Spata9 (spermatogenesis associated 9) - Rat Genome Database

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Gene: Spata9 (spermatogenesis associated 9) Rattus norvegicus
Analyze
Symbol: Spata9
Name: spermatogenesis associated 9
RGD ID: 1308291
Description: Predicted to be located in membrane. Orthologous to human SPATA9 (spermatogenesis associated 9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC294594; spermatogenesis-associated protein 9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr827,197,372 - 7,235,408 (+)NCBIGRCr8
mRatBN7.225,465,573 - 5,504,048 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl25,465,575 - 5,503,538 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx212,572,511 - 12,610,492 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0210,671,734 - 10,709,721 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.025,308,103 - 5,346,074 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.022,729,803 - 2,768,162 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl22,729,829 - 2,766,853 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.022,728,259 - 2,766,354 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.423,014,000 - 3,051,967 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.123,033,546 - 3,071,230 (+)NCBI
Celera21,935,165 - 1,973,135 (+)NCBICelera
Cytogenetic Map2q11NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Spata9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr827,197,372 - 7,235,408 (+)NCBIGRCr8
mRatBN7.225,465,573 - 5,504,048 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl25,465,575 - 5,503,538 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx212,572,511 - 12,610,492 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0210,671,734 - 10,709,721 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.025,308,103 - 5,346,074 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.022,729,803 - 2,768,162 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl22,729,829 - 2,766,853 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.022,728,259 - 2,766,354 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.423,014,000 - 3,051,967 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.123,033,546 - 3,071,230 (+)NCBI
Celera21,935,165 - 1,973,135 (+)NCBICelera
Cytogenetic Map2q11NCBI
SPATA9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38595,652,181 - 95,732,102 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl595,652,181 - 95,698,711 (-)EnsemblGRCh38hg38GRCh38
GRCh37594,987,885 - 95,067,806 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36595,019,775 - 95,044,470 (-)NCBINCBI36Build 36hg18NCBI36
Celera590,872,445 - 90,897,462 (-)NCBICelera
Cytogenetic Map5q15NCBI
HuRef590,184,363 - 90,209,377 (-)NCBIHuRef
CHM1_1594,426,692 - 94,451,378 (-)NCBICHM1_1
T2T-CHM13v2.0596,153,102 - 96,233,338 (-)NCBIT2T-CHM13v2.0
Spata9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391376,108,113 - 76,147,106 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1376,115,269 - 76,147,091 (+)EnsemblGRCm39 Ensembl
GRCm381375,959,970 - 75,998,987 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1375,967,150 - 75,998,972 (+)EnsemblGRCm38mm10GRCm38
MGSCv371376,105,187 - 76,136,416 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361376,433,741 - 76,464,970 (+)NCBIMGSCv36mm8
Celera1378,295,559 - 78,328,670 (+)NCBICelera
Cytogenetic Map13C1NCBI
cM Map1340.95NCBI
Spata9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541816,865,731 - 16,894,262 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541816,862,007 - 16,892,303 (+)NCBIChiLan1.0ChiLan1.0
SPATA9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2419,680,314 - 19,721,341 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1517,849,411 - 17,874,354 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0519,665,823 - 19,692,040 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1519,763,023 - 19,842,283 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl519,811,545 - 19,839,138 (+)Ensemblpanpan1.1panPan2
SPATA9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1313,905,515 - 13,960,117 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl313,921,077 - 13,946,458 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha315,215,304 - 15,314,253 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0313,785,787 - 13,855,587 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl313,801,189 - 13,826,419 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1313,718,897 - 13,818,370 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0313,716,947 - 13,801,940 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0313,915,876 - 14,027,067 (+)NCBIUU_Cfam_GSD_1.0
Spata9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213169,463,748 - 169,491,720 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365237,649,301 - 7,676,973 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365237,649,061 - 7,677,247 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPATA9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2102,256,239 - 102,287,484 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12102,257,240 - 102,287,285 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2295,734,140 - 95,741,091 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SPATA9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1489,535,911 - 89,560,910 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl489,536,106 - 89,560,226 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604938,181,086 - 38,206,199 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Spata9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474314,309,920 - 14,335,006 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474314,311,547 - 14,335,652 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Spata9
88 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:18
Count of miRNA genes:18
Interacting mature miRNAs:18
Transcripts:ENSRNOT00000017068
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat

