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

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Gene: Rtraf (RNA transcription, translation and transport factor) Mus musculus
Analyze
Symbol: Rtraf
Name: RNA transcription, translation and transport factor
RGD ID: 1312306
MGI Page MGI
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. Is expressed in several structures, including alimentary system; brain; cardiovascular system; genitourinary system; and respiratory system. Orthologous to human RTRAF (RNA transcription, translation and transport factor).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 2700060E02Rik; hypothetical protein LOC68045; RIKEN cDNA 2700060E02 gene; UPF0568 protein C14orf166 homolog
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Rtraf-ps  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391419,861,470 - 19,873,891 (-)NCBIGRCm39mm39
GRCm39 Ensembl1419,861,419 - 19,873,892 (-)Ensembl
GRCm381419,811,402 - 19,823,823 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1419,811,351 - 19,823,824 (-)EnsemblGRCm38mm10GRCm38
MGSCv371420,630,624 - 20,643,045 (-)NCBIGRCm37mm9NCBIm37
MGSCv361418,602,098 - 18,614,519 (-)NCBImm8
Celera1416,194,399 - 16,206,819 (-)NCBICelera
Cytogenetic Map14A3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12520002   PMID:14610273   PMID:15226823   PMID:15489334   PMID:16141072  
PMID:16141073   PMID:16512683   PMID:18799693   PMID:19521500   PMID:21862448   PMID:21873635   PMID:24194600   PMID:26265008   PMID:26336360   PMID:26370502   PMID:26426291   PMID:27113764  
PMID:27746211   PMID:29530978   PMID:30550785   PMID:31040226   PMID:31138677   PMID:32098917   PMID:32325033   PMID:34133714  


Genomics

Comparative Map Data
Rtraf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391419,861,470 - 19,873,891 (-)NCBIGRCm39mm39
GRCm39 Ensembl1419,861,419 - 19,873,892 (-)Ensembl
GRCm381419,811,402 - 19,823,823 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1419,811,351 - 19,823,824 (-)EnsemblGRCm38mm10GRCm38
MGSCv371420,630,624 - 20,643,045 (-)NCBIGRCm37mm9NCBIm37
MGSCv361418,602,098 - 18,614,519 (-)NCBImm8
Celera1416,194,399 - 16,206,819 (-)NCBICelera
Cytogenetic Map14A3NCBI
RTRAF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381451,989,546 - 52,010,694 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1451,989,514 - 52,010,694 (+)EnsemblGRCh38hg38GRCh38
GRCh371452,456,264 - 52,477,412 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361451,525,943 - 51,541,158 (+)NCBINCBI36hg18NCBI36
Build 341451,525,942 - 51,667,191NCBI
Celera1432,323,222 - 32,338,419 (+)NCBI
Cytogenetic Map14q22.1NCBI
HuRef1432,616,898 - 32,632,090 (+)NCBIHuRef
CHM1_11452,394,686 - 52,409,879 (+)NCBICHM1_1
Rtraf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2154,447,243 - 4,457,973 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl154,442,573 - 4,457,972 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1154,780,320 - 4,801,091 (+)NCBI
Celera15150,595 - 161,034 (-)NCBICelera
Cytogenetic Map15p16NCBI
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
PanPan1.11450,874,274 - 50,889,493 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1450,874,274 - 50,889,493 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01432,589,078 - 32,604,286 (+)NCBIMhudiblu_PPA_v0panPan3
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 (+)NCBI
ROS_Cfam_1.0828,402,398 - 28,417,391 (+)NCBI
ROS_Cfam_1.0 Ensembl828,402,487 - 28,417,249 (+)Ensembl
UMICH_Zoey_3.1828,071,637 - 28,086,629 (+)NCBI
UNSW_CanFamBas_1.0828,132,425 - 28,147,419 (+)NCBI
UU_Cfam_GSD_1.0828,479,155 - 28,494,152 (+)NCBI
Rtraf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864060,441,127 - 60,456,119 (+)NCBI
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 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605317,381,922 - 17,397,082 (+)NCBIVero_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_1.0hetGla2

