Spata17 (spermatogenesis associated 17) - Rat Genome Database

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Gene: Spata17 (spermatogenesis associated 17) Rattus norvegicus
Analyze
Symbol: Spata17
Name: spermatogenesis associated 17
RGD ID: 1565282
Description: Orthologous to human SPATA17 (spermatogenesis associated 17); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC498305; RGD1565282; similar to RIKEN cDNA 4930513F16; spermatogenesis-associated protein 17
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813101,137,415 - 101,316,221 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl13101,137,415 - 101,316,376 (-)EnsemblGRCr8
mRatBN7.21398,605,986 - 98,784,855 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1398,605,986 - 98,784,929 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx13101,121,463 - 101,300,415 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013102,510,639 - 102,689,336 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01399,707,437 - 99,886,371 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.013105,489,121 - 105,684,293 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13105,489,074 - 105,684,374 (-)Ensemblrn6Rnor6.0
Rnor_5.013110,139,348 - 110,334,033 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.413103,171,233 - 103,353,833 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1398,106,089 - 98,283,909 (-)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Spata17
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813101,137,415 - 101,316,221 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl13101,137,415 - 101,316,376 (-)EnsemblGRCr8
mRatBN7.21398,605,986 - 98,784,855 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1398,605,986 - 98,784,929 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx13101,121,463 - 101,300,415 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013102,510,639 - 102,689,336 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01399,707,437 - 99,886,371 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.013105,489,121 - 105,684,293 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13105,489,074 - 105,684,374 (-)Ensemblrn6Rnor6.0
Rnor_5.013110,139,348 - 110,334,033 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.413103,171,233 - 103,353,833 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1398,106,089 - 98,283,909 (-)NCBICelera
Cytogenetic Map13q26NCBI
SPATA17
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381217,631,344 - 217,871,696 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1217,631,324 - 217,871,696 (+)Ensemblhg38GRCh38
GRCh371217,804,686 - 218,045,038 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361215,871,318 - 216,107,107 (+)NCBIBuild 36Build 36hg18NCBI36
Celera1191,028,161 - 191,263,954 (+)NCBICelera
Cytogenetic Map1q41NCBI
HuRef1188,479,192 - 188,715,920 (+)NCBIHuRef
CHM1_11219,077,463 - 219,313,195 (+)NCBICHM1_1
T2T-CHM13v2.01216,872,358 - 217,112,494 (+)NCBIT2T-CHM13v2.0
Spata17
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391186,741,811 - 186,947,705 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1186,776,845 - 186,947,662 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381187,009,614 - 187,215,511 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1187,044,648 - 187,215,465 (-)Ensemblmm10GRCm38
MGSCv371188,872,286 - 189,039,325 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361188,749,194 - 188,916,253 (-)NCBIMGSCv36mm8
Celera1193,981,524 - 194,141,934 (-)NCBICelera
Cytogenetic Map1H5NCBI
cM Map190.23NCBI
Spata17
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955406616,018 - 800,383 (-)Ensembl
ChiLan1.0NW_004955406599,438 - 800,369 (-)NCBIChiLan1.0ChiLan1.0
SPATA17
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2131,531,425 - 31,762,905 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1131,493,977 - 31,725,490 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01193,205,670 - 193,437,171 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11198,059,692 - 198,285,900 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1198,059,692 - 198,287,313 (+)EnsemblpanPan2panpan1.1
SPATA17
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13812,850,773 - 13,058,137 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3812,850,469 - 13,146,096 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3812,893,459 - 13,100,316 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03812,883,600 - 13,091,323 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3812,883,299 - 13,055,928 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13812,893,896 - 13,101,103 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03813,240,510 - 13,447,681 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03813,549,364 - 13,757,219 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Spata17
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934458,799,654 - 58,995,960 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936628813,437 - 1,006,000 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936628813,437 - 1,006,000 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPATA17
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl107,797,502 - 7,971,824 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1107,797,448 - 8,120,892 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2109,884,741 - 10,017,266 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPATA17
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12511,729,382 - 11,956,102 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2511,728,433 - 11,955,926 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605512,139,439 - 12,375,225 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Spata17
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248351,796,302 - 1,982,664 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248351,796,181 - 1,979,668 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Spata17
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11065,165,487 - 65,338,714 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Spata17
1176 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:73
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000057326, ENSRNOT00000073142
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1321120177109350286Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)1365613454109350286Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1368983334109350286Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1367635937109350286Rat
1576318Schws5Schwannoma susceptibility QTL 50.0351nervous system integrity trait (VT:0010566)post-insult time to trigeminal nerve neurilemmoma formation (CMO:0002019)1364497900109350286Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1311081740103588154Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1338975045103588154Rat
8655951Rf63Renal function QTL 6312.2blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)1371610804109350286Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1383286150109350286Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1367635937109350286Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1364375743109350286Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131103588154Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1367635937109350286Rat

Markers in Region
D13Uia11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21398,618,608 - 98,618,895 (+)MAPPERmRatBN7.2
Rnor_6.013105,501,745 - 105,502,031NCBIRnor6.0
Rnor_5.013110,151,945 - 110,152,231UniSTSRnor5.0
RGSC_v3.413103,180,286 - 103,180,572UniSTSRGSC3.4
Celera1398,118,710 - 98,118,996UniSTS
Cytogenetic Map13q26UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 8 56 153 91 90 59 33 59 6 282 120 10 132 81 92 31 10 10

