Pramef12 (PRAME family member 12) - Rat Genome Database

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Gene: Pramef12 (PRAME family member 12) Rattus norvegicus
Analyze
Symbol: Pramef12
Name: PRAME family member 12
RGD ID: 1587431
Description: Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of Cul2-RING ubiquitin ligase complex. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in myeloid leukemia. Orthologous to several human genes including PRAMEF12 (PRAME family member 12); PRAMEF19 (PRAME family member 19); and PRAMEF7 (PRAME family member 7); INTERACTS WITH 1,2-dimethylhydrazine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC691157; similar to PRAME family member DJ1198H6.2
RGD Orthologs
Human
Mouse
Bonobo
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85161,476,048 - 161,487,195 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5161,476,051 - 161,487,235 (-)EnsemblGRCr8
mRatBN7.25156,193,666 - 156,197,199 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5156,193,745 - 156,197,195 (-)EnsemblmRatBN7.2
Rnor_6.05162,378,442 - 162,388,786 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5162,385,173 - 162,388,620 (+)Ensemblrn6Rnor6.0
Rnor_5.05166,075,868 - 166,079,359 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45162,768,599 - 162,772,223 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5154,497,256 - 154,507,601 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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

Genomics

Comparative Map Data
Pramef12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85161,476,048 - 161,487,195 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5161,476,051 - 161,487,235 (-)EnsemblGRCr8
mRatBN7.25156,193,666 - 156,197,199 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5156,193,745 - 156,197,195 (-)EnsemblmRatBN7.2
Rnor_6.05162,378,442 - 162,388,786 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5162,385,173 - 162,388,620 (+)Ensemblrn6Rnor6.0
Rnor_5.05166,075,868 - 166,079,359 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45162,768,599 - 162,772,223 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5154,497,256 - 154,507,601 (-)NCBICelera
Cytogenetic Map5q36NCBI
PRAMEF12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38112,773,738 - 12,777,906 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl112,773,738 - 12,777,906 (+)Ensemblhg38GRCh38
GRCh37112,833,881 - 12,838,049 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36112,757,571 - 12,760,636 (+)NCBIBuild 36Build 36hg18NCBI36
Celera111,947,529 - 11,950,594 (+)NCBICelera
Cytogenetic Map1p36.21NCBI
HuRef111,988,148 - 11,991,213 (+)NCBIHuRef
CHM1_1112,822,897 - 12,825,962 (+)NCBICHM1_1
T2T-CHM13v2.0112,318,012 - 12,322,180 (+)NCBIT2T-CHM13v2.0
Pramel13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394144,118,244 - 144,135,037 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4144,118,244 - 144,135,034 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm384144,391,674 - 144,408,467 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4144,391,674 - 144,408,464 (-)Ensemblmm10GRCm38
MGSCv374143,981,577 - 143,998,367 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv364143,658,361 - 143,675,151 (-)NCBIMGSCv36mm8
Celera4145,995,204 - 146,011,975 (-)NCBICelera
Cytogenetic Map4E1NCBI
cM Map477.98NCBI
PRAMEF12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21215,456,394 - 215,460,564 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11214,103,176 - 214,107,346 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0111,525,455 - 11,529,625 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LOC103225579
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120119,014,526 - 119,019,561 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20119,015,953 - 119,018,681 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366653427,916 - 30,863 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Pramef12
83 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:56
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000048232
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5130249266172190305Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116702075161702075Rat
1354583Despr3Despair related QTL34.980.0002locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)5132930505172190305Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5141212838172190305Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149642129171146538Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5160111176171146538Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)599905133172190305Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5133789363172190305Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134369199172190305Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)565089051166764498Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136631198172190305Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5156396728172190305Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133081618172190305Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5149805999162987697Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)551657967166600247Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138002522170842766Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133270647172190305Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5160071170172129029Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)5141764300172190305Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5148093485172129029Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125969677172190305Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5156396728167181764Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5131708216172190305Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5149661912166600247Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116702075161702075Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116702075161702075Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116702075161702075Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5156289283171137955Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133081618172190305Rat


Expression

RNA-SEQ Expression

circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
1 13 2 2 1 1 1 5 2 12 2 55 1

Sequence


Ensembl Acc Id: ENSRNOT00000048232   ⟹   ENSRNOP00000049620
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5161,476,051 - 161,487,235 (-)Ensembl
mRatBN7.2 Ensembl5156,193,745 - 156,197,195 (-)Ensembl
Rnor_6.0 Ensembl5162,385,173 - 162,388,620 (+)Ensembl
RefSeq Acc Id: XM_006239346   ⟹   XP_006239408
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85161,476,048 - 161,487,195 (-)NCBI
mRatBN7.25156,193,666 - 156,197,199 (-)NCBI
Rnor_6.05162,378,442 - 162,388,786 (+)NCBI
Rnor_5.05166,075,868 - 166,079,359 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001418217 (Get FASTA)   NCBI Sequence Viewer  
  XP_006239408 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL81056 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000049620
  ENSRNOP00000049620.6
RefSeq Acc Id: XP_006239408   ⟸   XM_006239346
- Sequence:
Ensembl Acc Id: ENSRNOP00000049620   ⟸   ENSRNOT00000048232

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M2Q6-F1-model_v2 AlphaFold F1M2Q6 1-463 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587431 AgrOrtholog
BioCyc Gene G2FUF-39273 BioCyc
Ensembl Genes ENSRNOG00000037035 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048232 ENTREZGENE
  ENSRNOT00000048232.6 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro L_dom-like UniProtKB/TrEMBL
  PRAME_domain UniProtKB/TrEMBL
  PRAME_family UniProtKB/TrEMBL
KEGG Report rno:691157 UniProtKB/TrEMBL
NCBI Gene 691157 ENTREZGENE
PANTHER PRAME FAMILY MEMBER 11-RELATED UniProtKB/TrEMBL
  SIMILAR TO PREFERENTIALLY EXPRESSED ANTIGEN IN MELANOMA-LIKE 3 UniProtKB/TrEMBL
PhenoGen Pramef12 PhenoGen
PIRSF PRAME UniProtKB/TrEMBL
RatGTEx ENSRNOG00000037035 RatGTEx
Superfamily-SCOP RNI-like UniProtKB/TrEMBL
UniProt A6IU05 ENTREZGENE, UniProtKB/TrEMBL
  F1M2Q6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Pramef12  PRAME family member 12  LOC691157  similar to PRAME family member DJ1198H6.2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691157  similar to PRAME family member DJ1198H6.2  LOC686451  similar to PRAME family member DJ1198H6.2  Data merged from RGD:1597633 1643240 APPROVED
2006-11-20 LOC686451  similar to PRAME family member DJ1198H6.2      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC691157  similar to PRAME family member DJ1198H6.2      Symbol and Name status set to provisional 70820 PROVISIONAL