZGENE
  ENSRNOT00000114572.1 UniProtKB/TrEMBL
  ENSRNOT00000115440 ENTREZGENE
  ENSRNOT00000115440.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.900.10 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
InterPro DBL_dom_sf UniProtKB/TrEMBL
  DH-domain UniProtKB/TrEMBL
  GDS_CDC24_CS UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  SH3-like_dom UniProtKB/TrEMBL
  SH3_domain UniProtKB/TrEMBL
NCBI Gene 305938 ENTREZGENE
Pfam PF00169 UniProtKB/TrEMBL
  RhoGEF UniProtKB/TrEMBL
  SH3_1 UniProtKB/TrEMBL
PhenoGen Spata13 PhenoGen
PROSITE DH_1 UniProtKB/TrEMBL
  DH_2 UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
SMART RhoGEF UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
Superfamily-SCOP DH-domain UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
UniProt A0A8I6A3P0_RAT UniProtKB/TrEMBL
  A0A8I6ACW7_RAT UniProtKB/TrEMBL
  D3ZWB4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Spata13  spermatogenesis associated 13   Spata13_predicted  spermatogenesis associated 13 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Spata13_predicted  spermatogenesis associated 13 (predicted)      Symbol and Name status set to approved 70820 APPROVED