Prm3 (protamine 3) - Rat Genome Database

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Gene: Prm3 (protamine 3) Rattus norvegicus
Analyze
Symbol: Prm3
Name: protamine 3
RGD ID: 1587265
Description: Predicted to enable DNA binding activity. Predicted to be involved in flagellated sperm motility. Predicted to be located in nucleus. Predicted to be part of nucleosome. Predicted to be active in cytoplasm. Orthologous to human PRM3 (protamine 3); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 3-chloropropane-1,2-diol; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: protamine-3; sperm protamine P3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8105,384,394 - 5,384,908 (+)NCBIGRCr8
mRatBN7.2104,877,471 - 4,877,985 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl104,877,471 - 4,877,985 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx109,574,046 - 9,574,560 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,095,162 - 9,095,676 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0104,733,443 - 4,733,957 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0104,951,557 - 4,952,071 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl104,951,557 - 4,952,071 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0103,778,043 - 3,778,557 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4104,814,767 - 4,815,281 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera103,899,067 - 3,899,581 (+)NCBICelera
Cytogenetic Map10q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,ISO)
nucleosome  (IEA)
nucleus  (IEA)

Molecular Function
DNA binding  (IEA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8521723   PMID:8720108   PMID:18256328  


Genomics

Comparative Map Data
Prm3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8105,384,394 - 5,384,908 (+)NCBIGRCr8
mRatBN7.2104,877,471 - 4,877,985 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl104,877,471 - 4,877,985 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx109,574,046 - 9,574,560 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,095,162 - 9,095,676 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0104,733,443 - 4,733,957 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0104,951,557 - 4,952,071 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl104,951,557 - 4,952,071 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0103,778,043 - 3,778,557 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4104,814,767 - 4,815,281 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera103,899,067 - 3,899,581 (+)NCBICelera
Cytogenetic Map10q11NCBI
PRM3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381611,273,199 - 11,273,629 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1611,273,199 - 11,273,629 (-)EnsemblGRCh38hg38GRCh38
GRCh371611,367,056 - 11,367,486 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361611,273,850 - 11,274,953 (-)NCBINCBI36Build 36hg18NCBI36
Build 341611,274,644 - 11,274,953NCBI
Celera1611,536,532 - 11,536,843 (-)NCBICelera
Cytogenetic Map16p13.13NCBI
HuRef1611,284,873 - 11,285,184 (-)NCBIHuRef
CHM1_11611,367,047 - 11,367,358 (-)NCBICHM1_1
T2T-CHM13v2.01611,309,421 - 11,309,851 (-)NCBIT2T-CHM13v2.0
Prm3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391610,608,372 - 10,608,778 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1610,608,369 - 10,608,778 (-)EnsemblGRCm39 Ensembl
GRCm381610,790,508 - 10,790,914 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1610,790,505 - 10,790,914 (-)EnsemblGRCm38mm10GRCm38
MGSCv371610,790,601 - 10,791,007 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361610,704,162 - 10,704,467 (-)NCBIMGSCv36mm8
Celera1611,417,938 - 11,418,344 (-)NCBICelera
Cytogenetic Map16A1NCBI
cM Map165.84NCBI
Prm3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554427,306,672 - 7,309,671 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554427,308,621 - 7,309,105 (+)NCBIChiLan1.0ChiLan1.0
PRM3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21811,820,086 - 11,824,473 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11615,590,874 - 15,594,935 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01610,215,159 - 10,215,812 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11611,436,997 - 11,437,447 (-)NCBIpanpan1.1PanPan1.1panPan2
PRM3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1631,493,084 - 31,494,775 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha632,875,950 - 32,877,652 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0631,675,724 - 31,677,423 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1631,489,021 - 31,490,709 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0631,363,314 - 31,364,995 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0631,787,543 - 31,789,245 (+)NCBIUU_Cfam_GSD_1.0
Prm3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344111,499,042 - 111,500,330 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365309,344,605 - 9,344,922 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365309,344,605 - 9,344,922 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRM3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1331,865,159 - 31,866,717 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2332,655,879 - 32,656,364 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRM3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1510,750,083 - 10,751,380 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl510,750,168 - 10,750,503 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606819,413,430 - 19,413,991 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Prm3
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:59
Count of miRNA genes:55
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000003451
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
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1549898Neuinf3Neuroinflammation QTL 326.4nervous system integrity trait (VT:0010566)MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio (CMO:0001980)1034063205387112Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat

Markers in Region
RH94725  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2104,876,873 - 4,876,979 (+)MAPPERmRatBN7.2
Rnor_6.0104,950,960 - 4,951,065NCBIRnor6.0
Rnor_5.0103,777,446 - 3,777,551UniSTSRnor5.0
RGSC_v3.4104,814,168 - 4,814,273UniSTSRGSC3.4
Celera103,898,470 - 3,898,575UniSTS
Cytogenetic Map10q11UniSTS
RH94726  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2104,876,095 - 4,876,196 (+)MAPPERmRatBN7.2
Rnor_6.0104,950,182 - 4,950,282NCBIRnor6.0
Rnor_5.0103,776,668 - 3,776,768UniSTSRnor5.0
RGSC_v3.4104,813,390 - 4,813,490UniSTSRGSC3.4
Celera103,897,692 - 3,897,792UniSTS
Cytogenetic Map10q11UniSTS
UniSTS:498766  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2104,876,885 - 4,876,960 (+)MAPPERmRatBN7.2
Rnor_6.0104,950,972 - 4,951,046NCBIRnor6.0
Rnor_5.0103,777,458 - 3,777,532UniSTSRnor5.0
RGSC_v3.4104,814,180 - 4,814,254UniSTSRGSC3.4
Celera103,898,482 - 3,898,556UniSTS
Cytogenetic Map10q11UniSTS


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 2
Medium 5
Low 1 1 2 1 1 1
Below cutoff 2 12 5 7 5 4 5 5 1 2 3 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003451   ⟹   ENSRNOP00000003451
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl104,877,471 - 4,877,985 (+)Ensembl
Rnor_6.0 Ensembl104,951,557 - 4,952,071 (+)Ensembl
RefSeq Acc Id: NM_001002855   ⟹   NP_001002855
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8105,384,394 - 5,384,908 (+)NCBI
mRatBN7.2104,877,471 - 4,877,985 (+)NCBI
Rnor_6.0104,951,557 - 4,952,071 (+)NCBI
Rnor_5.0103,778,043 - 3,778,557 (+)NCBI
RGSC_v3.4104,814,767 - 4,815,281 (+)RGD
Celera103,899,067 - 3,899,581 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001002855 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB35760 (Get FASTA)   NCBI Sequence Viewer  
  CAA87063 (Get FASTA)   NCBI Sequence Viewer  
  EDL96209 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003451
  ENSRNOP00000003451.2
  ENSRNOP00055026644
  ENSRNOP00060017833
  ENSRNOP00065002972
GenBank Protein Q64256 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001002855   ⟸   NM_001002855
- UniProtKB: Q64256 (UniProtKB/Swiss-Prot),   A6K4I7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003451   ⟸   ENSRNOT00000003451

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q64256-F1-model_v2 AlphaFold Q64256 1-104 view protein structure

Transcriptome

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

Promoters
RGD ID:13696940
Promoter ID:EPDNEW_R7465
Type:initiation region
Name:Prm3_1
Description:protamine 3
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_6.0104,951,653 - 4,951,713EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587265 AgrOrtholog
BioCyc Gene G2FUF-26144 BioCyc
Ensembl Genes ENSRNOG00000002564 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055019284 UniProtKB/Swiss-Prot
  ENSRNOG00060013207 UniProtKB/Swiss-Prot
  ENSRNOG00065002977 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003451 ENTREZGENE
  ENSRNOT00000003451.4 UniProtKB/Swiss-Prot
  ENSRNOT00055032894 UniProtKB/Swiss-Prot
  ENSRNOT00060022500 UniProtKB/Swiss-Prot
  ENSRNOT00065004166 UniProtKB/Swiss-Prot
InterPro PRMP3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:442921 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 442921 ENTREZGENE
PANTHER PROTAMINE-3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR14317 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Prm3 PhenoGen
RatGTEx ENSRNOG00000002564 RatGTEx
  ENSRNOG00055019284 RatGTEx
  ENSRNOG00060013207 RatGTEx
  ENSRNOG00065002977 RatGTEx
UniProt A6K4I7 ENTREZGENE, UniProtKB/TrEMBL
  PRM3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-19 Prm3  protamine 3      Symbol and Name status set to provisional 70820 PROVISIONAL