Raver1 (ribonucleoprotein, PTB-binding 1) - Rat Genome Database

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Gene: Raver1 (ribonucleoprotein, PTB-binding 1) Rattus norvegicus
Analyze
Symbol: Raver1
Name: ribonucleoprotein, PTB-binding 1
RGD ID: 1359190
Description: Predicted to enable RNA binding activity. Predicted to be located in cytoplasm and nucleus. Orthologous to human RAVER1 (ribonucleoprotein, PTB binding 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC298705; protein raver-1; RAVER1 homolog; RAVER1 homolog (human); Raver1h; ribonucleoprotein PTB-binding 1; similar to EXCretory canal abnormal EXC-7, ELAV type RNA binding protein (48.7 kD) (exc-7)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2819,610,464 - 19,629,188 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,610,466 - 19,629,152 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx823,629,875 - 23,648,565 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,927,729 - 21,946,421 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,840,134 - 19,858,824 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,092,084 - 22,111,863 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,092,094 - 22,111,863 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,148,754 - 22,168,072 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4820,096,974 - 20,115,289 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1820,096,980 - 20,115,289 (-)NCBI
Celera821,004,887 - 21,023,576 (-)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA)
nucleus  (IEA)

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. GOA pipeline RGD automated data pipeline
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
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:14633994   PMID:15489334   PMID:22681889  


Genomics

Comparative Map Data
Raver1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2819,610,464 - 19,629,188 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,610,466 - 19,629,152 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx823,629,875 - 23,648,565 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,927,729 - 21,946,421 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,840,134 - 19,858,824 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,092,084 - 22,111,863 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,092,094 - 22,111,863 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0822,148,754 - 22,168,072 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4820,096,974 - 20,115,289 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1820,096,980 - 20,115,289 (-)NCBI
Celera821,004,887 - 21,023,576 (-)NCBICelera
Cytogenetic Map8q13NCBI
RAVER1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381910,316,212 - 10,333,529 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1910,316,212 - 10,333,529 (-)EnsemblGRCh38hg38GRCh38
GRCh371910,426,888 - 10,444,205 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,287,888 - 10,305,314 (-)NCBINCBI36Build 36hg18NCBI36
Celera1910,322,277 - 10,339,705 (-)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef1910,007,146 - 10,024,575 (-)NCBIHuRef
CHM1_11910,427,421 - 10,444,848 (-)NCBICHM1_1
T2T-CHM13v2.01910,442,322 - 10,459,641 (-)NCBIT2T-CHM13v2.0
Raver1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39920,985,454 - 21,003,295 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl920,985,454 - 21,003,304 (-)EnsemblGRCm39 Ensembl
GRCm38921,074,158 - 21,091,999 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,074,158 - 21,092,008 (-)EnsemblGRCm38mm10GRCm38
MGSCv37920,878,602 - 20,896,432 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36920,817,922 - 20,842,389 (-)NCBIMGSCv36mm8
Celera918,342,872 - 18,360,702 (-)NCBICelera
Cytogenetic Map9A3NCBI
cM Map97.71NCBI
Raver1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554951,594,531 - 1,610,412 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554951,594,864 - 1,609,251 (-)NCBIChiLan1.0ChiLan1.0
RAVER1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11914,231,824 - 14,249,612 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0199,866,631 - 9,883,833 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11910,532,355 - 10,549,142 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1910,532,362 - 10,549,142 (-)Ensemblpanpan1.1panPan2
RAVER1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12050,784,068 - 50,798,303 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2050,653,826 - 50,668,049 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02051,305,704 - 51,319,929 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2051,304,534 - 51,319,931 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12050,511,848 - 50,526,071 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02050,940,625 - 50,954,836 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02051,181,734 - 51,195,963 (+)NCBIUU_Cfam_GSD_1.0
Raver1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,687,391 - 209,704,240 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936659650,473 - 667,382 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936659650,463 - 667,379 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAVER1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.169,364,903 - 9,387,874 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl69,366,151 - 9,383,633 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607410,655,263 - 10,673,534 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Raver1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248282,474,217 - 2,487,927 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248282,473,824 - 2,486,967 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Raver1
53 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:201
Count of miRNA genes:131
Interacting mature miRNAs:169
Transcripts:ENSRNOT00000046983
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat

Markers in Region
RH143439  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2819,619,528 - 19,619,628 (+)MAPPERmRatBN7.2
Rnor_6.0822,101,147 - 22,101,246NCBIRnor6.0
Rnor_5.0822,158,010 - 22,158,109UniSTSRnor5.0
RGSC_v3.4820,106,037 - 20,106,136UniSTSRGSC3.4
Celera821,013,943 - 21,014,042UniSTS
RH 3.4 Map8182.1UniSTS
Cytogenetic Map8q13UniSTS
UniSTS:236065  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2819,610,742 - 19,610,847 (+)MAPPERmRatBN7.2
Rnor_6.0822,092,361 - 22,092,465NCBIRnor6.0
Rnor_5.0822,149,033 - 22,149,137UniSTSRnor5.0
RGSC_v3.4820,097,251 - 20,097,355UniSTSRGSC3.4
Celera821,005,164 - 21,005,268UniSTS
Cytogenetic Map8q13UniSTS


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 3 35 40 29 19 29 1 66 29 41 11
Low 8 17 12 12 8 10 8 6 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000046983   ⟹   ENSRNOP00000048510
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl819,610,466 - 19,629,152 (-)Ensembl
Rnor_6.0 Ensembl822,092,094 - 22,111,863 (-)Ensembl
RefSeq Acc Id: NM_001013939   ⟹   NP_001013961
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2819,610,466 - 19,629,156 (-)NCBI
Rnor_6.0822,092,084 - 22,111,863 (-)NCBI
Rnor_5.0822,148,754 - 22,168,072 (-)NCBI
RGSC_v3.4820,096,974 - 20,115,289 (-)RGD
Celera821,004,887 - 21,023,576 (-)RGD
Sequence:
RefSeq Acc Id: XM_039080982   ⟹   XP_038936910
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2819,610,464 - 19,629,188 (-)NCBI
RefSeq Acc Id: NP_001013961   ⟸   NM_001013939
- UniProtKB: Q5XI28 (UniProtKB/Swiss-Prot),   A6JNN8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000048510   ⟸   ENSRNOT00000046983
RefSeq Acc Id: XP_038936910   ⟸   XM_039080982
- Peptide Label: isoform X1
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XI28-F1-model_v2 AlphaFold Q5XI28 1-748 view protein structure

Transcriptome

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

Promoters
RGD ID:13695775
Promoter ID:EPDNEW_R6299
Type:multiple initiation site
Name:Raver1_1
Description:ribonucleoprotein, PTB-binding 1
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_6.0822,111,869 - 22,111,929EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359190 AgrOrtholog
BioCyc Gene G2FUF-31439 BioCyc
Ensembl Genes ENSRNOG00000020710 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055012362 UniProtKB/Swiss-Prot
  ENSRNOG00060026098 UniProtKB/Swiss-Prot
  ENSRNOG00065012104 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000046983 ENTREZGENE
  ENSRNOT00000046983.4 UniProtKB/Swiss-Prot
  ENSRNOT00055021055 UniProtKB/Swiss-Prot
  ENSRNOT00060045179 UniProtKB/Swiss-Prot
  ENSRNOT00065019670 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7127766 IMAGE-MGC_LOAD
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RAVER1 UniProtKB/Swiss-Prot
  RAVER1_RRM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RAVER1_RRM3 UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:298705 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:95117 IMAGE-MGC_LOAD
NCBI Gene 298705 ENTREZGENE
PANTHER PTHR23189:SF46 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RNA RECOGNITION MOTIF-CONTAINING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Raver1 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020710 RatGTEx
  ENSRNOG00055012362 RatGTEx
  ENSRNOG00060026098 RatGTEx
  ENSRNOG00065012104 RatGTEx
SMART RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP RNA-binding domain, RBD UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6JNN8 ENTREZGENE, UniProtKB/TrEMBL
  Q5XI28 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Raver1  ribonucleoprotein, PTB-binding 1  Raver1h  RAVER1 homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Raver1h  RAVER1 homolog (human)  LOC298705  similar to EXCretory canal abnormal EXC-7, ELAV type RNA binding protein (48.7 kD) (exc-7)  Symbol and Name updated 1299863 APPROVED
2005-07-29 LOC298705  similar to EXCretory canal abnormal EXC-7, ELAV type RNA binding protein (48.7 kD) (exc-7)      Symbol and Name status set to provisional 70820 PROVISIONAL