Spata4 (spermatogenesis associated 4) - Rat Genome Database

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Gene: Spata4 (spermatogenesis associated 4) Rattus norvegicus
Analyze
Symbol: Spata4
Name: spermatogenesis associated 4
RGD ID: 1303065
Description: Predicted to enable microtubule binding activity. Predicted to be involved in regulation of cytoskeleton organization. Predicted to be located in cytoplasm. Predicted to be active in axoneme. Orthologous to human SPATA4 (spermatogenesis associated 4); INTERACTS WITH bisphenol A; cadmium dichloride; 1,2-dichloroethane (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: spermatogenesis related gene 2; spermatogenesis-associated 4; spermatogenesis-associated protein 4; Srg2; Tsarg2
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
GRCr81643,946,879 - 43,956,268 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1643,946,881 - 43,956,231 (-)EnsemblGRCr8
mRatBN7.21637,213,809 - 37,223,169 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1637,213,812 - 37,223,164 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1642,565,512 - 42,574,843 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01645,926,325 - 45,935,654 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01641,307,277 - 41,316,623 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01639,961,160 - 39,970,530 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1639,961,149 - 39,970,532 (-)Ensemblrn6Rnor6.0
Rnor_5.01639,736,325 - 39,745,690 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera1635,340,115 - 35,349,446 (-)NCBICelera
Cytogenetic Map16p11NCBI
JBrowse:




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

Biological Process

Cellular Component
axoneme  (IBA)
cytoplasm  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (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. Cloning and characterization of testis-specific spermatogenesis associated gene homologous to human SPATA4 in rat. Liu SF, etal., Biol Pharm Bull 2004 Nov;27(11):1867-70.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16336790   PMID:17662146  


Genomics

Comparative Map Data
Spata4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81643,946,879 - 43,956,268 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1643,946,881 - 43,956,231 (-)EnsemblGRCr8
mRatBN7.21637,213,809 - 37,223,169 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1637,213,812 - 37,223,164 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1642,565,512 - 42,574,843 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01645,926,325 - 45,935,654 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01641,307,277 - 41,316,623 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01639,961,160 - 39,970,530 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1639,961,149 - 39,970,532 (-)Ensemblrn6Rnor6.0
Rnor_5.01639,736,325 - 39,745,690 (-)NCBIRnor_5.0Rnor_5.0rn5
Celera1635,340,115 - 35,349,446 (-)NCBICelera
Cytogenetic Map16p11NCBI
SPATA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384176,184,579 - 176,195,585 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4176,184,579 - 176,195,585 (-)Ensemblhg38GRCh38
GRCh374177,105,730 - 177,116,736 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364177,342,719 - 177,353,816 (-)NCBIBuild 36Build 36hg18NCBI36
Build 344177,480,873 - 177,491,971NCBI
Celera4174,433,712 - 174,444,808 (-)NCBICelera
Cytogenetic Map4q34.2NCBI
HuRef4172,856,406 - 172,867,496 (-)NCBIHuRef
CHM1_14177,082,440 - 177,093,526 (-)NCBICHM1_1
T2T-CHM13v2.04179,522,953 - 179,533,935 (-)NCBIT2T-CHM13v2.0
Spata4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39855,053,816 - 55,063,133 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl855,053,816 - 55,063,133 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38854,600,781 - 54,610,098 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl854,600,781 - 54,610,098 (+)Ensemblmm10GRCm38
MGSCv37855,686,134 - 55,695,451 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36856,099,478 - 56,108,795 (+)NCBIMGSCv36mm8
Celera857,314,160 - 57,323,463 (+)NCBICelera
Cytogenetic Map8B1.3NCBI
cM Map829.27NCBI
Spata4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540331,548,676 - 31,556,182 (+)Ensembl
ChiLan1.0NW_00495540331,548,696 - 31,558,177 (+)NCBIChiLan1.0ChiLan1.0
SPATA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23173,900,209 - 173,911,434 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14174,281,912 - 174,293,129 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04168,366,918 - 168,378,630 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14180,601,038 - 180,612,014 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4180,601,038 - 180,612,014 (-)EnsemblpanPan2panpan1.1
SPATA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11653,358,359 - 53,369,569 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1653,358,371 - 53,369,452 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1648,859,131 - 48,871,328 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01655,672,037 - 55,684,245 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1655,671,975 - 55,684,243 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11653,566,116 - 53,578,293 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01654,161,695 - 54,173,917 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01654,400,417 - 54,412,636 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Spata4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494326,361,250 - 26,380,507 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365166,785,397 - 6,794,777 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365166,785,199 - 6,794,777 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPATA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1538,695,934 - 38,705,941 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11538,698,822 - 38,705,784 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21544,398,711 - 44,405,685 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SPATA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.17122,259,054 - 122,273,218 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl7122,259,066 - 122,272,691 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666037102,338,235 - 102,351,904 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Spata4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247697,224,690 - 7,234,220 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247697,222,835 - 7,234,161 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Spata4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11333,828,315 - 33,837,673 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Spata4
42 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:71
Interacting mature miRNAs:76
Transcripts:ENSRNOT00000071331
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
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16435482249354822Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)1638712345387123Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1638712345387123Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16423421249757901Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)163692878281928782Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16423421266955197Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162846870173468701Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)163236104377361043Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16423421253708481Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)163105803976058039Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)163439829479398294Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683908666195506Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338679049757901Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16474422249744222Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683908666195506Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)163188527176885271Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683908666195506Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161773081872536785Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683908652786090Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)161590580260905802Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683908666195506Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16330168348301683Rat


