Prima1 (proline rich membrane anchor 1) - Rat Genome Database

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Gene: Prima1 (proline rich membrane anchor 1) Rattus norvegicus
Analyze
Symbol: Prima1
Name: proline rich membrane anchor 1
RGD ID: 1583978
Description: Predicted to enable enzyme binding activity and protein-membrane adaptor activity. Predicted to be involved in neurotransmitter catabolic process. Predicted to act upstream of or within establishment of localization in cell. Predicted to be located in plasma membrane. Orthologous to human PRIMA1 (proline rich membrane anchor 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC362773; LOC690195; PRiMA; Prima1l; proline rich membrane anchor 1-like; proline-rich membrane anchor 1; similar to proline rich membrane anchor 1
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
mRatBN7.26122,338,365 - 122,390,955 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6122,338,370 - 122,389,921 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx6122,479,287 - 122,530,808 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.06122,774,553 - 122,826,076 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.06122,109,406 - 122,160,809 (-)NCBIRnor_WKY
Rnor_6.06127,075,954 - 127,127,985 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6127,075,954 - 127,127,413 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06136,279,361 - 136,331,457 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46127,473,126 - 127,524,588 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.16127,479,410 - 127,528,755 (-)NCBI
Celera6119,819,984 - 119,871,375 (-)NCBICelera
Cytogenetic Map6q32NCBI
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11804574   PMID:15632090   PMID:18511416   PMID:19368807   PMID:19490106   PMID:19680821   PMID:20147288  


Genomics

Comparative Map Data
Prima1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26122,338,365 - 122,390,955 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6122,338,370 - 122,389,921 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx6122,479,287 - 122,530,808 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.06122,774,553 - 122,826,076 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.06122,109,406 - 122,160,809 (-)NCBIRnor_WKY
Rnor_6.06127,075,954 - 127,127,985 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6127,075,954 - 127,127,413 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06136,279,361 - 136,331,457 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46127,473,126 - 127,524,588 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.16127,479,410 - 127,528,755 (-)NCBI
Celera6119,819,984 - 119,871,375 (-)NCBICelera
Cytogenetic Map6q32NCBI
PRIMA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381493,718,298 - 93,788,994 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1493,718,298 - 93,788,485 (-)EnsemblGRCh38hg38GRCh38
GRCh371494,184,644 - 94,254,831 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361493,254,397 - 93,324,519 (-)NCBINCBI36Build 36hg18NCBI36
Build 341493,257,136 - 93,324,519NCBI
Celera1474,238,652 - 74,308,549 (-)NCBICelera
Cytogenetic Map14q32.12NCBI
HuRef1474,364,500 - 74,434,354 (-)NCBIHuRef
CHM1_11494,122,661 - 94,192,768 (-)NCBICHM1_1
T2T-CHM13v2.01487,945,588 - 88,015,848 (-)NCBIT2T-CHM13v2.0
Prima1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912103,160,712 - 103,208,967 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12103,163,167 - 103,208,409 (-)EnsemblGRCm39 Ensembl
GRCm3812103,194,453 - 103,242,719 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12103,196,908 - 103,242,150 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712104,435,118 - 104,480,356 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3612103,597,958 - 103,643,196 (-)NCBIMGSCv36mm8
Celera12104,413,731 - 104,459,201 (-)NCBICelera
Cytogenetic Map12ENCBI
Prima1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543815,835,641 - 15,903,484 (-)NCBIChiLan1.0ChiLan1.0
PRIMA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11493,685,784 - 93,756,139 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1493,685,784 - 93,756,139 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01474,351,140 - 74,422,033 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PRIMA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1862,843,314 - 62,903,238 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl862,843,300 - 62,903,444 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha862,420,228 - 62,480,175 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0863,114,510 - 63,174,498 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl863,114,499 - 63,175,090 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1862,792,703 - 62,852,629 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0862,843,588 - 62,903,540 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0863,173,899 - 63,233,935 (-)NCBIUU_Cfam_GSD_1.0
Prima1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864011,753,509 - 11,799,860 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367331,670,004 - 1,712,558 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049367331,667,191 - 1,713,517 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRIMA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7115,038,630 - 115,100,756 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17115,038,626 - 115,101,431 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27121,670,412 - 121,710,761 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PRIMA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12471,466,023 - 71,540,482 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605358,711,841 - 58,783,437 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prima1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473410,167,449 - 10,222,792 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473410,167,407 - 10,223,052 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Prima1
272 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1143
Count of miRNA genes:332
Interacting mature miRNAs:442
Transcripts:ENSRNOT00000011906, ENSRNOT00000051429
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
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)685140138130140138Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)685140138130140138Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6104085867128713626Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6106752656132339866Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6112636280140994061Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6116506292130245370Rat