Markers in Region
RH128917  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.225,501,294 - 5,501,505 (+)MAPPERmRatBN7.2
Rnor_6.022,764,610 - 2,764,820NCBIRnor6.0
Rnor_5.022,763,057 - 2,763,267UniSTSRnor5.0
RGSC_v3.423,049,724 - 3,049,934UniSTSRGSC3.4
Celera21,970,892 - 1,971,102UniSTS
Cytogenetic Map2q11UniSTS


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 3 2 8 1
Low 3 11 27 11 16 11 8 11 9 11 5 10 8
Below cutoff 2 2 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017068   ⟹   ENSRNOP00000017068
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl25,465,575 - 5,503,538 (+)Ensembl
Rnor_6.0 Ensembl22,729,829 - 2,766,853 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116641   ⟹   ENSRNOP00000081820
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl25,465,673 - 5,503,538 (+)Ensembl
RefSeq Acc Id: NM_001106399   ⟹   NP_001099869
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr827,197,433 - 7,235,400 (+)NCBI
mRatBN7.225,465,575 - 5,503,538 (+)NCBI
Rnor_6.022,729,829 - 2,766,853 (+)NCBI
Rnor_5.022,728,259 - 2,766,354 (+)NCBI
RGSC_v3.423,014,000 - 3,051,967 (+)RGD
Celera21,935,165 - 1,973,135 (+)RGD
Sequence:
RefSeq Acc Id: XM_006231705   ⟹   XP_006231767
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr827,197,372 - 7,235,408 (+)NCBI
mRatBN7.225,465,573 - 5,504,048 (+)NCBI
Rnor_6.022,729,803 - 2,768,162 (+)NCBI
Rnor_5.022,728,259 - 2,766,354 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099869 (Get FASTA)   NCBI Sequence Viewer  
  XP_006231767 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM09912 (Get FASTA)   NCBI Sequence Viewer  
  EDM09913 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017068
  ENSRNOP00000017068.4
  ENSRNOP00000081820.1
Reference Protein Sequences
RefSeq Acc Id: NP_001099869   ⟸   NM_001106399
- UniProtKB: D3ZFQ7 (UniProtKB/TrEMBL),   A6I4F4 (UniProtKB/TrEMBL),   A0A8I6G8H0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006231767   ⟸   XM_006231705
- Peptide Label: isoform X1
- UniProtKB: A0A8I6G8H0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017068   ⟸   ENSRNOT00000017068
RefSeq Acc Id: ENSRNOP00000081820   ⟸   ENSRNOT00000116641

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZFQ7-F1-model_v2 AlphaFold D3ZFQ7 1-252 view protein structure

Transcriptome

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

Promoters
RGD ID:13691034
Promoter ID:EPDNEW_R1559
Type:initiation region
Name:Spata9_1
Description:spermatogenesis associated 9
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_6.022,729,861 - 2,729,921EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308291 AgrOrtholog
BioCyc Gene G2FUF-55086 BioCyc
Ensembl Genes ENSRNOG00000012770 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017068 ENTREZGENE
  ENSRNOT00000017068.6 UniProtKB/TrEMBL
  ENSRNOT00000116641.1 UniProtKB/TrEMBL
InterPro SPATA9 UniProtKB/TrEMBL
KEGG Report rno:294594 UniProtKB/TrEMBL
NCBI Gene 294594 ENTREZGENE
PANTHER PTHR35669 UniProtKB/TrEMBL
  SPERMATOGENESIS-ASSOCIATED PROTEIN 9 UniProtKB/TrEMBL
Pfam SPATA9 UniProtKB/TrEMBL
PhenoGen Spata9 PhenoGen
RatGTEx ENSRNOG00000012770 RatGTEx
UniProt A0A8I6G8H0 ENTREZGENE, UniProtKB/TrEMBL
  A6I4F4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZFQ7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Spata9  spermatogenesis associated 9   Spata9_predicted  spermatogenesis associated 9 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Spata9_predicted  spermatogenesis associated 9 (predicted)      Symbol and Name status set to approved 70820 APPROVED