Spmip7 (sperm microtubule inner protein 7) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Spmip7 (sperm microtubule inner protein 7) Rattus norvegicus
Analyze
Symbol: Spmip7 (Ensembl: Spata48)
Name: sperm microtubule inner protein 7 (Ensembl:spermatogenesis associated 48)
RGD ID: 1309870
Description: Predicted to be involved in spermatogenesis. Orthologous to human SPMIP7 (sperm microtubule inner protein 7); INTERACTS WITH 17beta-estradiol; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical LOC289778; hypothetical protein LOC289778; LOC289778; RGD1309870; Spata48; spermatogenesis associated 48; spermatogenesis-associated protein 48; uncharacterized protein C7orf72 homolog; uncharacterized protein LOC289778
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81490,244,087 - 90,299,294 (+)NCBIGRCr8
mRatBN7.21486,030,427 - 86,085,644 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1486,030,655 - 86,085,644 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1490,441,207 - 90,496,323 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01491,685,967 - 91,741,070 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01488,153,160 - 88,208,245 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01491,556,782 - 91,614,099 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1491,557,601 - 91,613,540 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01491,344,025 - 91,399,177 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41492,358,993 - 92,383,442 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11492,373,932 - 92,402,586 (+)NCBI
Celera1485,066,567 - 85,091,002 (+)NCBICelera
Cytogenetic Map14q21NCBI
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
spermatogenesis  (IBA,ISO)

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
Spmip7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81490,244,087 - 90,299,294 (+)NCBIGRCr8
mRatBN7.21486,030,427 - 86,085,644 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1486,030,655 - 86,085,644 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1490,441,207 - 90,496,323 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01491,685,967 - 91,741,070 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01488,153,160 - 88,208,245 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01491,556,782 - 91,614,099 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1491,557,601 - 91,613,540 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01491,344,025 - 91,399,177 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41492,358,993 - 92,383,442 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11492,373,932 - 92,402,586 (+)NCBI
Celera1485,066,567 - 85,091,002 (+)NCBICelera
Cytogenetic Map14q21NCBI
SPMIP7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38750,095,883 - 50,159,256 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl750,095,883 - 50,159,256 (+)EnsemblGRCh38hg38GRCh38
GRCh37750,135,479 - 50,198,852 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36750,106,348 - 50,169,398 (+)NCBINCBI36Build 36hg18NCBI36
Celera750,229,773 - 50,293,484 (+)NCBICelera
Cytogenetic Map7p12.2NCBI
HuRef750,016,509 - 50,079,746 (+)NCBIHuRef
CHM1_1750,137,668 - 50,201,160 (+)NCBICHM1_1
T2T-CHM13v2.0750,257,048 - 50,320,459 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2750,172,871 - 50,236,064 (+)NCBI
Spmip7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391111,412,089 - 11,465,658 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1111,412,094 - 11,465,192 (+)EnsemblGRCm39 Ensembl
GRCm381111,463,744 - 11,515,192 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1111,462,094 - 11,515,192 (+)EnsemblGRCm38mm10GRCm38
MGSCv371111,389,269 - 11,415,193 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361111,389,269 - 11,415,193 (+)NCBIMGSCv36mm8
Celera1111,948,754 - 11,974,675 (+)NCBICelera
Cytogenetic Map11A1NCBI
cM Map116.93NCBI
Spmip7
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554563,845,811 - 3,885,592 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554563,845,875 - 3,885,908 (-)NCBIChiLan1.0ChiLan1.0
SPMIP7
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2654,974,211 - 55,040,496 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17103,298,934 - 103,365,219 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0750,738,047 - 50,802,041 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1750,984,468 - 51,046,970 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl750,984,231 - 51,047,029 (+)Ensemblpanpan1.1panPan2
SPMIP7
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1181,591,336 - 1,652,140 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha181,453,660 - 1,517,130 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0181,519,619 - 1,583,103 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl181,520,878 - 1,580,617 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1181,494,091 - 1,557,561 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0181,491,000 - 1,554,464 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0181,627,204 - 1,690,691 (+)NCBIUU_Cfam_GSD_1.0
Spmip7
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118104,781,206 - 104,843,303 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366861,680,341 - 1,742,287 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366861,679,572 - 1,744,008 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPMIP7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9136,188,608 - 136,235,985 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19136,189,235 - 136,224,000 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29149,715,727 - 149,763,088 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPMIP7
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1218,646,498 - 8,710,205 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl218,646,586 - 8,709,554 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606213,567,473 - 13,630,525 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Spmip7
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247403,986,556 - 4,027,580 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247403,986,528 - 4,029,876 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Spmip7
250 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:50
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000057067
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
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)148205747195876975Rat


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 4 11 52 12 19
Below cutoff 2 16 22 17 8 17 2 2 22 22 13 3 2

