Spata19 (spermatogenesis associated 19) - Rat Genome Database

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Gene: Spata19 (spermatogenesis associated 19) Rattus norvegicus
Analyze
Symbol: Spata19
Name: spermatogenesis associated 19
RGD ID: 620628
Description: Predicted to be involved in sperm mitochondrion organization. Located in mitochondrion. Orthologous to human SPATA19 (spermatogenesis associated 19); INTERACTS WITH 1,3,5-trinitro-1,3,5-triazinane; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Spas1; spergen-1; spermatogenesis-associated protein 19, mitochondrial; spermatogenic cell-specific gene 1 protein; spermatogenic specific-gene1
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
GRCr8834,057,130 - 34,079,097 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl834,073,316 - 34,079,096 (+)EnsemblGRCr8
mRatBN7.2825,814,922 - 25,820,663 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl825,814,905 - 25,820,670 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx829,856,864 - 29,862,604 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0828,151,169 - 28,156,909 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0826,031,140 - 26,036,878 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0828,454,938 - 28,460,645 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl828,454,962 - 28,459,835 (+)Ensemblrn6Rnor6.0
Rnor_5.0828,472,561 - 28,478,881 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera827,302,047 - 27,307,898 (+)NCBICelera
RGSC_v3.1827,023,157 - 27,024,489 (+)NCBI
Cytogenetic Map8q13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
mitochondrial outer membrane  (IEA,ISO,ISS)
mitochondrion  (IDA,IEA)
motile cilium  (IEA)
sperm flagellum  (IEA,ISO,ISS)
sperm midpiece  (IBA,IEA,ISO,ISS)

References

References - curated
# Reference Title Reference Citation
1. Complementary DNA cloning and characterization of rat spergen-1, a spermatogenic cell-specific gene-1, containing a mitochondria-targeting signal. Doiguchi M, etal., Biol Reprod 2002 May;66(5):1462-70.
2. 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.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334  


Genomics

Comparative Map Data
Spata19
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8834,057,130 - 34,079,097 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl834,073,316 - 34,079,096 (+)EnsemblGRCr8
mRatBN7.2825,814,922 - 25,820,663 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl825,814,905 - 25,820,670 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx829,856,864 - 29,862,604 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0828,151,169 - 28,156,909 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0826,031,140 - 26,036,878 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0828,454,938 - 28,460,645 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl828,454,962 - 28,459,835 (+)Ensemblrn6Rnor6.0
Rnor_5.0828,472,561 - 28,478,881 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera827,302,047 - 27,307,898 (+)NCBICelera
RGSC_v3.1827,023,157 - 27,024,489 (+)NCBI
Cytogenetic Map8q13NCBI
SPATA19
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811133,835,930 - 133,845,513 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11133,840,631 - 133,845,538 (-)Ensemblhg38GRCh38
GRCh3711133,710,526 - 133,715,408 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611133,215,727 - 133,220,602 (-)NCBIBuild 36Build 36hg18NCBI36
Celera11130,884,494 - 130,889,369 (-)NCBICelera
Cytogenetic Map11q25NCBI
HuRef11129,665,529 - 129,670,404 (-)NCBIHuRef
CHM1_111133,598,442 - 133,603,317 (-)NCBICHM1_1
T2T-CHM13v2.011133,878,224 - 133,887,807 (-)NCBIT2T-CHM13v2.0
Spata19
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39927,308,103 - 27,313,007 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl927,308,096 - 27,313,081 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38927,396,807 - 27,401,711 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl927,396,800 - 27,401,785 (+)Ensemblmm10GRCm38
MGSCv37927,204,406 - 27,209,295 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36927,146,267 - 27,151,156 (+)NCBIMGSCv36mm8
Celera924,653,805 - 24,658,694 (+)NCBICelera
Cytogenetic Map9A4NCBI
cM Map912.9NCBI
Spata19
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541234,684,247 - 34,689,403 (-)Ensembl
ChiLan1.0NW_00495541234,684,298 - 34,689,163 (-)NCBIChiLan1.0ChiLan1.0
SPATA19
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v29134,552,496 - 134,557,408 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan111135,658,559 - 135,663,463 (-)NCBINHGRI_mPanPan1
PanPan1.1 Ensembl11132,550,916 - 132,555,821 (-)EnsemblpanPan2panpan1.1
SPATA19
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.151,357,720 - 1,362,312 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl51,357,750 - 1,362,270 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha51,476,752 - 1,481,343 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.051,313,419 - 1,318,021 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl51,313,448 - 1,317,979 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.151,346,357 - 1,350,948 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.051,346,728 - 1,351,321 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.051,384,655 - 1,389,252 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Spata19
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947115,549,177 - 115,610,895 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366841,992,541 - 1,996,813 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366841,992,463 - 1,996,877 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPATA19
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl960,426,621 - 60,433,458 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1960,426,620 - 60,433,458 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2966,934,893 - 66,941,731 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SPATA19
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11124,916,744 - 124,921,918 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1124,918,093 - 124,921,722 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660431,089,082 - 1,128,737 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Spata19
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248128,430,242 - 8,435,112 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248128,430,604 - 8,435,215 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Spata19
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1823,293,287 - 23,297,536 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Spata19
168 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:26
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000051573
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)83154366176543661Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat


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
nervous system
renal system
reproductive system
respiratory system
6 7 9 33 28 25 10 11 10 6 57 34 20 2 32 15

Sequence


Ensembl Acc Id: ENSRNOT00000051573   ⟹   ENSRNOP00000040918
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl834,073,316 - 34,079,096 (+)Ensembl
mRatBN7.2 Ensembl825,814,905 - 25,820,670 (+)Ensembl
Rnor_6.0 Ensembl828,454,962 - 28,459,835 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000112488   ⟹   ENSRNOP00000084720
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl834,073,828 - 34,079,096 (+)Ensembl
mRatBN7.2 Ensembl825,815,398 - 25,820,670 (+)Ensembl
RefSeq Acc Id: NM_134384   ⟹   NP_599211
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8834,073,352 - 34,079,089 (+)NCBI
mRatBN7.2825,814,922 - 25,820,663 (+)NCBI
Rnor_6.0828,454,938 - 28,460,645 (+)NCBI
Rnor_5.0828,472,561 - 28,478,881 (+)NCBI
Celera827,302,047 - 27,307,898 (+)RGD
Sequence:
RefSeq Acc Id: XM_063264838   ⟹   XP_063120908
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8834,057,130 - 34,079,097 (+)NCBI
Protein Sequences
Protein RefSeqs NP_599211 (Get FASTA)   NCBI Sequence Viewer  
  XP_063120908 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81729 (Get FASTA)   NCBI Sequence Viewer  
  BAB69061 (Get FASTA)   NCBI Sequence Viewer  
  EDL83332 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000040918
  ENSRNOP00000040918.5
GenBank Protein Q920Q3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_599211   ⟸   NM_134384
- Peptide Label: precursor
- UniProtKB: Q920Q3 (UniProtKB/Swiss-Prot),   A6JYE3 (UniProtKB/TrEMBL),   F1M9B7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000040918   ⟸   ENSRNOT00000051573
Ensembl Acc Id: ENSRNOP00000084720   ⟸   ENSRNOT00000112488
RefSeq Acc Id: XP_063120908   ⟸   XM_063264838
- Peptide Label: isoform X1
- UniProtKB: Q920Q3 (UniProtKB/Swiss-Prot),   A6JYE3 (UniProtKB/TrEMBL),   F1M9B7 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q920Q3-F1-model_v2 AlphaFold Q920Q3 1-154 view protein structure

Transcriptome

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

Promoters
RGD ID:13695821
Promoter ID:EPDNEW_R6346
Type:multiple initiation site
Name:Spata19_1
Description:spermatogenesis associated 19
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_6.0828,454,903 - 28,454,963EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620628 AgrOrtholog
BioCyc Gene G2FUF-31297 BioCyc
Ensembl Genes ENSRNOG00000031438 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000051573 ENTREZGENE
  ENSRNOT00000051573.5 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7132055 IMAGE-MGC_LOAD
InterPro SPATA19 UniProtKB/Swiss-Prot
KEGG Report rno:171403 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93204 IMAGE-MGC_LOAD
NCBI Gene 171403 ENTREZGENE
PANTHER PTHR36468 UniProtKB/Swiss-Prot
  SPERMATOGENESIS-ASSOCIATED PROTEIN 19, MITOCHONDRIAL UniProtKB/Swiss-Prot
Pfam SPATA19 UniProtKB/Swiss-Prot
PhenoGen Spata19 PhenoGen
RatGTEx ENSRNOG00000031438 RatGTEx
UniProt A0A8I5ZYJ6_RAT UniProtKB/TrEMBL
  A6JYE3 ENTREZGENE, UniProtKB/TrEMBL
  F1M9B7 ENTREZGENE, UniProtKB/TrEMBL
  Q920Q3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-22 Spata19  spermatogenesis associated 19  Spas1  spermatogenic specific-gene1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-11 Spas1  suppressor of Mec and Unc defects 1 homolog (C. elegans)  spergen-1  spermatogenic specific-gene1  Symbol updated to reflect Human and Mouse nomenclature 625702 APPROVED
2002-08-07 spergen-1  spermatogenic specific-gene1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the haploid spermatid mitochondria of the seminiferous tubules 634180
gene_regulation expression upregulated during the development of the testis 634180