Pramef20 (PRAME family member 20) - Rat Genome Database

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Gene: Pramef20 (PRAME family member 20) Rattus norvegicus
Analyze
Symbol: Pramef20
Name: PRAME family member 20
RGD ID: 1587437
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. Orthologous to human PRAMEF20 (PRAME family member 20); INTERACTS WITH bisphenol A; tributylstannane; 2,3',4,4',5-Pentachlorobiphenyl (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: PRAME family member 20-like; PRAME family member 25-like; pramef25; preferentially expressed antigen in melanoma-like 1-like; similar to PRAME family member 5
RGD Orthologs
Human
Mouse
Bonobo
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Pramef20-ps3  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85161,454,398 - 161,458,874 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5161,453,893 - 161,459,073 (-)EnsemblGRCr8
mRatBN7.25156,171,125 - 156,175,601 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5156,171,125 - 156,175,601 (-)EnsemblmRatBN7.2
Rnor_6.05162,406,599 - 162,411,066 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5162,406,599 - 162,411,063 (+)Ensemblrn6Rnor6.0
Rnor_5.05166,097,294 - 166,101,846 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45162,746,264 - 162,750,628 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5154,474,742 - 154,479,271 (-)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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Pramef20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85161,454,398 - 161,458,874 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5161,453,893 - 161,459,073 (-)EnsemblGRCr8
mRatBN7.25156,171,125 - 156,175,601 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5156,171,125 - 156,175,601 (-)EnsemblmRatBN7.2
Rnor_6.05162,406,599 - 162,411,066 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5162,406,599 - 162,411,063 (+)Ensemblrn6Rnor6.0
Rnor_5.05166,097,294 - 166,101,846 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45162,746,264 - 162,750,628 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5154,474,742 - 154,479,271 (-)NCBICelera
Cytogenetic Map5q36NCBI
PRAMEF20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38113,410,450 - 13,421,328 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl113,410,450 - 13,421,328 (+)Ensemblhg38GRCh38
GRCh37113,736,907 - 13,747,803 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36113,609,494 - 13,620,390 (+)NCBIBuild 36Build 36hg18NCBI36
Celera112,219,063 - 12,229,938 (+)NCBICelera
Cytogenetic Map1p36.21NCBI
HuRef112,253,404 - 12,264,251 (+)NCBIHuRef
CHM1_1113,535,692 - 13,546,570 (+)NCBICHM1_1
T2T-CHM13v2.0112,851,719 - 12,862,598 (+)NCBIT2T-CHM13v2.0
Pramel15
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394144,099,330 - 144,104,503 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4144,099,330 - 144,104,530 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm384144,372,760 - 144,377,933 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4144,372,760 - 144,377,933 (-)Ensemblmm10GRCm38
MGSCv374143,962,663 - 143,967,836 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv364143,639,447 - 143,644,620 (-)NCBIMGSCv36mm8
MGSCv364141,694,228 - 141,699,541 (-)NCBIMGSCv36mm8
Celera4145,973,855 - 145,979,151 (-)NCBICelera
Cytogenetic Map4E1NCBI
cM Map477.98NCBI
PRAMEF20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21213,494,300 - 213,506,635 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11212,745,084 - 212,760,561 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0112,006,813 - 12,010,964 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1113,553,798 - 13,564,608 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl113,553,798 - 13,564,608 (+)EnsemblpanPan2panpan1.1

Variants

.
Variants in Pramef20
34 total Variants

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
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
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5149805999162987697Rat
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
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5148093485172129029Rat
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

Markers in Region
D17S1835  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25156,176,205 - 156,177,162 (-)MAPPERmRatBN7.2
Rnor_6.05162,405,038 - 162,405,994NCBIRnor6.0
Rnor_5.05166,095,733 - 166,096,689UniSTSRnor5.0
Cytogenetic Map5q36UniSTS


Expression

RNA-SEQ Expression

appendage
ectoderm
integumental system
mesenchyme
nervous system
reproductive system
1 7 3 1 4 16

Sequence


Ensembl Acc Id: ENSRNOT00000091592   ⟹   ENSRNOP00000072516
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5161,453,893 - 161,459,073 (-)Ensembl
mRatBN7.2 Ensembl5156,171,125 - 156,175,601 (-)Ensembl
Rnor_6.0 Ensembl5162,406,599 - 162,411,063 (+)Ensembl
RefSeq Acc Id: XM_001077012   ⟹   XP_001077012
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85161,454,398 - 161,458,874 (-)NCBI
mRatBN7.25156,171,125 - 156,175,601 (-)NCBI
Rnor_6.05162,406,599 - 162,411,066 (+)NCBI
Rnor_5.05166,097,294 - 166,101,846 (+)NCBI
RGSC_v3.45162,746,264 - 162,750,628 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001421580 (Get FASTA)   NCBI Sequence Viewer  
  XP_001077012 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000072516
  ENSRNOP00000072516.1
RefSeq Acc Id: XP_001077012   ⟸   XM_001077012
- Sequence:
Ensembl Acc Id: ENSRNOP00000072516   ⟸   ENSRNOT00000091592

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K364-F1-model_v2 AlphaFold A0A0G2K364 1-477 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:1587437 AgrOrtholog
BioCyc Gene G2FUF-39274 BioCyc
Ensembl Genes ENSRNOG00000053942 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000091592 ENTREZGENE
  ENSRNOT00000091592.3 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:691150 UniProtKB/TrEMBL
NCBI Gene 691150 ENTREZGENE
PANTHER MELANOMA ANTIGEN PREFERENTIALLY EXPRESSED IN TUMORS UniProtKB/TrEMBL
  SIMILAR TO PREFERENTIALLY EXPRESSED ANTIGEN IN MELANOMA-LIKE 3 UniProtKB/TrEMBL
PhenoGen Pramef20 PhenoGen
PIRSF PRAME UniProtKB/TrEMBL
RatGTEx ENSRNOG00000053942 RatGTEx
Superfamily-SCOP RNI-like UniProtKB/TrEMBL
UniProt A0A0G2K364 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Pramef20  PRAME family member 20  LOC100364819  preferentially expressed antigen in melanoma-like 1-like  Data merged from RGD:2320246 1643240 APPROVED
2013-01-22 Pramef20  PRAME family member 20  pramef25  PRAME family member 25-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-09-18 pramef25  PRAME family member 25-like  Pramef20  PRAME family member 20  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100364819  preferentially expressed antigen in melanoma-like 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-01-09 LOC691150  similar to PRAME family member 5  LOC686447  similar to PRAME family member 5  Data merged from RGD:1597637 1643240 APPROVED
2006-11-20 LOC686447  similar to PRAME family member 5      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC691150  similar to PRAME family member 5      Symbol and Name status set to provisional 70820 PROVISIONAL