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: PROVISIONAL
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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81643,946,879 - 43,956,268 (-)NCBIGRCr8
mRatBN7.21637,213,809 - 37,223,169 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1637,213,812 - 37,223,164 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1642,565,512 - 42,574,843 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01645,926,325 - 45,935,654 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01641,307,277 - 41,316,623 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01639,961,160 - 39,970,530 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1639,961,149 - 39,970,532 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01639,736,325 - 39,745,690 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1635,340,115 - 35,349,446 (-)NCBICelera
Cytogenetic Map16p11NCBI
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

Biological Process

Cellular Component
axoneme  (IBA)
cytoplasm  (ISO)

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 (-)NCBIGRCr8
mRatBN7.21637,213,809 - 37,223,169 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1637,213,812 - 37,223,164 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1642,565,512 - 42,574,843 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01645,926,325 - 45,935,654 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01641,307,277 - 41,316,623 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01639,961,160 - 39,970,530 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1639,961,149 - 39,970,532 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01639,736,325 - 39,745,690 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
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 (-)EnsemblGRCh38hg38GRCh38
GRCh374177,105,730 - 177,116,736 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364177,342,719 - 177,353,816 (-)NCBINCBI36Build 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 Ensembl
GRCm38854,600,781 - 54,610,098 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl854,600,781 - 54,610,098 (+)EnsemblGRCm38mm10GRCm38
MGSCv37855,686,134 - 55,695,451 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1648,859,131 - 48,871,328 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01655,672,037 - 55,684,245 (+)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247697,222,835 - 7,234,161 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Spata4
49 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
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)162173597566735975Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)163195152060148445Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat


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 7
Low 1 2 2 6 1 1 2
Below cutoff 1 2 11 6 6 6 5 6 35 1 10 5 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071331   ⟹   ENSRNOP00000067346
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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: PROVISIONAL
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
Protein Sequences
Protein RefSeqs NP_001002852 (Get FASTA)   NCBI Sequence Viewer  
  XP_006253157 (Get FASTA)   NCBI Sequence Viewer  
  XP_038950433 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT70838 (Get FASTA)   NCBI Sequence Viewer  
  EDL78951 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000067346
  ENSRNOP00000067346.3
Reference Protein Sequences
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
- UniProtKB: A6JPH1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq 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
  ENSRNOT00000071331.3 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
InterPro Calponin-like_dom_sf UniProtKB/TrEMBL
  CH-domain UniProtKB/TrEMBL
  DUF1042 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