Sequence


Ensembl Acc Id: ENSRNOT00000073142   ⟹   ENSRNOP00000065902
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl13101,137,415 - 101,316,376 (-)Ensembl
mRatBN7.2 Ensembl1398,605,986 - 98,784,929 (-)Ensembl
Rnor_6.0 Ensembl13105,489,074 - 105,684,374 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000093941   ⟹   ENSRNOP00000094726
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl13101,137,415 - 101,316,143 (-)Ensembl
mRatBN7.2 Ensembl1398,605,986 - 98,784,717 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000096992   ⟹   ENSRNOP00000091799
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl13101,216,558 - 101,316,376 (-)Ensembl
mRatBN7.2 Ensembl1398,685,854 - 98,784,929 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000117771   ⟹   ENSRNOP00000088127
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1398,605,986 - 98,784,875 (-)Ensembl
RefSeq Acc Id: NM_001398667   ⟹   NP_001385596
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813101,137,415 - 101,316,143 (-)NCBI
mRatBN7.21398,605,986 - 98,784,723 (-)NCBI
RefSeq Acc Id: XM_006250449   ⟹   XP_006250511
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813101,137,415 - 101,316,221 (-)NCBI
mRatBN7.21398,605,986 - 98,784,855 (-)NCBI
Rnor_6.013105,489,121 - 105,684,293 (-)NCBI
Rnor_5.013110,139,348 - 110,334,033 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091497   ⟹   XP_038947425
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813101,137,415 - 101,225,891 (-)NCBI
mRatBN7.21398,605,986 - 98,692,844 (-)NCBI
RefSeq Acc Id: XM_039091498   ⟹   XP_038947426
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813101,137,415 - 101,225,885 (-)NCBI
mRatBN7.21398,605,986 - 98,694,029 (-)NCBI
RefSeq Acc Id: XM_039091499   ⟹   XP_038947427
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813101,137,415 - 101,275,832 (-)NCBI
mRatBN7.21398,605,986 - 98,744,411 (-)NCBI
RefSeq Acc Id: XM_063272549   ⟹   XP_063128619
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813101,137,415 - 101,225,891 (-)NCBI
RefSeq Acc Id: XM_063272550   ⟹   XP_063128620
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813101,137,415 - 101,270,424 (-)NCBI
RefSeq Acc Id: XP_006250511   ⟸   XM_006250449
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000065902   ⟸   ENSRNOT00000073142
RefSeq Acc Id: XP_038947427   ⟸   XM_039091499
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038947426   ⟸   XM_039091498
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947425   ⟸   XM_039091497
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000094726   ⟸   ENSRNOT00000093941
Ensembl Acc Id: ENSRNOP00000091799   ⟸   ENSRNOT00000096992
Ensembl Acc Id: ENSRNOP00000088127   ⟸   ENSRNOT00000117771
RefSeq Acc Id: NP_001385596   ⟸   NM_001398667
- UniProtKB: M0R8U7 (UniProtKB/TrEMBL),   A6JGT1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063128620   ⟸   XM_063272550
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063128619   ⟸   XM_063272549
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R8U7-F1-model_v2 AlphaFold M0R8U7 1-363 view protein structure

Transcriptome

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

Promoters
RGD ID:13699101
Promoter ID:EPDNEW_R9624
Type:multiple initiation site
Name:Spata17_1
Description:spermatogenesis associated 17
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_6.013105,684,200 - 105,684,260EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565282 AgrOrtholog
BioCyc Gene G2FUF-16939 BioCyc
Ensembl Genes ENSRNOG00000002504 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073142 ENTREZGENE
  ENSRNOT00000073142.5 UniProtKB/TrEMBL
  ENSRNOT00000093941.2 UniProtKB/TrEMBL
  ENSRNOT00000096992.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.190 UniProtKB/TrEMBL
InterPro ASPM UniProtKB/TrEMBL
  IQ_motif_EF-hand-BS UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
NCBI Gene 498305 ENTREZGENE
PANTHER SPERMATOGENESIS-ASSOCIATED PROTEIN 17 UniProtKB/TrEMBL
  UNCHARACTERIZED UniProtKB/TrEMBL
Pfam PF00612 UniProtKB/TrEMBL
PhenoGen Spata17 PhenoGen
PROSITE PS50096 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002504 RatGTEx
SMART SM00015 UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A8I6AF71 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ALD0_RAT UniProtKB/TrEMBL
  A6JGT1 ENTREZGENE, UniProtKB/TrEMBL
  M0R8U7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Spata17  spermatogenesis associated 17  RGD1565282_predicted  similar to RIKEN cDNA 4930513F16 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565282_predicted  similar to RIKEN cDNA 4930513F16 (predicted)  LOC498305  similar to RIKEN cDNA 4930513F16  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498305  similar to RIKEN cDNA 4930513F16      Symbol and Name status set to provisional 70820 PROVISIONAL