Tspyl1 (TSPY-like 1) - Rat Genome Database

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Gene: Tspyl1 (TSPY-like 1) Rattus norvegicus
Analyze
Symbol: Tspyl1
Name: TSPY-like 1
RGD ID: 1307726
Description: Predicted to enable several functions, including chromatin binding activity; histone binding activity; and identical protein binding activity. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of chromatin. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in gonadal dysgenesis and sudden infant death syndrome. Orthologous to several human genes including TSPYL1 (TSPY like 1); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding (Ensembl: lncRNA)
RefSeq Status: PROVISIONAL
Previously known as: Al8; testis-specific protein, Y-encoded-like; testis-specific protein, Y-encoded-like 1; testis-specific Y-encoded-like protein 1; Tspyl
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
GRCr82039,637,035 - 39,639,594 (+)NCBIGRCr8
mRatBN7.22038,082,003 - 38,084,562 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2038,081,951 - 38,084,554 (-)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl2038,082,009 - 38,084,563 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2039,799,041 - 39,801,600 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02039,458,158 - 39,460,717 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02040,177,989 - 40,180,548 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02041,083,317 - 41,085,876 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2041,083,317 - 41,085,875 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02042,813,240 - 42,815,799 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42038,622,288 - 38,624,847 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12038,645,298 - 38,647,857 (+)NCBI
Celera2038,864,524 - 38,867,083 (+)NCBICelera
Cytogenetic Map20q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleolus  (ISO)
nucleoplasm  (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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function. Puffenberger EG, etal., Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11689-94. Epub 2004 Jul 23.
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. 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:23382074  


Genomics

Comparative Map Data
Tspyl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82039,637,035 - 39,639,594 (+)NCBIGRCr8
mRatBN7.22038,082,003 - 38,084,562 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2038,081,951 - 38,084,554 (-)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl2038,082,009 - 38,084,563 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2039,799,041 - 39,801,600 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02039,458,158 - 39,460,717 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02040,177,989 - 40,180,548 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02041,083,317 - 41,085,876 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2041,083,317 - 41,085,875 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02042,813,240 - 42,815,799 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42038,622,288 - 38,624,847 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12038,645,298 - 38,647,857 (+)NCBI
Celera2038,864,524 - 38,867,083 (+)NCBICelera
Cytogenetic Map20q12NCBI
TSPYL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386116,274,858 - 116,279,930 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6116,267,760 - 116,279,930 (-)EnsemblGRCh38hg38GRCh38
GRCh376116,596,021 - 116,601,093 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366116,704,437 - 116,707,973 (-)NCBINCBI36Build 36hg18NCBI36
Build 346116,705,909 - 116,706,596NCBI
Celera6117,339,059 - 117,344,311 (-)NCBICelera
Cytogenetic Map6q22.1NCBI
HuRef6114,176,189 - 114,181,447 (-)NCBIHuRef
CHM1_16116,859,915 - 116,865,188 (-)NCBICHM1_1
T2T-CHM13v2.06117,458,843 - 117,463,912 (-)NCBIT2T-CHM13v2.0
Tspyl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391034,158,186 - 34,160,881 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1034,158,186 - 34,161,271 (+)EnsemblGRCm39 Ensembl
GRCm381034,282,190 - 34,284,885 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1034,282,190 - 34,285,275 (+)EnsemblGRCm38mm10GRCm38
MGSCv371034,001,996 - 34,004,691 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361033,971,659 - 33,974,302 (+)NCBIMGSCv36mm8
Celera1035,191,843 - 35,194,538 (+)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1018.85NCBI
Tspyl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955526539,178 - 552,120 (+)NCBIChiLan1.0ChiLan1.0
TSPYL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25136,284,880 - 136,288,191 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16134,177,858 - 134,181,032 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06114,079,317 - 114,082,540 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16118,224,975 - 118,228,365 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6118,226,765 - 118,228,081 (-)Ensemblpanpan1.1panPan2
TSPYL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11271,933,904 - 71,937,508 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1271,935,792 - 71,937,285 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1271,694,379 - 71,697,628 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01272,815,541 - 72,818,775 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11272,168,461 - 72,170,993 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01272,009,251 - 72,012,170 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01272,398,241 - 72,400,894 (-)NCBIUU_Cfam_GSD_1.0
Tspyl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946107,132,709 - 107,135,622 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936824859,235 - 860,503 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936824857,696 - 860,604 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TSPYL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl181,908,075 - 81,909,249 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1181,906,168 - 81,909,461 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2192,021,582 - 92,025,154 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TSPYL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11357,536,638 - 57,538,810 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1357,536,749 - 57,538,071 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604029,860,269 - 29,863,858 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tspyl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248562,222,446 - 2,225,405 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tspyl1
4 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:139
Count of miRNA genes:113
Interacting mature miRNAs:120
Transcripts:ENSRNOT00000000660
Prediction methods: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
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203161428444396023Rat

Markers in Region
BE102382  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,084,095 - 38,084,283 (+)MAPPERmRatBN7.2
Rnor_6.02041,085,410 - 41,085,597NCBIRnor6.0
Rnor_5.02042,815,333 - 42,815,520UniSTSRnor5.0
RGSC_v3.42038,624,381 - 38,624,568UniSTSRGSC3.4
Celera2038,866,617 - 38,866,804UniSTS
RH 3.4 Map20415.2UniSTS
Cytogenetic Map20q12UniSTS
Tspyl  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,082,832 - 38,083,266 (+)MAPPERmRatBN7.2
Rnor_6.02041,084,147 - 41,084,580NCBIRnor6.0
Rnor_5.02042,814,070 - 42,814,503UniSTSRnor5.0
RGSC_v3.42038,623,118 - 38,623,551UniSTSRGSC3.4
Celera2038,865,354 - 38,865,787UniSTS
Cytogenetic Map20q12UniSTS
RH133775  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22038,084,362 - 38,084,542 (+)MAPPERmRatBN7.2
Rnor_6.02041,085,677 - 41,085,856NCBIRnor6.0
Rnor_5.02042,815,600 - 42,815,779UniSTSRnor5.0
RGSC_v3.42038,624,648 - 38,624,827UniSTSRGSC3.4
Celera2038,866,884 - 38,867,063UniSTS
RH 3.4 Map20404.43UniSTS
Cytogenetic Map20q12UniSTS


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000660   ⟹   ENSRNOP00000000660
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2038,081,951 - 38,084,554 (-)Ensembl
Rnor_6.0 Ensembl2041,083,317 - 41,085,875 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102871
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2038,082,009 - 38,084,563 (+)Ensembl
RefSeq Acc Id: NM_001013033   ⟹   NP_001013051
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82039,637,035 - 39,639,594 (+)NCBI
mRatBN7.22038,082,003 - 38,084,562 (+)NCBI
Rnor_6.02041,083,317 - 41,085,876 (+)NCBI
Rnor_5.02042,813,240 - 42,815,799 (+)NCBI
RGSC_v3.42038,622,288 - 38,624,847 (+)RGD
Celera2038,864,524 - 38,867,083 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001013051 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81955 (Get FASTA)   NCBI Sequence Viewer  
  EDL87782 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001013051   ⟸   NM_001013033
- UniProtKB: Q642B1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000660   ⟸   ENSRNOT00000000660

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q642B1-F1-model_v2 AlphaFold Q642B1 1-379 view protein structure

Transcriptome

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

Promoters
RGD ID:13701640
Promoter ID:EPDNEW_R12163
Type:initiation region
Name:Tspyl1_1
Description:TSPY-like 1
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_6.02041,083,317 - 41,083,377EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307726 AgrOrtholog
BioCyc Gene G2FUF-3553 BioCyc
Ensembl Genes ENSRNOG00000000549 Ensembl
  ENSRNOG00000063919 Ensembl
Gene3D-CATH 1.20.5.1500 UniProtKB/TrEMBL
  Nucleosome assembly protein UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7123128 IMAGE-MGC_LOAD
InterPro NAP-like_sf UniProtKB/TrEMBL
  NAP_family UniProtKB/TrEMBL
KEGG Report rno:29544 UniProtKB/TrEMBL
MGC_CLONE MGC:94049 IMAGE-MGC_LOAD
NCBI Gene 29544 ENTREZGENE
PANTHER NAP_family UniProtKB/TrEMBL
  TESTIS-SPECIFIC Y-ENCODED-LIKE PROTEIN 1 UniProtKB/TrEMBL
Pfam NAP UniProtKB/TrEMBL
PhenoGen Tspyl1 PhenoGen
RatGTEx ENSRNOG00000000549 RatGTEx
  ENSRNOG00000063919 RatGTEx
Superfamily-SCOP SSF143113 UniProtKB/TrEMBL
UniProt Q642B1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Tspyl1  TSPY-like 1  Tspyl1  testis-specific protein, Y-encoded-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Tspyl1  testis-specific protein, Y-encoded-like 1  Tspyl  testis-specific protein, Y-encoded-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Tspyl  testis-specific protein, Y-encoded-like  Tspyl_predicted  testis-specific protein, Y-encoded-like (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tspyl_predicted  testis-specific protein, Y-encoded-like (predicted)      Symbol and Name status set to approved 70820 APPROVED