Tprn (taperin) - Rat Genome Database

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Gene: Tprn (taperin) Rattus norvegicus
Analyze
Symbol: Tprn
Name: taperin
RGD ID: 1562935
Description: Predicted to enable phosphatase binding activity. Predicted to be involved in auditory receptor cell stereocilium organization; sensory perception of sound; and stereocilium maintenance. Predicted to be located in stereocilium. Predicted to be active in stereocilium base. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 79. Orthologous to human TPRN (taperin); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC499749; LOC499749; similar to RIKEN cDNA C430004E15
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
mRatBN7.238,076,164 - 8,083,642 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,075,137 - 8,083,642 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,180,673 - 11,188,141 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0319,766,903 - 19,774,371 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0317,956,746 - 17,964,214 (+)NCBIRnor_WKY
Rnor_6.032,480,232 - 2,487,710 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,480,232 - 2,487,710 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,461,645 - 2,469,123 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,426,263 - 3,433,741 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera32,902,712 - 2,910,187 (+)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
stereocilium  (ISO,ISS)
stereocilium base  (IBA,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. OMIM Disease Annotation Pipeline OMIM Disease Annotation 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
5. 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:20170898   PMID:20170899   PMID:27269051   PMID:27693694   PMID:30380417  


Genomics

Comparative Map Data
Tprn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.238,076,164 - 8,083,642 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,075,137 - 8,083,642 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,180,673 - 11,188,141 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0319,766,903 - 19,774,371 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0317,956,746 - 17,964,214 (+)NCBIRnor_WKY
Rnor_6.032,480,232 - 2,487,710 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,480,232 - 2,487,710 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,461,645 - 2,469,123 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,426,263 - 3,433,741 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera32,902,712 - 2,910,187 (+)NCBICelera
Cytogenetic Map3p13NCBI
TPRN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389137,191,619 - 137,200,741 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl9137,191,617 - 137,204,193 (-)EnsemblGRCh38hg38GRCh38
GRCh379140,086,071 - 140,095,193 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,205,890 - 139,214,378 (-)NCBINCBI36Build 36hg18NCBI36
Build 349137,361,905 - 137,370,394NCBI
Celera9110,600,193 - 110,608,787 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,546,086 - 109,554,965 (-)NCBIHuRef
CHM1_19140,234,758 - 140,243,897 (-)NCBICHM1_1
T2T-CHM13v2.09149,429,282 - 149,438,404 (-)NCBIT2T-CHM13v2.0
Tprn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,152,610 - 25,159,898 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,152,630 - 25,159,897 (+)EnsemblGRCm39 Ensembl
GRCm38225,262,598 - 25,269,886 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,262,618 - 25,269,885 (+)EnsemblGRCm38mm10GRCm38
MGSCv37225,118,118 - 25,125,406 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,084,627 - 25,091,891 (+)NCBIMGSCv36mm8
Celera224,990,289 - 24,997,577 (+)NCBICelera
Cytogenetic Map2A3NCBI
Tprn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,197,280 - 5,203,445 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,196,871 - 5,205,945 (-)NCBIChiLan1.0ChiLan1.0
TPRN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19137,220,640 - 137,229,053 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v09108,251,235 - 108,261,541 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TPRN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha947,655,400 - 47,663,450 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,330,256 - 49,338,306 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,329,451 - 49,338,321 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,106,655 - 48,114,705 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,405,468 - 48,413,517 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,452,626 - 48,460,676 (+)NCBIUU_Cfam_GSD_1.0
Tprn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,580,345 - 202,588,325 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936669786,808 - 794,155 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936669786,569 - 794,713 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TPRN
(Sus scrofa - pig)		 No map positions available.
TPRN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112988,225 - 997,914 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660584,307,339 - 4,317,459 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tprn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624760750,871 - 758,433 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624760750,833 - 758,329 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tprn
6 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:207
Count of miRNA genes:138
Interacting mature miRNAs:153
Transcripts:ENSRNOT00000014489
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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat

Markers in Region
RH128666  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.238,083,372 - 8,083,584 (+)MAPPERmRatBN7.2
Rnor_6.032,487,441 - 2,487,652NCBIRnor6.0
Rnor_5.032,468,854 - 2,469,065UniSTSRnor5.0
RGSC_v3.433,433,472 - 3,433,683UniSTSRGSC3.4
Celera32,909,918 - 2,910,129UniSTS
Cytogenetic Map3p13UniSTS


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 27 10
Low 43 57 41 19 41 8 11 31 8 31 11 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014489   ⟹   ENSRNOP00000014489
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,075,137 - 8,083,642 (+)Ensembl
Rnor_6.0 Ensembl32,480,232 - 2,487,710 (+)Ensembl
RefSeq Acc Id: NM_001024309   ⟹   NP_001019480
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,076,164 - 8,083,642 (+)NCBI
Rnor_6.032,480,232 - 2,487,710 (+)NCBI
Rnor_5.032,461,645 - 2,469,123 (+)NCBI
RGSC_v3.433,426,263 - 3,433,741 (+)RGD
Celera32,902,712 - 2,910,187 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001019480 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83928 (Get FASTA)   NCBI Sequence Viewer  
  EDL93622 (Get FASTA)   NCBI Sequence Viewer  
  Q5XHX2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001019480   ⟸   NM_001024309
- UniProtKB: Q5XHX2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000014489   ⟸   ENSRNOT00000014489

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XHX2-F1-model_v2 AlphaFold Q5XHX2 1-753 view protein structure

Transcriptome

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

Promoters
RGD ID:13691866
Promoter ID:EPDNEW_R2390
Type:initiation region
Name:Tprn_1
Description:taperin
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_6.032,480,181 - 2,480,241EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562935 AgrOrtholog
BioCyc Gene G2FUF-50467 BioCyc
Ensembl Genes ENSRNOG00000010896 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000014489 ENTREZGENE
  ENSRNOP00000014489.4 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014489 ENTREZGENE
  ENSRNOT00000014489.6 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7135551 IMAGE-MGC_LOAD
InterPro Phostensin/Taperin_N_dom UniProtKB/Swiss-Prot
  Phostensin/Taperin_PP1-bd_dom UniProtKB/Swiss-Prot
  PPP1R18/Tprn UniProtKB/Swiss-Prot
KEGG Report rno:499749 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95335 IMAGE-MGC_LOAD
NCBI Gene 499749 ENTREZGENE
PANTHER PTHR21685 UniProtKB/Swiss-Prot
  PTHR21685:SF1 UniProtKB/Swiss-Prot
Pfam Phostensin UniProtKB/Swiss-Prot
  Phostensin_N UniProtKB/Swiss-Prot
PhenoGen Tprn PhenoGen
UniProt Q5XHX2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-05-26 Tprn  taperin  LOC499749  similar to RIKEN cDNA C430004E15  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC499749  similar to RIKEN cDNA C430004E15      Symbol and Name status set to provisional 70820 PROVISIONAL