Rtraf-ps2 (RNA transcription, translation and transport factor, pseudogene 2) - Rat Genome Database

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Gene: Rtraf-ps2 (RNA transcription, translation and transport factor, pseudogene 2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Rtraf-ps2
Name: RNA transcription, translation and transport factor, pseudogene 2
RGD ID: 1565933
Description: Predicted to enable RNA binding activity. Predicted to be involved in tRNA splicing, via endonucleolytic cleavage and ligation. Predicted to be part of tRNA-splicing ligase complex. Orthologous to human RTRAF (RNA transcription, translation and transport factor).
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: VALIDATED
Previously known as: Ac1591; hypothetical protein LOC360933; LOC360933; similar to Ac1591; uncharacterized protein LOC360933
RGD Orthologs
Alliance Genes
More Info homologs ...
Related Functional Gene: Rtraf  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21439,745,222 - 39,791,427 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1439,745,720 - 39,791,430 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1440,101,325 - 40,147,520 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01441,401,390 - 41,447,587 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01439,882,208 - 39,928,403 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01441,380,939 - 41,433,918 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1441,388,563 - 41,433,915 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01441,185,952 - 41,231,346 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41442,329,680 - 42,382,683 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1438,927,840 - 38,973,379 (+)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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
Additional References at PubMed
PMID:25931508  


Genomics

Variants

.
Variants in Rtraf-ps2
346 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:19
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000048329
Prediction methods: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
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
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
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat


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
Low 1 1 18 4 16 4 9 7 8 9
Below cutoff 1 9 8 6 2 6 7 9 1 3 3 1 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048329   ⟹   ENSRNOP00000039645
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1439,745,720 - 39,791,430 (+)Ensembl
Rnor_6.0 Ensembl1441,388,563 - 41,433,915 (+)Ensembl
RefSeq Acc Id: NR_172022
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21439,745,222 - 39,791,427 (+)NCBI
Protein Sequences
GenBank Protein AAP78768 (Get FASTA)   NCBI Sequence Viewer  
  EDL90017 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000039645   ⟸   ENSRNOT00000048329

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7TQ71-F1-model_v2 AlphaFold Q7TQ71 1-333 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:1565933 AgrOrtholog
BioCyc Gene G2FUF-15804 BioCyc
Ensembl Genes ENSRNOG00000029734 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039645.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048329 ENTREZGENE
  ENSRNOT00000048329.4 UniProtKB/TrEMBL
InterPro Putative_carnitine_def-assoc UniProtKB/TrEMBL
KEGG Report rno:360933 UniProtKB/TrEMBL
NCBI Gene 360933 ENTREZGENE
PANTHER PTHR15924 UniProtKB/TrEMBL
  RNA TRANSCRIPTION, TRANSLATION AND TRANSPORT FACTOR PROTEIN UniProtKB/TrEMBL
Pfam RLL UniProtKB/TrEMBL
PhenoGen Rtraf-ps2 PhenoGen
UniProt A6JD95_RAT UniProtKB/TrEMBL
  F7EZS3_RAT UniProtKB/TrEMBL
UniProt Secondary Q7TQ71 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-10 Rtraf-ps2  RNA transcription, translation and transport factor, pseudogene 2  LOC360933  similar to Ac1591  Symbol and Name Changed 1299863 APPROVED
2006-02-09 LOC360933  similar to Ac1591      Symbol and Name status set to provisional 70820 PROVISIONAL