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

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Gene: Rtraf (RNA transcription, translation and transport factor) Rattus norvegicus
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Symbol: Rtraf
Name: RNA transcription, translation and transport factor
RGD ID: 1304704
Description: Predicted to enable RNA binding activity; RNA polymerase II complex binding activity; and identical protein binding activity. Predicted to be involved in negative regulation of protein kinase activity; positive regulation of transcription by RNA polymerase II; and tRNA splicing, via endonucleolytic cleavage and ligation. Predicted to be located in microtubule cytoskeleton; nucleoplasm; and perinuclear region of cytoplasm. Predicted to be part of tRNA-splicing ligase complex. Orthologous to human RTRAF (RNA transcription, translation and transport factor); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; ethanol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC302247; LOC302247; LRRGT00192; RGD1304704; similar to Hypothetical protein CGI-99; uncharacterized protein LOC302247; UPF0568 protein C14orf166 homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Rtraf-ps2  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8154,482,699 - 4,507,115 (+)NCBIGRCr8
mRatBN7.2154,447,243 - 4,457,973 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl154,442,573 - 4,457,972 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx154,457,639 - 4,468,370 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0155,844,087 - 5,854,816 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0154,456,473 - 4,467,202 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0154,882,925 - 4,893,890 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl154,882,947 - 4,893,919 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,973,714 - 8,984,679 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,790,458 - 4,800,905 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1154,780,320 - 4,801,091 (+)NCBI
Celera15150,595 - 161,034 (-)NCBICelera
Cytogenetic Map15p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Landscape of the hnRNP K protein-protein interactome. Mikula M, etal., Proteomics. 2006 Apr;6(8):2395-406.
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
Additional References at PubMed
PMID:15147888   PMID:16950395   PMID:21311021   PMID:22658674   PMID:24608264   PMID:24870230   PMID:25931508   PMID:35352799  


Genomics

Comparative Map Data
Rtraf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8154,482,699 - 4,507,115 (+)NCBIGRCr8
mRatBN7.2154,447,243 - 4,457,973 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl154,442,573 - 4,457,972 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx154,457,639 - 4,468,370 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0155,844,087 - 5,854,816 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0154,456,473 - 4,467,202 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0154,882,925 - 4,893,890 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl154,882,947 - 4,893,919 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,973,714 - 8,984,679 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,790,458 - 4,800,905 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1154,780,320 - 4,801,091 (+)NCBI
Celera15150,595 - 161,034 (-)NCBICelera
Cytogenetic Map15p16NCBI
RTRAF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381451,989,546 - 52,010,694 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1451,989,514 - 52,010,694 (+)EnsemblGRCh38hg38GRCh38
GRCh371452,456,264 - 52,477,412 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361451,525,943 - 51,541,158 (+)NCBINCBI36Build 36hg18NCBI36
Build 341451,525,942 - 51,667,191NCBI
Celera1432,323,222 - 32,338,419 (+)NCBICelera
Cytogenetic Map14q22.1NCBI
HuRef1432,616,898 - 32,632,090 (+)NCBIHuRef
CHM1_11452,394,686 - 52,409,879 (+)NCBICHM1_1
T2T-CHM13v2.01446,196,590 - 46,217,738 (+)NCBIT2T-CHM13v2.0
Rtraf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391419,861,470 - 19,873,891 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1419,861,419 - 19,873,892 (-)EnsemblGRCm39 Ensembl
GRCm381419,811,402 - 19,823,823 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1419,811,351 - 19,823,824 (-)EnsemblGRCm38mm10GRCm38
MGSCv371420,630,624 - 20,643,045 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361418,602,098 - 18,614,519 (-)NCBIMGSCv36mm8
Celera1416,194,399 - 16,206,819 (-)NCBICelera
Cytogenetic Map14A3NCBI
cM Map1410.95NCBI
Rtraf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540911,034,815 - 11,049,878 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540911,034,815 - 11,049,400 (-)NCBIChiLan1.0ChiLan1.0
RTRAF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21553,123,300 - 53,138,555 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11452,339,811 - 52,355,066 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01432,589,078 - 32,604,286 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11450,874,274 - 50,889,493 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1450,874,274 - 50,889,493 (+)Ensemblpanpan1.1panPan2
RTRAF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1828,224,365 - 28,243,129 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha827,977,089 - 27,995,838 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0828,402,398 - 28,417,391 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl828,402,487 - 28,417,249 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1828,071,637 - 28,086,629 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0828,132,425 - 28,147,419 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0828,479,155 - 28,494,152 (+)NCBIUU_Cfam_GSD_1.0
Rtraf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864060,441,127 - 60,456,119 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493649513,735,580 - 13,750,554 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTRAF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1181,681,352 - 181,698,979 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11181,681,368 - 181,698,980 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21201,953,129 - 201,970,820 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RTRAF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12429,091,241 - 29,106,349 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605317,381,922 - 17,397,082 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rtraf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473117,032,638 - 17,047,165 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rtraf
367 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:24
Count of miRNA genes:20
Interacting mature miRNAs:24
Transcripts:ENSRNOT00000049255
Prediction methods:Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15231575947315759Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15139411584Rat
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15132342855Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15144836456Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
1300142Bp191Blood pressure QTL 1913.14arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)15115177511Rat

