TNP1 (transition protein 1) - Rat Genome Database

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Gene: TNP1 (transition protein 1) Homo sapiens
Analyze
Symbol: TNP1
Name: transition protein 1
RGD ID: 733923
HGNC Page HGNC
Description: Enables DNA binding activity. Involved in several processes, including chromatin organization; single strand break repair; and spermatid nucleus elongation. Part of nucleosome.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: spermatid nuclear transition protein 1; STP-1; TP-1; TP1; transition protein 1 (during histone to protamine replacement)
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2216,859,458 - 216,860,064 (-)EnsemblGRCh38hg38GRCh38
GRCh382216,859,458 - 216,860,064 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372217,724,181 - 217,724,787 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362217,432,426 - 217,433,027 (-)NCBINCBI36hg18NCBI36
Build 342217,549,689 - 217,550,288NCBI
Celera2211,492,069 - 211,492,670 (-)NCBI
Cytogenetic Map2q35NCBI
HuRef2209,578,223 - 209,578,824 (-)NCBIHuRef
CHM1_12217,730,235 - 217,730,836 (-)NCBICHM1_1
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

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

Molecular Function
DNA binding  (IBA,IMP)
protein binding  (IPI)

References

References - curated
1. GOA_HUMAN data from the GO Consortium
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:2040274   PMID:2249851   PMID:2250010   PMID:3382664   PMID:3412903   PMID:8019440   PMID:9809674   PMID:9837753   PMID:10781074   PMID:11315969   PMID:12477932   PMID:12743712  
PMID:15489334   PMID:16291974   PMID:16989827   PMID:17207965   PMID:17852044   PMID:18292840   PMID:18727729   PMID:20378615   PMID:20522125   PMID:20524034   PMID:21873635   PMID:21931568  
PMID:21967852   PMID:25416956   PMID:26098692   PMID:31515488   PMID:32296183   PMID:33440036  


Genomics

Comparative Map Data
TNP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2216,859,458 - 216,860,064 (-)EnsemblGRCh38hg38GRCh38
GRCh382216,859,458 - 216,860,064 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372217,724,181 - 217,724,787 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362217,432,426 - 217,433,027 (-)NCBINCBI36hg18NCBI36
Build 342217,549,689 - 217,550,288NCBI
Celera2211,492,069 - 211,492,670 (-)NCBI
Cytogenetic Map2q35NCBI
HuRef2209,578,223 - 209,578,824 (-)NCBIHuRef
CHM1_12217,730,235 - 217,730,836 (-)NCBICHM1_1
Tnp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39173,054,233 - 73,055,058 (-)NCBIGRCm39mm39
GRCm39 Ensembl173,054,233 - 73,055,068 (-)Ensembl
GRCm38173,015,074 - 73,015,899 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl173,015,074 - 73,015,909 (-)EnsemblGRCm38mm10GRCm38
MGSCv37173,061,648 - 73,062,473 (-)NCBIGRCm37mm9NCBIm37
MGSCv36172,948,284 - 72,949,079 (-)NCBImm8
Celera173,589,038 - 73,589,863 (-)NCBICelera
Cytogenetic Map1C3NCBI
cM Map136.94NCBI
Tnp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2974,594,463 - 74,595,072 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl974,594,466 - 74,595,274 (-)Ensembl
Rnor_6.0980,294,837 - 80,295,446 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl980,294,840 - 80,295,446 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0980,066,299 - 80,066,908 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4972,397,750 - 72,398,359 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1972,544,732 - 72,545,341 (-)NCBI
Celera972,188,091 - 72,188,700 (-)NCBICelera
Cytogenetic Map9q33NCBI
Tnp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545316,387,527 - 16,388,890 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545316,387,897 - 16,388,513 (+)NCBIChiLan1.0ChiLan1.0
TNP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B222,723,606 - 222,724,212 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B222,723,606 - 222,724,212 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B104,122,748 - 104,123,349 (-)NCBIMhudiblu_PPA_v0panPan3
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Tnp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303172,120,406 - 172,121,032 (-)NCBI
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)NCBI
ChlSab1.1 Ensembl10102,703,325 - 102,703,691 (-)Ensembl
Vero_WHO_p1.0NW_02366604096,709,921 - 96,711,971 (+)NCBI
Tnp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248238,269,758 - 8,270,134 (+)NCBI