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
sensory system
visual system
3 8 5 67 22 22 11 8 11 4 47 24 58 2 32 11 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000071331   ⟹   ENSRNOP00000067346
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1643,946,881 - 43,956,231 (-)Ensembl
mRatBN7.2 Ensembl1637,213,812 - 37,223,164 (-)Ensembl
Rnor_6.0 Ensembl1639,961,149 - 39,970,532 (-)Ensembl
RefSeq Acc Id: NM_001002852   ⟹   NP_001002852
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81643,946,881 - 43,956,231 (-)NCBI
mRatBN7.21637,213,812 - 37,223,164 (-)NCBI
Rnor_6.01639,961,174 - 39,970,524 (-)NCBI
Rnor_5.01639,736,325 - 39,745,690 (-)NCBI
Celera1635,340,115 - 35,349,446 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253095   ⟹   XP_006253157
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81643,946,879 - 43,956,268 (-)NCBI
mRatBN7.21637,213,809 - 37,223,169 (-)NCBI
Rnor_6.01639,961,160 - 39,970,530 (-)NCBI
Rnor_5.01639,736,325 - 39,745,690 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039094505   ⟹   XP_038950433
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81643,946,879 - 43,956,244 (-)NCBI
mRatBN7.21637,213,809 - 37,223,060 (-)NCBI
RefSeq Acc Id: NP_001002852   ⟸   NM_001002852
- UniProtKB: Q6DNA4 (UniProtKB/TrEMBL),   M0RCM3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253157   ⟸   XM_006253095
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000067346   ⟸   ENSRNOT00000071331
RefSeq Acc Id: XP_038950433   ⟸   XM_039094505
- Peptide Label: isoform X2
Protein Domains
Calponin-homology (CH)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RCM3-F1-model_v2 AlphaFold M0RCM3 1-316 view protein structure

Transcriptome

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

Promoters
RGD ID:13700081
Promoter ID:EPDNEW_R10605
Type:initiation region
Name:Spata4_1
Description:spermatogenesis associated 4
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_6.01639,970,506 - 39,970,566EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303065 AgrOrtholog
BioCyc Gene G2FUF-11471 BioCyc
Ensembl Genes ENSRNOG00000048035 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071331 ENTREZGENE
  ENSRNOT00000071331.4 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
InterPro Calponin-like_dom_sf UniProtKB/TrEMBL
  CH-domain UniProtKB/TrEMBL
  DUF1042 UniProtKB/TrEMBL
  Spermatogenesis_Ciliary_MAP UniProtKB/TrEMBL
KEGG Report rno:306441 UniProtKB/TrEMBL
NCBI Gene 306441 ENTREZGENE
PANTHER SPERMATOGENESIS-ASSOCIATED 4-RELATED UniProtKB/TrEMBL
  SPERMATOGENESIS-ASSOCIATED PROTEIN 4 UniProtKB/TrEMBL
Pfam DUF1042 UniProtKB/TrEMBL
PhenoGen Spata4 PhenoGen
PROSITE PS50021 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000048035 RatGTEx
UniProt A6JPH1 ENTREZGENE, UniProtKB/TrEMBL
  M0RCM3 ENTREZGENE, UniProtKB/TrEMBL
  Q6DNA4 ENTREZGENE
UniProt Secondary Q6DNA4 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Spata4  spermatogenesis associated 4    spermatogenesis-associated 4  Name updated 1299863 APPROVED
2005-02-14 Spata4  spermatogenesis-associated 4      Symbol and Name status set to provisional 70820 PROVISIONAL