Position Markers
AB017202  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381419,811,014 - 19,811,274UniSTSGRCm38
MGSCv371420,630,236 - 20,630,496UniSTSGRCm37
Celera1416,194,011 - 16,194,271UniSTS
Cytogenetic Map14A3UniSTS
Whitehead/MRC_RH1426.79UniSTS
AW547149  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381419,811,518 - 19,811,597UniSTSGRCm38
MGSCv371420,630,740 - 20,630,819UniSTSGRCm37
Celera1416,194,515 - 16,194,594UniSTS
Cytogenetic Map14A3UniSTS
Whitehead/MRC_RH1424.69UniSTS
UniSTS:235896  
Mouse AssemblyChrPosition (strand)SourceJBrowse
MGSCv37388,380,953 - 88,381,063UniSTSGRCm37
MGSCv37859,999,575 - 59,999,685UniSTSGRCm37
Celera388,616,822 - 88,616,932UniSTS
Celera860,159,935 - 60,160,045UniSTS
UniSTS:237133  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381419,811,300 - 19,811,481UniSTSGRCm38
MGSCv371420,630,522 - 20,630,703UniSTSGRCm37
Celera1416,194,297 - 16,194,478UniSTS
Cytogenetic Map14A3UniSTS


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301991Wta3_mweight adult 3 (mouse)Not determined14388747337887650Mouse
1300779Dyscalc4_mdystrophic cardiac calcinosis 4 (mouse)Not determined141221287146213007Mouse
1300544Hypn_mhyperinsulinemia (mouse)Not determined141516061649160765Mouse
1301372Sluc13_msusceptibility to lung cancer 13 (mouse)Not determined141882760452827726Mouse
4141265Appd2_mAPP associated premature death 2 (mouse)Not determined14594555230114862Mouse
4141550Dbm3_mdiabetes modifier 3 (mouse)Not determined514347339143596Mouse
10412071Ssen3_msuseptibility to Sendai virus 3 (mouse)Not determined14126987934Mouse
4141864Mrdq4_mmodifier of retinal degeneration QTL 4 (mouse)Not determined992324548765082Mouse
27226748Femd8_mfemur midshaft diameter 8, 10 week (mouse)141376927346737457Mouse
11532711Sluc40_msusceptibility to lung cancer 40 (mouse)14127379943Mouse
27226752Femd4_mfemur midshaft diameter 4, 5 week (mouse)141376927347237457Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:194
Count of miRNA genes:172
Interacting mature miRNAs:181
Transcripts:ENSMUST00000022341
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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000022341   ⟹   ENSMUSP00000022341
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1419,861,419 - 19,873,892 (-)Ensembl
GRCm38.p6 Ensembl1419,811,351 - 19,823,824 (-)Ensembl
RefSeq Acc Id: ENSMUST00000225615
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1419,870,065 - 19,873,123 (-)Ensembl
GRCm38.p6 Ensembl1419,819,997 - 19,823,055 (-)Ensembl
RefSeq Acc Id: NM_026528   ⟹   NP_080804
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391419,861,470 - 19,873,891 (-)NCBI
GRCm381419,811,402 - 19,823,823 (-)ENTREZGENE
MGSCv371420,630,624 - 20,643,045 (-)RGD
Celera1416,194,399 - 16,206,819 (-)RGD
cM Map14 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_080804   ⟸   NM_026528
- UniProtKB: Q9CQE8 (UniProtKB/Swiss-Prot),   Q4VA29 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000022341   ⟸   ENSMUST00000022341

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9CQE8-F1-model_v2 AlphaFold Q9CQE8 1-244 view protein structure

Promoters
RGD ID:8681574
Promoter ID:EPDNEW_M18818
Type:initiation region
Name:Rtraf_1
Description:Mus musculus RNA transcription, translation and transport factor, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381419,823,824 - 19,823,884EPDNEW
RGD ID:6848633
Promoter ID:MM_TRO:2949
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:MEF_B6
Transcripts:MTR003116.14.340.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361420,642,291 - 20,642,791 (-)MPROMDB
RGD ID:6824564
Promoter ID:MM_KWN:15777
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B6,   Spleen
Transcripts:NM_026528
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361420,642,926 - 20,643,497 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1915295 AgrOrtholog
Ensembl Genes ENSMUSG00000021807 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000022341 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000022341 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro RTRAF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:68045 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1915295 ENTREZGENE
NCBI Gene 68045 ENTREZGENE
PANTHER PTHR15924 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RLL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rtraf PhenoGen
UniProt Q4VA29 ENTREZGENE, UniProtKB/TrEMBL
  Q9CQE8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-09-26 Rtraf  RNA transcription, translation and transport factor  2700060E02Rik  RIKEN cDNA 2700060E02 gene  Symbol and/or name change 5135510 APPROVED