Praf2 (PRA1 domain family, member 2) - Rat Genome Database

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Gene: Praf2 (PRA1 domain family, member 2) Rattus norvegicus
Analyze
Symbol: Praf2
Name: PRA1 domain family, member 2 (Ensembl:PRA1 domain family 2)
RGD ID: 1566287
Description: Predicted to be active in membrane. Orthologous to human PRAF2 (PRA1 domain family member 2); INTERACTS WITH aflatoxin B1; bisphenol A; cobalt dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC367743; PRA1 domain family 2; PRA1 family protein 2; RGD1566287; similar to DXImx39e protein
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
mRatBN7.2X14,773,398 - 14,776,035 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX14,773,420 - 14,775,909 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX19,587,417 - 19,590,054 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X20,493,062 - 20,495,699 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X16,758,229 - 16,760,866 (+)NCBIRnor_WKY
Rnor_6.0X15,618,324 - 15,620,992 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,618,991 - 15,620,841 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,399,546 - 16,402,441 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
CeleraX14,857,586 - 14,860,236 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IBA)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Praf2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,773,398 - 14,776,035 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX14,773,420 - 14,775,909 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX19,587,417 - 19,590,054 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X20,493,062 - 20,495,699 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0X16,758,229 - 16,760,866 (+)NCBIRnor_WKY
Rnor_6.0X15,618,324 - 15,620,992 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,618,991 - 15,620,841 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,399,546 - 16,402,441 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
CeleraX14,857,586 - 14,860,236 (-)NCBICelera
Cytogenetic MapXq12NCBI
PRAF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X49,071,161 - 49,074,002 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX49,071,161 - 49,074,002 (-)EnsemblGRCh38hg38GRCh38
GRCh37X48,928,818 - 48,931,661 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,815,762 - 48,818,606 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X48,685,066 - 48,687,911NCBI
CeleraX52,732,829 - 52,735,673 (+)NCBICelera
Cytogenetic MapXp11.23NCBI
HuRefX46,585,451 - 46,588,295 (-)NCBIHuRef
CHM1_1X48,960,139 - 48,962,983 (-)NCBICHM1_1
T2T-CHM13v2.0X48,482,886 - 48,485,729 (-)NCBIT2T-CHM13v2.0
Praf2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,594,810 - 7,597,302 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX7,594,678 - 7,597,303 (+)EnsemblGRCm39 Ensembl
GRCm38X7,728,571 - 7,731,063 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,728,439 - 7,731,064 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,305,697 - 7,308,189 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X6,885,530 - 6,888,022 (+)NCBIMGSCv36mm8
CeleraX3,739,495 - 3,741,987 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.48NCBI
Praf2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543594,606 - 598,264 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955543594,662 - 597,695 (-)NCBIChiLan1.0ChiLan1.0
PRAF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X49,224,864 - 49,227,782 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX49,224,864 - 49,233,960 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X41,369,432 - 41,372,322 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PRAF2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X42,218,038 - 42,221,075 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX42,218,046 - 42,226,422 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,593,685 - 16,596,572 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X42,354,289 - 42,357,178 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX42,354,298 - 42,357,058 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X42,340,622 - 42,343,507 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X42,328,272 - 42,331,153 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X42,423,017 - 42,425,908 (-)NCBIUU_Cfam_GSD_1.0
Praf2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,731,706 - 34,734,384 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936721971,744 - 975,580 (-)EnsemblSpeTri2.0
SpeTri2.0NW_004936721972,095 - 974,738 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRAF2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X43,147,473 - 43,150,350 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X47,995,413 - 47,998,290 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PRAF2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X46,179,842 - 46,182,769 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX46,179,835 - 46,183,552 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607611,745,320 - 11,748,234 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Praf2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624893842,071 - 846,170 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624893842,293 - 845,494 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Praf2
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:158
Count of miRNA genes:117
Interacting mature miRNAs:129
Transcripts:ENSRNOT00000042525
Prediction methods:Miranda, Pita, 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
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat

Markers in Region
AI178741  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,773,521 - 14,773,758 (+)MAPPERmRatBN7.2
Rnor_6.0X15,618,448 - 15,618,684NCBIRnor6.0
Rnor_5.0X16,399,670 - 16,399,906UniSTSRnor5.0
RGSC_v3.4X26,812,551 - 26,812,787UniSTSRGSC3.4
CeleraX14,857,710 - 14,857,946UniSTS
RH 3.4 MapX146.9UniSTS
Cytogenetic MapXq13UniSTS


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 26 10 10 3 10 74 20 30 3
Low 17 47 31 16 31 8 11 15 11 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000085397   ⟹   ENSRNOP00000068878
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,773,420 - 14,775,909 (-)Ensembl
Rnor_6.0 EnsemblX15,618,991 - 15,620,841 (-)Ensembl
RefSeq Acc Id: NM_001109013   ⟹   NP_001102483
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,773,398 - 14,776,035 (-)NCBI
Rnor_6.0X15,618,324 - 15,620,992 (-)NCBI
Rnor_5.0X16,399,546 - 16,402,441 (-)NCBI
CeleraX14,857,586 - 14,860,236 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102483 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL83833 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102483   ⟸   NM_001109013
- UniProtKB: A0A0G2JTX2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068878   ⟸   ENSRNOT00000085397

Transcriptome

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

Promoters
RGD ID:13701744
Promoter ID:EPDNEW_R12268
Type:multiple initiation site
Name:Praf2_1
Description:PRA1 domain family, member 2
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_6.0X15,620,864 - 15,620,924EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566287 AgrOrtholog
BioCyc Gene G2FUF-2917 BioCyc
Ensembl Genes ENSRNOG00000057147 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000068878 ENTREZGENE
  ENSRNOP00000068878.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000085397 ENTREZGENE
  ENSRNOT00000085397.2 UniProtKB/TrEMBL
InterPro Prenylated_rab_accept_PRA1 UniProtKB/TrEMBL
NCBI Gene 367743 ENTREZGENE
PANTHER PTHR12859 UniProtKB/TrEMBL
Pfam PRA1 UniProtKB/TrEMBL
PhenoGen Praf2 PhenoGen
UniProt A0A0G2JTX2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-12-15 Praf2  PRA1 domain family, member 2  Praf2  PRA1 domain family 2   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Praf2  PRA1 domain family 2   Praf2_predicted  PRA1 domain family 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Praf2_predicted  PRA1 domain family 2 (predicted)  RGD1566287_predicted  similar to DXImx39e protein (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1566287_predicted  similar to DXImx39e protein (predicted)  LOC367743  similar to DXImx39e protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367743  similar to DXImx39e protein      Symbol and Name status set to provisional 70820 PROVISIONAL