Position Markers
GDB:186871  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372217,724,131 - 217,725,860UniSTSGRCh37
Build 362217,432,376 - 217,434,105RGDNCBI36
Celera2211,492,019 - 211,493,748RGD
HuRef2209,578,173 - 209,579,902UniSTS
D2S2720  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372217,724,190 - 217,724,370UniSTSGRCh37
Build 362217,432,435 - 217,432,615RGDNCBI36
Celera2211,492,078 - 211,492,258RGD
Cytogenetic Map2q35-q36UniSTS
HuRef2209,578,232 - 209,578,412UniSTS
Whitehead-YAC Contig Map2 UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:157
Count of miRNA genes:153
Interacting mature miRNAs:157
Transcripts:ENST00000236979
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.


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 sensory system adipose tissue appendage pharyngeal arch
High 1 1 1 1 1 348
Medium 22 16 29 6 5 5 36 11 14 2 40 23 1 11 21
Low 787 695 961 171 291 102 1159 548 788 36 393 813 68 351 748 1
Below cutoff 681 815 339 175 304 124 1222 649 1174 76 236 220 51 304 818

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000236979   ⟹   ENSP00000236979
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2216,859,458 - 216,860,064 (-)Ensembl
RefSeq Acc Id: NM_003284   ⟹   NP_003275
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382216,859,458 - 216,860,064 (-)NCBI
GRCh372217,724,181 - 217,724,782 (-)ENTREZGENE
Build 362217,432,426 - 217,433,027 (-)NCBI Archive
HuRef2209,578,223 - 209,578,824 (-)ENTREZGENE
CHM1_12217,730,235 - 217,730,836 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_003275   ⟸   NM_003284
- UniProtKB: P09430 (UniProtKB/Swiss-Prot),   Q4ZG82 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000236979   ⟸   ENST00000236979

Promoters
RGD ID:6862762
Promoter ID:EPDNEW_H4546
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:
Human AssemblyChrPosition (strand)Source
GRCh382216,860,064 - 216,860,124EPDNEW
RGD ID:6849414
Promoter ID:EP33023
Type:multiple initiation site
Name:HS_TNP1
Description:Transition protein 1.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Notes:homology_group=Homology group 192; Mammalian transition protein 1.
Tissues & Cell Lines:spermatids
Experiment Methods:Primer extension; NEDO full length human cDNA sequencing project.; Oligo-capping
Position:
Human AssemblyChrPosition (strand)Source
Build 362217,433,030 - 217,433,090EPD

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q32.3-37.3(chr2:194898783-236473913)x3 copy number gain See cases [RCV000051119] Chr2:194898783..236473913 [GRCh38]
Chr2:195763507..237382556 [GRCh37]
Chr2:195471752..237047295 [NCBI36]
Chr2:2q32.3-37.3
pathogenic
GRCh38/hg38 2q32.2-37.3(chr2:188818195-242065208)x3 copy number gain See cases [RCV000052958] Chr2:188818195..242065208 [GRCh38]
Chr2:189682921..243007359 [GRCh37]
Chr2:189391166..242656032 [NCBI36]
Chr2:2q32.2-37.3
pathogenic
GRCh38/hg38 2q32.2-37.3(chr2:190310736-241892770)x3 copy number gain See cases [RCV000052959] Chr2:190310736..241892770 [GRCh38]
Chr2:191175462..242834921 [GRCh37]
Chr2:190883707..242483594 [NCBI36]
Chr2:2q32.2-37.3
pathogenic
GRCh38/hg38 2q32.3-37.3(chr2:193122313-241074980)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052960]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052960]|See cases [RCV000052960] Chr2:193122313..241074980 [GRCh38]
Chr2:193987039..242014395 [GRCh37]
Chr2:193695284..241663068 [NCBI36]
Chr2:2q32.3-37.3
pathogenic
GRCh38/hg38 2q34-36.3(chr2:212614422-227121230)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052964]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052964]|See cases [RCV000052964] Chr2:212614422..227121230 [GRCh38]
Chr2:213479146..227985946 [GRCh37]
Chr2:213187391..227694190 [NCBI36]
Chr2:2q34-36.3
pathogenic
GRCh38/hg38 2q34-37.3(chr2:210579676-242126245)x3 copy number gain See cases [RCV000135934] Chr2:210579676..242126245 [GRCh38]
Chr2:211444400..243059659 [GRCh37]
Chr2:211152645..242717069 [NCBI36]
Chr2:2q34-37.3
pathogenic
GRCh38/hg38 2q31.3-36.2(chr2:180513793-224302848)x3 copy number gain See cases [RCV000139446] Chr2:180513793..224302848 [GRCh38]
Chr2:181378520..225167565 [GRCh37]
Chr2:181086765..224875809 [NCBI36]
Chr2:2q31.3-36.2
pathogenic
GRCh38/hg38 2q32.2-37.3(chr2:189436149-241841232)x3 copy number gain See cases [RCV000142307] Chr2:189436149..241841232 [GRCh38]
Chr2:190300875..242783384 [GRCh37]
Chr2:190009120..242432057 [NCBI36]
Chr2:2q32.2-37.3
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384) copy number gain See cases [RCV000512056] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2q34-37.3(chr2:213518431-242783384)x3 copy number gain See cases [RCV000512009] Chr2:213518431..242783384 [GRCh37]
Chr2:2q34-37.3
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3 copy number gain See cases [RCV000511212] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2q35-36.3(chr2:217374144-227643620)x1 copy number loss not provided [RCV000585275] Chr2:217374144..227643620 [GRCh37]
Chr2:2q35-36.3
likely pathogenic
GRCh37/hg19 2q33.3-35(chr2:205169148-219149293)x3 copy number gain not provided [RCV000682166] Chr2:205169148..219149293 [GRCh37]
Chr2:2q33.3-35
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3 copy number gain not provided [RCV000752802] Chr2:14238..243048760 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3 copy number gain not provided [RCV000752804] Chr2:15672..243101834 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2q34-37.3(chr2:210779657-239879183)x3 copy number gain See cases [RCV000790568] Chr2:210779657..239879183 [GRCh37]
Chr2:2q34-37.3
pathogenic
Single allele duplication Neurodevelopmental disorder [RCV000787403] Chr2:188926928..225298653 [GRCh37]
Chr2:2q32.1-36.2
pathogenic
GRCh37/hg19 2q35(chr2:216883237-220953003)x3 copy number gain not provided [RCV001007510] Chr2:216883237..220953003 [GRCh37]
Chr2:2q35
pathogenic
GRCh37/hg19 2q34-35(chr2:215122019-220397907)x1 copy number loss not provided [RCV001259180] Chr2:215122019..220397907 [GRCh37]
Chr2:2q34-35
likely pathogenic
GRCh37/hg19 2q31.2-37.3(chr2:178397959-243007457)x3 copy number gain See cases [RCV001263052] Chr2:178397959..243007457 [GRCh37]
Chr2:2q31.2-37.3
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:11951 AgrOrtholog
COSMIC TNP1 COSMIC
Ensembl Genes ENSG00000118245 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000236979 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000236979 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000118245 GTEx
HGNC ID HGNC:11951 ENTREZGENE
Human Proteome Map TNP1 Human Proteome Map
InterPro Nuclear_transition_prot1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_transition_prot1_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:7141 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 7141 ENTREZGENE
OMIM 190231 OMIM
PANTHER PTHR17486 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA36640 PharmGKB
PROSITE TP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt P09430 ENTREZGENE
  Q4ZG82 ENTREZGENE, UniProtKB/TrEMBL
  STP1_HUMAN UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-24 TNP1  transition protein 1  TNP1  transition protein 1 (during histone to protamine replacement)  Symbol and/or name change 5135510 APPROVED