Markers in Region
AA945900  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2154,458,226 - 4,458,364 (+)MAPPERmRatBN7.2
Rnor_6.0154,894,144 - 4,894,281NCBIRnor6.0
Rnor_5.0158,984,933 - 8,985,070UniSTSRnor5.0
RGSC_v3.4154,801,328 - 4,801,465UniSTSRGSC3.4
Celera15150,035 - 150,172UniSTS
RH 3.4 Map1568.1UniSTS
Cytogenetic Map15p16UniSTS
UniSTS:235896  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8154,496,498 - 4,497,473 (+)Marker Load Pipeline
mRatBN7.2154,447,355 - 4,448,330 (+)MAPPERmRatBN7.2
Rnor_6.0154,883,033 - 4,884,007NCBIRnor6.0
Rnor_5.0158,973,822 - 8,974,796UniSTSRnor5.0
RGSC_v3.4154,790,458 - 4,791,432UniSTSRGSC3.4
Celera15160,060 - 161,034UniSTS
Cytogenetic Map15p16UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000049255   ⟹   ENSRNOP00000049155
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl154,442,573 - 4,457,970 (+)Ensembl
Rnor_6.0 Ensembl154,882,947 - 4,893,919 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092002   ⟹   ENSRNOP00000070052
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl154,447,356 - 4,457,972 (+)Ensembl
Rnor_6.0 Ensembl154,883,033 - 4,893,721 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101009   ⟹   ENSRNOP00000084953
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl154,447,270 - 4,457,970 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000120090   ⟹   ENSRNOP00000089550
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl154,447,272 - 4,457,970 (+)Ensembl
RefSeq Acc Id: NM_001395114   ⟹   NP_001382043
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8154,496,394 - 4,507,115 (+)NCBI
mRatBN7.2154,447,251 - 4,457,973 (+)NCBI
RefSeq Acc Id: XM_006251638   ⟹   XP_006251700
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8154,496,383 - 4,507,112 (+)NCBI
mRatBN7.2154,447,243 - 4,457,973 (+)NCBI
Rnor_6.0154,882,925 - 4,893,890 (+)NCBI
Rnor_5.0158,973,714 - 8,984,679 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063274191   ⟹   XP_063130261
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8154,482,699 - 4,507,112 (+)NCBI
RefSeq Acc Id: XP_006251700   ⟸   XM_006251638
- Peptide Label: isoform X2
- UniProtKB: A0A8I6GBA2 (UniProtKB/TrEMBL),   A0A8I6AA36 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000070052   ⟸   ENSRNOT00000092002
Ensembl Acc Id: ENSRNOP00000049155   ⟸   ENSRNOT00000049255
Ensembl Acc Id: ENSRNOP00000084953   ⟸   ENSRNOT00000101009
Ensembl Acc Id: ENSRNOP00000089550   ⟸   ENSRNOT00000120090
RefSeq Acc Id: NP_001382043   ⟸   NM_001395114
- UniProtKB: F7EMB2 (UniProtKB/TrEMBL),   A6KKK9 (UniProtKB/TrEMBL),   A0A8I6AA36 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063130261   ⟸   XM_063274191
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AA36 (UniProtKB/TrEMBL),   A6KKK9 (UniProtKB/TrEMBL),   F7EMB2 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6QI16-F1-model_v2 AlphaFold Q6QI16 1-296 view protein structure

Transcriptome

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

Promoters
RGD ID:13699573
Promoter ID:EPDNEW_R10095
Type:initiation region
Name:Rtraf_1
Description:RNA transcription, translation and transport factor
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_6.0154,882,981 - 4,883,041EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304704 AgrOrtholog
BioCyc Gene G2FUF-14518 BioCyc
Ensembl Genes ENSRNOG00000000340 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049255 ENTREZGENE
  ENSRNOT00000049255.4 UniProtKB/TrEMBL
  ENSRNOT00000092002 ENTREZGENE
  ENSRNOT00000092002.2 UniProtKB/TrEMBL
  ENSRNOT00000101009 ENTREZGENE
  ENSRNOT00000101009.1 UniProtKB/TrEMBL
  ENSRNOT00000120090.1 UniProtKB/TrEMBL
InterPro Putative_carnitine_def-assoc UniProtKB/TrEMBL
NCBI Gene 302247 ENTREZGENE
PANTHER PTHR15924 UniProtKB/TrEMBL
Pfam RLL UniProtKB/TrEMBL
PhenoGen Rtraf PhenoGen
RatGTEx ENSRNOG00000000340 RatGTEx
UniProt A0A8I6AA36 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GBA2 ENTREZGENE, UniProtKB/TrEMBL
  A6KKK9 ENTREZGENE, UniProtKB/TrEMBL
  F7EMB2 ENTREZGENE, UniProtKB/TrEMBL
  Q6QI16_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-09-26 Rtraf  RNA transcription, translation and transport factor  RGD1304704  similar to Hypothetical protein CGI-99  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1304704  similar to Hypothetical protein CGI-99  RGD1304704_predicted  similar to Hypothetical protein CGI-99 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1304704_predicted  similar to Hypothetical protein CGI-99 (predicted)  LOC302247_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC302247_predicted  similar to Hypothetical protein CGI-99 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL