Spag6l (sperm associated antigen 6-like) - Rat Genome Database

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Gene: Spag6l (sperm associated antigen 6-like) Rattus norvegicus
Analyze
Symbol: Spag6l
Name: sperm associated antigen 6-like
RGD ID: 1310892
Description: Predicted to enable microtubule binding activity. Predicted to be involved in epithelial cilium movement involved in extracellular fluid movement and plasma membrane bounded cell projection organization. Predicted to act upstream of or within several processes, including cilium assembly; epithelial cilium movement involved in extracellular fluid movement; and stress fiber assembly. Predicted to be located in several cellular components, including cytoskeleton; cytosol; and lateral wall of outer hair cell. Predicted to be active in acrosomal vesicle; cytoskeleton; and sperm principal piece. Orthologous to human SPAG6 (sperm associated antigen 6); INTERACTS WITH 17alpha-ethynylestradiol; bisphenol A; 2,3',4,4',5-Pentachlorobiphenyl (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC360747; RGD1310892; similar to axoneme central apparatus protein; Spag6; sperm associated antigen 6; sperm-associated antigen 6
RGD Orthologs
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81197,677,840 - 97,773,580 (+)NCBIGRCr8
mRatBN7.21184,173,628 - 84,269,374 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1184,173,526 - 84,269,364 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1192,897,912 - 92,992,752 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01185,559,039 - 85,653,877 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01184,612,643 - 84,707,491 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01188,424,493 - 88,517,910 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1188,424,414 - 88,508,601 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01191,480,026 - 91,573,812 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,208,991 - 86,321,358 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11186,249,590 - 86,361,168 (+)NCBI
Celera1182,948,415 - 83,020,335 (+)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10684790   PMID:12167721   PMID:12391165   PMID:12477932   PMID:17699735   PMID:37169167  


Genomics

Comparative Map Data
Spag6l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81197,677,840 - 97,773,580 (+)NCBIGRCr8
mRatBN7.21184,173,628 - 84,269,374 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1184,173,526 - 84,269,364 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1192,897,912 - 92,992,752 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01185,559,039 - 85,653,877 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01184,612,643 - 84,707,491 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01188,424,493 - 88,517,910 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1188,424,414 - 88,508,601 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01191,480,026 - 91,573,812 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41186,208,991 - 86,321,358 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11186,249,590 - 86,361,168 (+)NCBI
Celera1182,948,415 - 83,020,335 (+)NCBICelera
Cytogenetic Map11q23NCBI
Spag6l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391616,570,880 - 16,647,177 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1616,570,880 - 16,647,320 (-)EnsemblGRCm39 Ensembl
GRCm381616,753,016 - 16,829,363 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1616,753,016 - 16,829,456 (-)EnsemblGRCm38mm10GRCm38
MGSCv371616,753,109 - 16,829,456 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361616,666,579 - 16,742,857 (-)NCBIMGSCv36mm8
Celera1617,324,276 - 17,401,286 (-)NCBICelera
Cytogenetic Map16A3NCBI
cM Map1610.39NCBI

Variants

.
Variants in Spag6l
559 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:120
Count of miRNA genes:102
Interacting mature miRNAs:106
Transcripts:ENSRNOT00000002513, ENSRNOT00000022328
Prediction methods:Microtar, 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
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat


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 10 11
Low 2 1 1 64 10 1
Below cutoff 2 4 14 4 15 4 4 5 2 1 11 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022328   ⟹   ENSRNOP00000022328
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1184,173,526 - 84,269,364 (+)Ensembl
Rnor_6.0 Ensembl1188,424,414 - 88,508,601 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106349   ⟹   ENSRNOP00000088293
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1184,173,628 - 84,269,364 (+)Ensembl
RefSeq Acc Id: NM_001034960   ⟹   NP_001030132
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81197,677,840 - 97,773,580 (+)NCBI
mRatBN7.21184,173,628 - 84,269,374 (+)NCBI
Rnor_6.01188,424,493 - 88,517,910 (+)NCBI
Rnor_5.01191,480,026 - 91,573,812 (+)NCBI
RGSC_v3.41186,208,991 - 86,321,358 (+)RGD
Celera1182,948,415 - 83,020,335 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001030132 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI04679 (Get FASTA)   NCBI Sequence Viewer  
  EDL77861 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022328.8
  ENSRNOP00000088293
  ENSRNOP00000088293.1
Reference Protein Sequences
RefSeq Acc Id: NP_001030132   ⟸   NM_001034960
- UniProtKB: Q3MHU1 (UniProtKB/TrEMBL),   A6JSP6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022328   ⟸   ENSRNOT00000022328
RefSeq Acc Id: ENSRNOP00000088293   ⟸   ENSRNOT00000106349

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LXV9-F1-model_v2 AlphaFold F1LXV9 1-487 view protein structure

Transcriptome

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

Promoters
RGD ID:13698342
Promoter ID:EPDNEW_R8867
Type:initiation region
Name:Spag6l_1
Description:sperm associated antigen 6-like
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_6.01188,424,466 - 88,424,526EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310892 AgrOrtholog
BioCyc Gene G2FUF-20557 BioCyc
Ensembl Genes ENSRNOG00000025787 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022328.8 UniProtKB/TrEMBL
  ENSRNOT00000106349 ENTREZGENE
  ENSRNOT00000106349.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7454069 IMAGE-MGC_LOAD
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Armadillo UniProtKB/TrEMBL
KEGG Report rno:360747 UniProtKB/TrEMBL
MGC_CLONE MGC:125222 IMAGE-MGC_LOAD
NCBI Gene 360747 ENTREZGENE
PANTHER SPERM-ASSOCIATED ANTIGEN 6 UniProtKB/TrEMBL
  SPERM-ASSOCIATED ANTIGEN 6 ARMADILLO REPEAT-CONTAINING UniProtKB/TrEMBL
Pfam Arm UniProtKB/TrEMBL
PhenoGen Spag6l PhenoGen
RatGTEx ENSRNOG00000025787 RatGTEx
SMART ARM UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt A6JSP6 ENTREZGENE, UniProtKB/TrEMBL
  F1LXV9_RAT UniProtKB/TrEMBL
  Q3MHU1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-13 Spag6l  sperm associated antigen 6-like  Spag6  sperm associated antigen 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-27 Spag6  sperm associated antigen 6  RGD1310892  similar to axoneme central apparatus protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1310892  similar to axoneme central apparatus protein  RGD1310892_predicted  similar to axoneme central apparatus protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1310892_predicted  similar to axoneme central apparatus protein (predicted)  LOC360747_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC360747_predicted  similar to axoneme central apparatus protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL