Pramef20l1 (PRAME family member 20 like 1) - Rat Genome Database

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Gene: Pramef20l1 (PRAME family member 20 like 1) Rattus norvegicus
Analyze
Symbol: Pramef20l1 (Ensembl: RGD1561699)
Name: PRAME family member 20 like 1 (Ensembl:similar to DNA segment, Chr 5, ERATO Doi 577, expressed)
RGD ID: 1561699
Description: Predicted to be involved in several processes, including negative regulation of DNA-templated transcription; negative regulation of apoptotic process; and positive regulation of cell population proliferation. Predicted to be active in cytoplasm. Orthologous to several human genes including PRAMEF1 (PRAME family member 1); PRAMEF10 (PRAME family member 10); and PRAMEF11 (PRAME family member 11).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC501890; LOC501900; PRAME family member 20-like; PRAME family member 3-like; PRAME family member 8-like; RGD1559999; RGD1561699; similar to DNA segment, Chr 5, ERATO Doi 577, expressed
RGD Orthologs
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81414,362,506 - 14,365,164 (+)NCBIGRCr8
mRatBN7.21414,058,560 - 14,061,218 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1414,058,525 - 14,061,218 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01415,424,025 - 15,426,702 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1415,424,044 - 15,426,702 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01415,363,285 - 15,365,943 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41415,328,520 - 15,331,174 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1413,788,718 - 13,791,397 (-)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA)

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
Pramef20l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81414,362,506 - 14,365,164 (+)NCBIGRCr8
mRatBN7.21414,058,560 - 14,061,218 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1414,058,525 - 14,061,218 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01415,424,025 - 15,426,702 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1415,424,044 - 15,426,702 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01415,363,285 - 15,365,943 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41415,328,520 - 15,331,174 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1413,788,718 - 13,791,397 (-)NCBICelera
Cytogenetic Map14p22NCBI
LOC108168685
(Mus musculus - house mouse)		 No map positions available.

Variants

.
Variants in Pramef20l1
21 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:102
Count of miRNA genes:84
Interacting mature miRNAs:88
Transcripts:ENSRNOT00000068306
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14121760616960180Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14381307418274691Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14381307418274691Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat


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

reproductive system
High
Medium
Low
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000051054   ⟹   ENSRNOP00000047988
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1415,706,961 - 15,709,518 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000068306   ⟹   ENSRNOP00000059812
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1415,424,044 - 15,426,702 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101209   ⟹   ENSRNOP00000084586
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1414,058,525 - 14,061,218 (+)Ensembl
RefSeq Acc Id: XM_006250714   ⟹   XP_006250776
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81414,362,506 - 14,365,164 (+)NCBI
mRatBN7.21414,058,560 - 14,061,218 (+)NCBI
Rnor_6.01415,424,025 - 15,426,702 (-)NCBI
Rnor_5.01415,363,285 - 15,365,943 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063273872   ⟹   XP_063129942
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81414,362,506 - 14,364,731 (+)NCBI
Protein Sequences
Protein RefSeqs XP_006250776 (Get FASTA)   NCBI Sequence Viewer  
  XP_063129942 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000084586
  ENSRNOP00000084586.1
Reference Protein Sequences
RefSeq Acc Id: XP_006250776   ⟸   XM_006250714
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A1M8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000059812   ⟸   ENSRNOT00000068306
RefSeq Acc Id: ENSRNOP00000047988   ⟸   ENSRNOT00000051054
RefSeq Acc Id: ENSRNOP00000084586   ⟸   ENSRNOT00000101209
RefSeq Acc Id: XP_063129942   ⟸   XM_063273872
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRT5-F1-model_v2 AlphaFold D3ZRT5 1-481 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:1561699 AgrOrtholog
BioCyc Gene G2FUF-16302 BioCyc
Ensembl Genes ENSRNOG00000047839 Ensembl
  ENSRNOG00000048778 Ensembl
  ENSRNOG00000065680 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000101209 ENTREZGENE
  ENSRNOT00000101209.1 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro LRR_dom_sf UniProtKB/TrEMBL
  PRAME_family UniProtKB/TrEMBL
NCBI Gene 501890 ENTREZGENE
PANTHER D5ERTD577E PROTEIN-RELATED UniProtKB/TrEMBL
  SIMILAR TO PREFERENTIALLY EXPRESSED ANTIGEN IN MELANOMA-LIKE 3 UniProtKB/TrEMBL
PhenoGen Pramef20l1 PhenoGen
PIRSF PRAME UniProtKB/TrEMBL
RatGTEx ENSRNOG00000047839 RatGTEx
  ENSRNOG00000048778 RatGTEx
  ENSRNOG00000065680 RatGTEx
Superfamily-SCOP RNI-like UniProtKB/TrEMBL
UniProt A0A8I6A1M8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Pramef20l1  PRAME family member 20 like 1  RGD1561699  similar to DNA segment, Chr 5, ERATO Doi 577, expressed  Symbol and Name Changed 1299863 APPROVED
2022-06-02 RGD1561699  similar to DNA segment, Chr 5, ERATO Doi 577, expressed  RGD1561699  similar to DNA segment, Chr 5, ERATO Doi 577, expressed  Data merged from RGD:149736186 737654 PROVISIONAL
2021-08-09 RGD1561699  similar to DNA segment, Chr 5, ERATO Doi 577, expressed      Symbol and Name status set to provisional 45752 PROVISIONAL
2021-03-09 RGD1561699  similar to DNA segment, Chr 5, ERATO Doi 577, expressed  RGD1559999  similar to DNA segment, Chr 5, ERATO Doi 577, expressed  Data merged from RGD:1559999 737654 PROVISIONAL
2008-04-30 RGD1561699  similar to DNA segment, Chr 5, ERATO Doi 577, expressed   RGD1561699_predicted  similar to DNA segment, Chr 5, ERATO Doi 577, expressed (predicted)  'predicted' is removed 2292626 APPROVED
2008-04-30 RGD1559999  similar to DNA segment, Chr 5, ERATO Doi 577, expressed   RGD1559999_predicted  similar to DNA segment, Chr 5, ERATO Doi 577, expressed (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1559999_predicted  similar to DNA segment, Chr 5, ERATO Doi 577, expressed (predicted)  LOC501900  similar to DNA segment, Chr 5, ERATO Doi 577, expressed  Symbol and Name status set to approved 1299863 APPROVED
2006-03-07 RGD1561699_predicted  similar to DNA segment, Chr 5, ERATO Doi 577, expressed (predicted)  LOC501890  similar to DNA segment, Chr 5, ERATO Doi 577, expressed  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501890  similar to DNA segment, Chr 5, ERATO Doi 577, expressed      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-02-09 LOC501900  similar to DNA segment, Chr 5, ERATO Doi 577, expressed      Symbol and Name status set to provisional 70820 PROVISIONAL