Rp1l1 (RP1 like 1) - Rat Genome Database

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Gene: Rp1l1 (RP1 like 1) Rattus norvegicus
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Symbol: Rp1l1
Name: RP1 like 1
RGD ID: 1586886
Description: Predicted to be involved in several processes, including axoneme assembly; photoreceptor cell development; and photoreceptor cell maintenance. Predicted to be located in photoreceptor connecting cilium and photoreceptor outer segment. Predicted to be active in axoneme. Human ortholog(s) of this gene implicated in occult macular dystrophy and retinitis pigmentosa 88. Orthologous to human RP1L1 (RP1 like 1); INTERACTS WITH 1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ortholog); 1,2-dichloroethane (ortholog); 2,2',4,4',5,5'-hexachlorobiphenyl (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC683404; retinitis pigmentosa 1-like 1; similar to Retinitis pigmentosa 1-like 1 protein (Retinitis pigmentosa 1-like protein 1)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81542,435,803 - 42,447,165 (+)NCBIGRCr8
GRCr8 Ensembl1542,435,803 - 42,447,165 (+)EnsemblGRCr8 Ensembl
mRatBN7.21538,259,907 - 38,271,269 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1538,259,928 - 38,270,316 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01547,344,380 - 47,384,461 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1547,373,120 - 47,383,508 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01551,117,811 - 51,143,753 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1537,912,769 - 37,952,844 (+)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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:19657028   PMID:23281133   PMID:23376485  


Genomics

Comparative Map Data
Rp1l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81542,435,803 - 42,447,165 (+)NCBIGRCr8
GRCr8 Ensembl1542,435,803 - 42,447,165 (+)EnsemblGRCr8 Ensembl
mRatBN7.21538,259,907 - 38,271,269 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1538,259,928 - 38,270,316 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01547,344,380 - 47,384,461 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1547,373,120 - 47,383,508 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01551,117,811 - 51,143,753 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1537,912,769 - 37,952,844 (+)NCBICelera
Cytogenetic Map15p12NCBI
RP1L1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38810,606,349 - 10,655,143 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl810,606,349 - 10,712,187 (-)EnsemblGRCh38hg38GRCh38
GRCh37810,463,859 - 10,512,653 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36810,501,269 - 10,550,027 (-)NCBINCBI36Build 36hg18NCBI36
Build 34810,501,270 - 10,550,027NCBI
Celera89,591,303 - 9,640,515 (-)NCBICelera
Cytogenetic Map8p23.1NCBI
HuRef89,394,231 - 9,443,153 (-)NCBIHuRef
CHM1_1810,529,596 - 10,578,235 (-)NCBICHM1_1
T2T-CHM13v2.089,083,816 - 9,132,787 (+)NCBIT2T-CHM13v2.0
Rp1l1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391464,229,880 - 64,270,955 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1464,229,955 - 64,272,474 (+)EnsemblGRCm39 Ensembl
GRCm381463,992,431 - 64,033,506 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1463,992,506 - 64,035,025 (+)EnsemblGRCm38mm10GRCm38
MGSCv371464,611,268 - 64,652,343 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361462,946,541 - 62,987,953 (+)NCBIMGSCv36mm8
Celera1461,769,430 - 61,810,604 (+)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1433.34NCBI
Rp1l1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540352,180,612 - 52,200,569 (-)NCBIChiLan1.0ChiLan1.0
RP1L1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2727,058,051 - 27,078,116 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan183,090,439 - 3,110,497 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v088,586,410 - 8,605,275 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RP1L1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12527,317,102 - 27,332,075 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2527,325,658 - 27,330,556 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2527,977,022 - 27,991,705 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02527,474,859 - 27,489,549 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12527,429,640 - 27,444,331 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02527,323,498 - 27,338,179 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02527,477,657 - 27,492,342 (+)NCBIUU_Cfam_GSD_1.0
Rp1l1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049436,021,659 - 6,058,745 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366752,527,406 - 2,564,464 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RP1L1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11413,790,287 - 13,841,230 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21415,156,836 - 15,192,516 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RP1L1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.188,479,768 - 8,499,497 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605233,925,836 - 33,944,748 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rp1l1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475824,480,805 - 24,516,524 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rp1l1
42 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:42
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000070815
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
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
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154046315285463152Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
4 2 25 36 11 21 2 5 47 34 5 28 7 45 21 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000070815   ⟹   ENSRNOP00000064085
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1542,435,803 - 42,447,165 (+)Ensembl
mRatBN7.2 Ensembl1538,259,928 - 38,270,316 (+)Ensembl
Rnor_6.0 Ensembl1547,373,120 - 47,383,508 (+)Ensembl
RefSeq Acc Id: NM_001421085   ⟹   NP_001408014
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81542,435,803 - 42,447,165 (+)NCBI
mRatBN7.21538,259,907 - 38,271,269 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001408014 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL85330 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064085
  ENSRNOP00000064085.3
Ensembl Acc Id: ENSRNOP00000064085   ⟸   ENSRNOT00000070815
RefSeq Acc Id: NP_001408014   ⟸   NM_001421085
- UniProtKB: A6K6H0 (UniProtKB/TrEMBL),   M0R410 (UniProtKB/TrEMBL)
Protein Domains
Doublecortin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R410-F1-model_v2 AlphaFold M0R410 1-1860 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:1586886 AgrOrtholog
BioCyc Gene G2FUF-13392 BioCyc
Ensembl Genes ENSRNOG00000046326 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000070815 ENTREZGENE
  ENSRNOT00000070815.3 UniProtKB/TrEMBL
Gene3D-CATH 3.10.20.230 UniProtKB/TrEMBL
InterPro Doublecortin_dom UniProtKB/TrEMBL
  Doublecortin_dom_sf UniProtKB/TrEMBL
NCBI Gene 683404 ENTREZGENE
PANTHER PTHR23005 UniProtKB/TrEMBL
  RETINITIS PIGMENTOSA 1-LIKE 1 PROTEIN UniProtKB/TrEMBL
Pfam DCX UniProtKB/TrEMBL
PhenoGen Rp1l1 PhenoGen
PROSITE PS50309 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000046326 RatGTEx
SMART DCX UniProtKB/TrEMBL
Superfamily-SCOP SSF89837 UniProtKB/TrEMBL
UniProt A6K6H0 ENTREZGENE, UniProtKB/TrEMBL
  M0R410 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-01-03 Rp1l1  RP1 like 1  Rp1l1  retinitis pigmentosa 1-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-10-03 Rp1l1  retinitis pigmentosa 1-like 1  LOC683404  similar to Retinitis pigmentosa 1-like 1 protein (Retinitis pigmentosa 1-like protein 1)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC683404  similar to Retinitis pigmentosa 1-like 1 protein (Retinitis pigmentosa 1-like protein 1)      Symbol and Name status set to provisional 70820 PROVISIONAL