Markers in Region
D6Hmgc14  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26122,379,987 - 122,380,207 (+)MAPPERmRatBN7.2
Rnor_6.06127,117,566 - 127,117,783NCBIRnor6.0
Rnor_5.06136,320,973 - 136,321,190UniSTSRnor5.0
Celera6119,861,539 - 119,861,748UniSTS
Cytogenetic Map6q32UniSTS
RH132423  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26122,385,260 - 122,385,479 (+)MAPPERmRatBN7.2
Rnor_6.06127,122,839 - 127,123,057NCBIRnor6.0
Rnor_5.06136,326,296 - 136,326,514UniSTSRnor5.0
RGSC_v3.46127,520,014 - 127,520,232UniSTSRGSC3.4
Celera6119,866,801 - 119,867,019UniSTS
RH 3.4 Map6841.89UniSTS
Cytogenetic Map6q32UniSTS
RH134181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26122,338,423 - 122,338,615 (+)MAPPERmRatBN7.2
Rnor_6.06127,076,008 - 127,076,199NCBIRnor6.0
Rnor_5.06136,279,415 - 136,279,606UniSTSRnor5.0
RGSC_v3.46127,473,180 - 127,473,371UniSTSRGSC3.4
Celera6119,819,999 - 119,820,192UniSTS
RH 3.4 Map6841.89UniSTS
Cytogenetic Map6q32UniSTS


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 13 18 1
Low 3 42 16 6 5 6 7 10 59 17 39 11 7
Below cutoff 1 41 35 14 35 1 1 2 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011906   ⟹   ENSRNOP00000011906
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6122,338,370 - 122,389,921 (-)Ensembl
Rnor_6.0 Ensembl6127,075,954 - 127,127,413 (-)Ensembl
RefSeq Acc Id: NM_001108721   ⟹   NP_001102191
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26122,338,370 - 122,389,835 (-)NCBI
Rnor_6.06127,075,954 - 127,127,413 (-)NCBI
Rnor_5.06136,279,361 - 136,331,457 (-)NCBI
RGSC_v3.46127,473,126 - 127,524,588 (-)RGD
Celera6119,819,984 - 119,871,375 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240495   ⟹   XP_006240557
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26122,338,365 - 122,390,955 (-)NCBI
Rnor_6.06127,075,954 - 127,127,985 (-)NCBI
Rnor_5.06136,279,361 - 136,331,457 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594373   ⟹   XP_017449862
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26122,338,365 - 122,389,840 (-)NCBI
Rnor_6.06127,078,844 - 127,127,477 (-)NCBI
Sequence:
RefSeq Acc Id: XR_355067
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26122,341,218 - 122,389,840 (-)NCBI
Rnor_6.06127,078,851 - 127,127,477 (-)NCBI
Rnor_5.06136,279,361 - 136,331,457 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102191 (Get FASTA)   NCBI Sequence Viewer  
  XP_006240557 (Get FASTA)   NCBI Sequence Viewer  
  XP_017449862 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3ZZP4 (Get FASTA)   NCBI Sequence Viewer  
  EDL81765 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102191   ⟸   NM_001108721
- Peptide Label: precursor
- UniProtKB: D4ACH8 (UniProtKB/Swiss-Prot),   D3ZZP4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006240557   ⟸   XM_006240495
- Peptide Label: isoform X1
- UniProtKB: D4ACH8 (UniProtKB/Swiss-Prot),   D3ZZP4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449862   ⟸   XM_017594373
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000011906   ⟸   ENSRNOT00000011906
Protein Domains
PRAD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZZP4-F1-model_v2 AlphaFold D3ZZP4 1-153 view protein structure

Transcriptome

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

Promoters
RGD ID:13694791
Promoter ID:EPDNEW_R5314
Type:single initiation site
Name:Prima1_1
Description:proline rich membrane anchor 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_6.06127,127,419 - 127,127,479EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1583978 AgrOrtholog
BioCyc Gene G2FUF-36425 BioCyc
Ensembl Genes ENSRNOG00000008915 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011906.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011906.7 UniProtKB/TrEMBL
KEGG Report rno:690195 UniProtKB/Swiss-Prot
NCBI Gene 690195 ENTREZGENE
PhenoGen Prima1 PhenoGen
UniProt A0A8L2Q5U1_RAT UniProtKB/TrEMBL
  D3ZZP4 ENTREZGENE
  D4ACH8 ENTREZGENE
  PRIMA_RAT UniProtKB/Swiss-Prot
UniProt Secondary D4ACH8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-22 Prima1  proline rich membrane anchor 1  Prima1l  proline rich membrane anchor 1-like  Data Merged 737654 APPROVED
2008-04-30 Prima1l  proline rich membrane anchor 1-like  Prima1_predicted  proline rich membrane anchor 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Prima1  proline rich membrane anchor 1  LOC690195  similar to proline rich membrane anchor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC690195  similar to proline rich membrane anchor 1  LOC683544  similar to proline rich membrane anchor 1  Data Merged 1643240 APPROVED
2006-11-19 LOC690195  similar to proline rich membrane anchor 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC683544  similar to proline rich membrane anchor 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Prima1_predicted  proline rich membrane anchor 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED