Linc00176 (long intergenic non-protein coding RNA 176) - Rat Genome Database

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Gene: Linc00176 (long intergenic non-protein coding RNA 176) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Linc00176 (Ensembl: Prpf6)
Name: long intergenic non-protein coding RNA 176 (Ensembl:pre-mRNA processing factor 6)
RGD ID: 1561282
Description: Predicted to enable several functions, including identical protein binding activity; protein-macromolecule adaptor activity; and ribonucleoprotein complex binding activity. Predicted to be involved in RNA localization; positive regulation of transcription by RNA polymerase II; and spliceosomal tri-snRNP complex assembly. Predicted to be located in nuclear speck. Predicted to be part of nucleus. Orthologous to human C20orf204 (chromosome 20 open reading frame 204); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC499958; LOC499958; RGD1561282; RGD1561282; uncharacterized protein LOC499958
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83189,148,857 - 189,152,647 (+)NCBIGRCr8
mRatBN7.23168,771,350 - 168,775,133 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,704,299 - 168,774,991 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3173,152,112 - 173,154,490 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03182,111,204 - 182,113,582 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,773,567 - 178,775,945 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03177,163,038 - 177,166,874 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,164,359 - 177,166,737 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,871,757 - 180,876,260 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,806,096 - 170,808,474 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3163,812,737 - 163,815,115 (-)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Linc00176
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:86
Count of miRNA genes:76
Interacting mature miRNAs:78
Transcripts:ENSRNOT00000066837
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat


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 10 49 112 90 89 58 25 58 6 216 96 92 45 59 31

Sequence


Ensembl Acc Id: ENSRNOT00000066837   ⟹   ENSRNOP00000062368
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,772,613 - 168,774,991 (+)Ensembl
Rnor_6.0 Ensembl3177,164,359 - 177,166,737 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000083423   ⟹   ENSRNOP00000073536
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,706,935 - 168,771,190 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000110479   ⟹   ENSRNOP00000097317
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,704,299 - 168,771,191 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000117191   ⟹   ENSRNOP00000096663
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,706,935 - 168,772,737 (+)Ensembl
RefSeq Acc Id: NM_001109213   ⟹   NP_001102683
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,150,127 - 189,152,505 (+)NCBI
mRatBN7.23168,772,613 - 168,774,991 (+)NCBI
Rnor_6.03177,164,359 - 177,166,737 (+)NCBI
Rnor_5.03180,871,757 - 180,876,260 (+)NCBI
RGSC_v3.43170,806,096 - 170,808,474 (+)RGD
Celera3163,812,737 - 163,815,115 (-)RGD
Sequence:
RefSeq Acc Id: XM_039105721   ⟹   XP_038961649
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,148,857 - 189,152,647 (+)NCBI
mRatBN7.23168,771,350 - 168,775,133 (+)NCBI
RefSeq Acc Id: XM_039105722   ⟹   XP_038961650
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,148,857 - 189,152,647 (+)NCBI
mRatBN7.23168,771,350 - 168,775,133 (+)NCBI
RefSeq Acc Id: XM_039105723   ⟹   XP_038961651
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,148,857 - 189,152,647 (+)NCBI
mRatBN7.23168,771,350 - 168,775,133 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102683 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961649 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961650 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961651 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL88694 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000062368.1
  ENSRNOP00000097317.1
RefSeq Acc Id: NP_001102683   ⟸   NM_001109213
- Peptide Label: precursor
- UniProtKB: D3ZCA7 (UniProtKB/TrEMBL),   A6KLY6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000062368   ⟸   ENSRNOT00000066837
RefSeq Acc Id: XP_038961649   ⟸   XM_039105721
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038961650   ⟸   XM_039105722
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038961651   ⟸   XM_039105723
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000073536   ⟸   ENSRNOT00000083423
Ensembl Acc Id: ENSRNOP00000097317   ⟸   ENSRNOT00000110479
Ensembl Acc Id: ENSRNOP00000096663   ⟸   ENSRNOT00000117191
Protein Domains
PRP1 splicing factor N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZCA7-F1-model_v2 AlphaFold D3ZCA7 1-188 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:1561282 AgrOrtholog
BioCyc Gene G2FUF-46269 BioCyc
Ensembl Genes ENSRNOG00000043071 Ensembl
  ENSRNOG00000051498 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066837.2 UniProtKB/TrEMBL
  ENSRNOT00000110479.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
InterPro HAT UniProtKB/TrEMBL
  PRP1_N UniProtKB/TrEMBL
  Syf1-like UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/TrEMBL
  TPR_repeat UniProtKB/TrEMBL
KEGG Report rno:499958 UniProtKB/TrEMBL
NCBI Gene 499958 ENTREZGENE
PANTHER PTHR11246 UniProtKB/TrEMBL
  PTHR11246:SF1 UniProtKB/TrEMBL
Pfam PRP1_N UniProtKB/TrEMBL
  TPR_16 UniProtKB/TrEMBL
  TPR_19 UniProtKB/TrEMBL
PhenoGen Linc00176 PhenoGen
PROSITE PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000043071 RatGTEx
  ENSRNOG00000051498 RatGTEx
SMART HAT UniProtKB/TrEMBL
  TPR UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A0A8I6AW80_RAT UniProtKB/TrEMBL
  A6KLY6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZCA7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-02-01 Linc00176  long intergenic non-protein coding RNA 176  RGD1561282  RGD1561282  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1561282  RGD1561282   RGD1561282_predicted  RGD1561282 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1561282_predicted  RGD1561282 (predicted)  LOC499958  LOC499958  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499958  LOC499958      Symbol and Name status set to provisional 70820 PROVISIONAL