Rp9 (RP9, pre-mRNA splicing factor) - Rat Genome Database

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Gene: Rp9 (RP9, pre-mRNA splicing factor) Rattus norvegicus
Analyze
Symbol: Rp9
Name: RP9, pre-mRNA splicing factor
RGD ID: 1559759
Description: Predicted to be involved in cognition. Predicted to be part of signal recognition particle receptor complex. Human ortholog(s) of this gene implicated in retinitis pigmentosa 9. Orthologous to human RP9 (RP9 pre-mRNA splicing factor); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; aflatoxin B1.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC363032; retinitis pigmentosa 9; retinitis pigmentosa 9 (human); retinitis pigmentosa 9 homolog; retinitis pigmentosa 9 homolog (human); RGD1559759; Rp9h; similar to PAP-1
RGD Orthologs
Human
Mouse
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8829,218,564 - 29,281,211 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl829,217,346 - 29,281,150 (-)EnsemblGRCr8
mRatBN7.2820,955,447 - 21,005,225 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,941,362 - 21,005,175 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx825,003,304 - 25,033,903 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0823,300,254 - 23,330,855 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0821,204,052 - 21,234,651 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0823,450,111 - 23,482,939 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl823,450,111 - 23,482,939 (-)Ensemblrn6Rnor6.0
Rnor_5.0823,502,288 - 23,522,447 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4821,775,021 - 21,795,978 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera822,360,579 - 22,391,176 (-)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cognition  (ISO)
RNA splicing  (IEA)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15652350   PMID:22681889   PMID:23227193  


Genomics

Comparative Map Data
Rp9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8829,218,564 - 29,281,211 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl829,217,346 - 29,281,150 (-)EnsemblGRCr8
mRatBN7.2820,955,447 - 21,005,225 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,941,362 - 21,005,175 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx825,003,304 - 25,033,903 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0823,300,254 - 23,330,855 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0821,204,052 - 21,234,651 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0823,450,111 - 23,482,939 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl823,450,111 - 23,482,939 (-)Ensemblrn6Rnor6.0
Rnor_5.0823,502,288 - 23,522,447 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4821,775,021 - 21,795,978 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera822,360,579 - 22,391,176 (-)NCBICelera
Cytogenetic Map8q13NCBI
RP9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38733,094,797 - 33,109,404 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl733,094,797 - 33,109,405 (-)Ensemblhg38GRCh38
GRCh37733,134,409 - 33,149,016 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36733,100,934 - 33,115,527 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34732,907,651 - 32,922,242NCBI
Celera733,116,207 - 33,130,800 (-)NCBICelera
Cytogenetic Map7p14.3NCBI
HuRef733,013,685 - 33,028,278 (-)NCBIHuRef
CHM1_1733,134,259 - 33,148,851 (-)NCBICHM1_1
T2T-CHM13v2.0733,234,370 - 33,248,976 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2733,178,937 - 33,193,530 (-)NCBI
Rp9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39922,359,607 - 22,379,652 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl922,322,343 - 22,381,039 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38922,448,311 - 22,468,356 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl922,411,047 - 22,469,743 (-)Ensemblmm10GRCm38
MGSCv37922,252,755 - 22,272,800 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36922,198,740 - 22,218,725 (-)NCBIMGSCv36mm8
Celera919,718,699 - 19,738,744 (-)NCBICelera
Cytogenetic Map9A3NCBI
cM Map99.16NCBI
RP9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11445,167,392 - 45,187,687 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1445,167,842 - 45,187,672 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1444,598,445 - 44,622,357 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01445,102,720 - 45,126,648 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.11445,206,671 - 45,230,597 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01444,888,764 - 44,912,693 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01445,262,725 - 45,286,654 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Rp9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511889,475,933 - 89,510,566 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364788,704,450 - 8,722,430 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364788,687,584 - 8,722,345 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100738822
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1840,539,046 - 40,564,228 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11840,397,551 - 40,415,127 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21844,339,762 - 44,357,345 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RP9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12125,315,612 - 25,330,256 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2125,315,565 - 25,334,399 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604281,224,808 - 81,239,386 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rp9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248962,968,652 - 2,982,098 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248962,968,652 - 2,982,098 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Rp9
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1818,659,746 - 18,690,260 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rp9
676 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:33
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000065367
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

Markers in Region
RH129794  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,983,583 - 20,983,733 (+)MAPPERmRatBN7.2
Rnor_6.0823,459,124 - 23,459,273NCBIRnor6.0
Rnor_5.0823,511,301 - 23,511,450UniSTSRnor5.0
RGSC_v3.4821,784,034 - 21,784,183UniSTSRGSC3.4
Celera822,369,592 - 22,369,741UniSTS
RH 3.4 Map8182.9UniSTS
Cytogenetic Map8q13UniSTS
AA850211  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,990,027 - 20,990,138 (+)MAPPERmRatBN7.2
Rnor_6.0823,465,290 - 23,465,400NCBIRnor6.0
Rnor_5.0823,517,109 - 23,517,219UniSTSRnor5.0
RGSC_v3.4821,790,871 - 21,790,981UniSTSRGSC3.4
Celera822,376,033 - 22,376,143UniSTS
RH 3.4 Map8207.69UniSTS
Cytogenetic Map8q13UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000065367   ⟹   ENSRNOP00000060995
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl829,250,553 - 29,281,150 (-)Ensembl
mRatBN7.2 Ensembl820,974,570 - 21,005,175 (-)Ensembl
Rnor_6.0 Ensembl823,450,111 - 23,482,939 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000107195   ⟹   ENSRNOP00000087499
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl829,259,527 - 29,281,150 (-)Ensembl
mRatBN7.2 Ensembl820,983,545 - 21,005,175 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000116516   ⟹   ENSRNOP00000091532
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl829,217,346 - 29,281,150 (-)Ensembl
mRatBN7.2 Ensembl820,941,362 - 21,005,175 (-)Ensembl
RefSeq Acc Id: NM_001108756   ⟹   NP_001102226
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8829,250,553 - 29,281,150 (-)NCBI
mRatBN7.2820,974,570 - 21,005,175 (-)NCBI
Rnor_6.0823,450,111 - 23,482,939 (-)NCBI
Rnor_5.0823,502,288 - 23,522,447 (-)NCBI
RGSC_v3.4821,775,021 - 21,795,978 (-)RGD
Celera822,360,579 - 22,391,176 (-)RGD
Sequence:
RefSeq Acc Id: NM_001401177   ⟹   NP_001388106
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8829,259,527 - 29,281,150 (-)NCBI
mRatBN7.2820,983,545 - 21,005,175 (-)NCBI
RefSeq Acc Id: XM_039081715   ⟹   XP_038937643
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8829,250,393 - 29,281,211 (-)NCBI
mRatBN7.2820,974,769 - 21,005,225 (-)NCBI
RefSeq Acc Id: XM_039081716   ⟹   XP_038937644
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8829,218,564 - 29,281,211 (-)NCBI
mRatBN7.2820,955,447 - 21,005,225 (-)NCBI
RefSeq Acc Id: NP_001102226   ⟸   NM_001108756
- Peptide Label: isoform 2
- UniProtKB: F1LYD8 (UniProtKB/TrEMBL),   A6JP01 (UniProtKB/TrEMBL),   A0A8I6AFT5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000060995   ⟸   ENSRNOT00000065367
RefSeq Acc Id: XP_038937644   ⟸   XM_039081716
- Peptide Label: isoform X2
- UniProtKB: A0A8I6AFT5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038937643   ⟸   XM_039081715
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AFT5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000091532   ⟸   ENSRNOT00000116516
Ensembl Acc Id: ENSRNOP00000087499   ⟸   ENSRNOT00000107195
RefSeq Acc Id: NP_001388106   ⟸   NM_001401177
- Peptide Label: isoform 1
- UniProtKB: A0A8I6A7C2 (UniProtKB/TrEMBL),   A6JP02 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LYD8-F1-model_v2 AlphaFold F1LYD8 1-150 view protein structure

Transcriptome

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

Promoters
RGD ID:13695808
Promoter ID:EPDNEW_R6332
Type:multiple initiation site
Name:Rp9_1
Description:retinitis pigmentosa 9
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_6.0823,482,964 - 23,483,024EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559759 AgrOrtholog
BioCyc Gene G2FUF-31375 BioCyc
Ensembl Genes ENSRNOG00000029456 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065367 ENTREZGENE
  ENSRNOT00000065367.4 UniProtKB/TrEMBL
  ENSRNOT00000107195 ENTREZGENE
  ENSRNOT00000107195.2 UniProtKB/TrEMBL
  ENSRNOT00000116516.2 UniProtKB/TrEMBL
InterPro PAP-1 UniProtKB/TrEMBL
KEGG Report rno:363032 UniProtKB/TrEMBL
NCBI Gene 363032 ENTREZGENE
PANTHER PTHR35252 UniProtKB/TrEMBL
  RETINITIS PIGMENTOSA 9 PROTEIN UniProtKB/TrEMBL
PhenoGen Rp9 PhenoGen
RatGTEx ENSRNOG00000029456 RatGTEx
UniProt A0A8I6A7C2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AFT5 ENTREZGENE, UniProtKB/TrEMBL
  A6JP01 ENTREZGENE, UniProtKB/TrEMBL
  A6JP02 ENTREZGENE, UniProtKB/TrEMBL
  F1LYD8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-04-04 Rp9  RP9, pre-mRNA splicing factor  Rp9  retinitis pigmentosa 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-03-16 Rp9  retinitis pigmentosa 9  Rp9  retinitis pigmentosa 9 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-06 Rp9  retinitis pigmentosa 9 (human)  rp9  retinitis pigmentosa 9 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 rp9  retinitis pigmentosa 9 (human)  Rp9h_predicted  retinitis pigmentosa 9 homolog (human) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Rp9h_predicted  retinitis pigmentosa 9 homolog (human) (predicted)  RGD1559759_predicted  similar to PAP-1 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1559759_predicted  similar to PAP-1 (predicted)  LOC363032  similar to PAP-1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363032  similar to PAP-1      Symbol and Name status set to provisional 70820 PROVISIONAL