Tnp1 (transition protein 1) - Rat Genome Database

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Gene: Tnp1 (transition protein 1) Rattus norvegicus
Analyze
Symbol: Tnp1
Name: transition protein 1
RGD ID: 3884
Description: Predicted to enable DNA binding activity. Predicted to be involved in several processes, including nucleosome disassembly; regulation of gene expression; and spermatid nucleus differentiation. Predicted to act upstream of or within spermatogenesis. Located in male germ cell nucleus. Orthologous to human TNP1 (transition protein 1); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; allethrin; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: spermatid nuclear transition protein 1; STP-1; testis-specific basic protein; TP-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8982,043,669 - 82,044,278 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl982,043,672 - 82,044,278 (-)EnsemblGRCr8
mRatBN7.2974,594,463 - 74,595,072 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl974,594,466 - 74,595,274 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx983,049,184 - 83,049,793 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0988,178,079 - 88,178,688 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0986,564,825 - 86,565,434 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0980,294,837 - 80,295,446 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl980,294,840 - 80,295,446 (-)Ensemblrn6Rnor6.0
Rnor_5.0980,066,299 - 80,066,908 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4972,397,750 - 72,398,359 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera972,188,091 - 72,188,700 (-)NCBICelera
RGSC_v3.1972,544,732 - 72,545,341 (-)NCBI
Cytogenetic Map9q33NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromosome  (IEA)
male germ cell nucleus  (IBA,IDA)
nucleosome  (IBA,IEA,ISO,ISS)
nucleus  (IEA,ISO)

Molecular Function
DNA binding  (IBA,IEA,ISO,ISS)
protein binding  (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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Isolation of a cDNA clone for transition protein 1 (TP1), a major chromosomal protein of mammalian spermatids. Heidaran MA and Kistler WS, Gene 1987;54(2-3):281-4.
4. Nucleotide sequence of the Stp-1 gene coding for rat spermatid nuclear transition protein 1 (TP1): homology with protamine P1 and assignment of the mouse Stp-1 gene to chromosome 1. Heidaran MA, etal., Gene 1989 Jan 30;75(1):39-46.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. GOA pipeline RGD automated data pipeline
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
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:1112834   PMID:1627265   PMID:4829397   PMID:10781074   PMID:11315969   PMID:12573823   PMID:12743712   PMID:15083521   PMID:15163613   PMID:15189834   PMID:15489334   PMID:17261847  
PMID:19506090   PMID:28366643  


Genomics

Comparative Map Data
Tnp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8982,043,669 - 82,044,278 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl982,043,672 - 82,044,278 (-)EnsemblGRCr8
mRatBN7.2974,594,463 - 74,595,072 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl974,594,466 - 74,595,274 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx983,049,184 - 83,049,793 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0988,178,079 - 88,178,688 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0986,564,825 - 86,565,434 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0980,294,837 - 80,295,446 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl980,294,840 - 80,295,446 (-)Ensemblrn6Rnor6.0
Rnor_5.0980,066,299 - 80,066,908 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4972,397,750 - 72,398,359 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera972,188,091 - 72,188,700 (-)NCBICelera
RGSC_v3.1972,544,732 - 72,545,341 (-)NCBI
Cytogenetic Map9q33NCBI
TNP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382216,859,458 - 216,860,064 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2216,859,458 - 216,860,064 (-)Ensemblhg38GRCh38
GRCh372217,724,181 - 217,724,787 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362217,432,426 - 217,433,027 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342217,549,689 - 217,550,288NCBI
Celera2211,492,069 - 211,492,670 (-)NCBICelera
Cytogenetic Map2q35NCBI
HuRef2209,578,223 - 209,578,824 (-)NCBIHuRef
CHM1_12217,730,235 - 217,730,836 (-)NCBICHM1_1
T2T-CHM13v2.02217,341,898 - 217,342,504 (-)NCBIT2T-CHM13v2.0
Tnp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39173,054,233 - 73,055,058 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl173,054,233 - 73,055,068 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38173,015,074 - 73,015,899 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl173,015,074 - 73,015,909 (-)Ensemblmm10GRCm38
MGSCv37173,061,648 - 73,062,473 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36172,948,284 - 72,949,079 (-)NCBIMGSCv36mm8
Celera173,589,038 - 73,589,863 (-)NCBICelera
Cytogenetic Map1C3NCBI
cM Map136.94NCBI
Tnp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545316,387,527 - 16,388,890 (+)Ensembl
ChiLan1.0NW_00495545316,387,897 - 16,388,513 (+)NCBIChiLan1.0ChiLan1.0
TNP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213119,489,569 - 119,490,175 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B119,504,535 - 119,505,141 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B104,122,748 - 104,123,349 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B222,723,606 - 222,724,212 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B222,723,606 - 222,724,212 (-)EnsemblpanPan2panpan1.1
TNP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13723,742,875 - 23,743,417 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3723,727,538 - 23,743,365 (-)EnsemblcanFam3CanFam3.1
Tnp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303172,120,406 - 172,121,032 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936586504,864 - 505,447 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936586504,864 - 505,447 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15119,037,496 - 119,038,105 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.115119,037,492 - 119,038,099 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215131,800,371 - 131,801,028 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TNP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110102,703,116 - 102,703,747 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10102,703,325 - 102,703,691 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604096,709,921 - 96,711,971 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248238,269,758 - 8,270,134 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tnp1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14146,516,184 - 146,516,786 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tnp1
3 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000023769
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)94002992585029925Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)94445825685262605Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92956766483835942Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)94172029586720295Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1581517Bp284Blood pressure QTL 284arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)93922018684220186Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)94002992585029925Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat

Markers in Region
PMC141152P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2974,594,689 - 74,595,055 (+)MAPPERmRatBN7.2
Rnor_6.0980,295,064 - 80,295,429NCBIRnor6.0
Rnor_5.0980,066,526 - 80,066,891UniSTSRnor5.0
RGSC_v3.4972,397,977 - 72,398,342UniSTSRGSC3.4
Celera972,188,318 - 72,188,683UniSTS
Cytogenetic Map9q33UniSTS
Tnp1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2974,594,689 - 74,595,055 (+)MAPPERmRatBN7.2
Rnor_6.0980,295,064 - 80,295,429NCBIRnor6.0
Rnor_5.0980,066,526 - 80,066,891UniSTSRnor5.0
RGSC_v3.4972,397,977 - 72,398,342UniSTSRGSC3.4
Celera972,188,318 - 72,188,683UniSTS
Cytogenetic Map9q33UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
1 9 7 24 27 31 14 13 14 2 59 28 1 18 10 37 17

Sequence


Ensembl Acc Id: ENSRNOT00000023769   ⟹   ENSRNOP00000023769
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl982,043,672 - 82,044,278 (-)Ensembl
mRatBN7.2 Ensembl974,594,466 - 74,595,274 (-)Ensembl
Rnor_6.0 Ensembl980,294,840 - 80,295,446 (-)Ensembl
RefSeq Acc Id: NM_017056   ⟹   NP_058752
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8982,043,669 - 82,044,278 (-)NCBI
mRatBN7.2974,594,463 - 74,595,072 (-)NCBI
Rnor_6.0980,294,837 - 80,295,446 (-)NCBI
Rnor_5.0980,066,299 - 80,066,908 (-)NCBI
RGSC_v3.4972,397,750 - 72,398,359 (-)RGD
Celera972,188,091 - 72,188,700 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_058752 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA42260 (Get FASTA)   NCBI Sequence Viewer  
  AAH78850 (Get FASTA)   NCBI Sequence Viewer  
  CAA30264 (Get FASTA)   NCBI Sequence Viewer  
  EDL75321 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000023769
GenBank Protein P02317 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_058752   ⟸   NM_017056
- UniProtKB: P02317 (UniProtKB/Swiss-Prot),   A6JVR3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000023769   ⟸   ENSRNOT00000023769

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P02317-F1-model_v2 AlphaFold P02317 1-55 view protein structure

Transcriptome

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

Promoters
RGD ID:13696741
Promoter ID:EPDNEW_R7266
Type:multiple initiation site
Name:Tnp1_1
Description:transition protein 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_6.0980,295,458 - 80,295,518EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3884 AgrOrtholog
BioCyc Gene G2FUF-27187 BioCyc
Ensembl Genes ENSRNOG00000017611 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000023769 ENTREZGENE
IMAGE_CLONE IMAGE:7131725 IMAGE-MGC_LOAD
InterPro Nuclear_transition_prot1 UniProtKB/Swiss-Prot
  Nuclear_transition_prot1_CS UniProtKB/Swiss-Prot
KEGG Report rno:24839 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93498 IMAGE-MGC_LOAD
NCBI Gene 24839 ENTREZGENE
PANTHER PTHR17486 UniProtKB/Swiss-Prot
  SPERMATID NUCLEAR TRANSITION PROTEIN 1 UniProtKB/Swiss-Prot
Pfam TP1 UniProtKB/Swiss-Prot
PhenoGen Tnp1 PhenoGen
PROSITE TP1 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000017611 RatGTEx
UniProt A0A8L2QC99_RAT UniProtKB/TrEMBL
  A6JVR3 ENTREZGENE, UniProtKB/TrEMBL
  P02317 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Tnp1  Transition protein 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein protein contains 54 aa residues 729972