Sequence


RefSeq Acc Id: ENSRNOT00000038733   ⟹   ENSRNOP00000033938
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1486,030,655 - 86,085,644 (+)Ensembl
Rnor_6.0 Ensembl1491,557,601 - 91,613,540 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000057067   ⟹   ENSRNOP00000053899
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1491,588,940 - 91,613,483 (+)Ensembl
RefSeq Acc Id: NM_001106018   ⟹   NP_001099488
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81490,274,851 - 90,299,294 (+)NCBI
mRatBN7.21486,061,198 - 86,085,644 (+)NCBI
Rnor_6.01491,588,940 - 91,613,483 (+)NCBI
Rnor_5.01491,344,025 - 91,399,177 (+)NCBI
RGSC_v3.41492,358,993 - 92,383,442 (+)RGD
Celera1485,066,567 - 85,091,002 (+)RGD
Sequence:
RefSeq Acc Id: NM_001401548   ⟹   NP_001388477
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81490,245,911 - 90,299,293 (+)NCBI
mRatBN7.21486,032,251 - 86,085,643 (+)NCBI
RefSeq Acc Id: NM_001401549   ⟹   NP_001388478
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81490,245,911 - 90,299,293 (+)NCBI
mRatBN7.21486,032,251 - 86,085,643 (+)NCBI
RefSeq Acc Id: NM_001401550   ⟹   NP_001388479
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81490,244,087 - 90,299,293 (+)NCBI
mRatBN7.21486,030,427 - 86,085,643 (+)NCBI
RefSeq Acc Id: NM_001401551   ⟹   NP_001388480
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81490,267,377 - 90,299,293 (+)NCBI
mRatBN7.21486,053,724 - 86,085,643 (+)NCBI
RefSeq Acc Id: NM_001401552   ⟹   NP_001388481
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81490,267,884 - 90,299,293 (+)NCBI
mRatBN7.21486,054,231 - 86,085,643 (+)NCBI
RefSeq Acc Id: XM_063272955   ⟹   XP_063129025
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81490,267,404 - 90,299,293 (+)NCBI
RefSeq Acc Id: NP_001099488   ⟸   NM_001106018
- Peptide Label: isoform e
- UniProtKB: A6KJA1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000053899   ⟸   ENSRNOT00000057067
RefSeq Acc Id: ENSRNOP00000033938   ⟸   ENSRNOT00000038733
RefSeq Acc Id: NP_001388479   ⟸   NM_001401550
- Peptide Label: isoform c
RefSeq Acc Id: NP_001388477   ⟸   NM_001401548
- Peptide Label: isoform a
- UniProtKB: D4A9H9 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001388478   ⟸   NM_001401549
- Peptide Label: isoform b
RefSeq Acc Id: NP_001388480   ⟸   NM_001401551
- Peptide Label: isoform d
RefSeq Acc Id: NP_001388481   ⟸   NM_001401552
- Peptide Label: isoform e
- UniProtKB: A6KJA1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063129025   ⟸   XM_063272955
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A9H9-F1-model_v2 AlphaFold D4A9H9 1-445 view protein structure

Transcriptome

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

Promoters
RGD ID:13699493
Promoter ID:EPDNEW_R10015
Type:initiation region
Name:RGD1309870_1
Description:hypothetical LOC289778
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_6.01491,557,598 - 91,557,658EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309870 AgrOrtholog
BioCyc Gene G2FUF-15000 BioCyc
Ensembl Genes ENSRNOG00000037621 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038733 ENTREZGENE
  ENSRNOT00000038733.3 UniProtKB/TrEMBL
InterPro DUF4540 UniProtKB/TrEMBL
KEGG Report rno:289778 UniProtKB/TrEMBL
NCBI Gene 289778 ENTREZGENE
PANTHER PTHR34759 UniProtKB/TrEMBL
  SPERMATOGENESIS-ASSOCIATED PROTEIN 48 UniProtKB/TrEMBL
Pfam DUF4540 UniProtKB/TrEMBL
PhenoGen Spmip7 PhenoGen
RatGTEx ENSRNOG00000037621 RatGTEx
UniProt A6KJA1 ENTREZGENE, UniProtKB/TrEMBL
  D4A9H9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-05-08 Spmip7  sperm microtubule inner protein 7  Spata48  spermatogenesis associated 48  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2018-09-05 Spata48  spermatogenesis associated 48  RGD1309870  hypothetical LOC289778  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1309870  hypothetical LOC289778   RGD1309870_predicted  hypothetical LOC289778 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1309870_predicted  hypothetical LOC289778 (predicted)  LOC289778_predicted  hypothetical LOC289778 (predicted)  Symbol and Name status set to approved 1331353 APPROVED