Prpf6 (pre-mRNA processing factor 6) - Rat Genome Database

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Gene: Prpf6 (pre-mRNA processing factor 6) Rattus norvegicus
Analyze
Symbol: Prpf6
Name: pre-mRNA processing factor 6
RGD ID: 1307103
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 spliceosomal tri-snRNP complex assembly. Predicted to act upstream of or within RNA localization and positive regulation of transcription by RNA polymerase II. Predicted to be located in nuclear speck. Predicted to be part of nucleus. Human ortholog(s) of this gene implicated in retinitis pigmentosa 60. Orthologous to human PRPF6 (pre-mRNA processing factor 6); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 6-propyl-2-thiouracil; Aroclor 1254; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC366276; MGC156816; pre-mRNA-processing factor 6; PRP6 homolog; PRP6 pre-mRNA processing factor 6 homolog; PRP6 pre-mRNA processing factor 6 homolog (S. cerevisiae); PRP6 pre-mRNA splicing factor 6 homolog; PRP6 pre-mRNA splicing factor 6 homolog (S. cerevisiae); RGD1307103; similar to RIKEN cDNA 1190003A07; U5 snRNP-associated 102 kDa protein; U5-102 kDa protein
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83189,084,465 - 189,148,705 (+)NCBIGRCr8
mRatBN7.23168,706,952 - 168,771,191 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,704,299 - 168,774,991 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3173,086,155 - 173,150,690 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03182,045,248 - 182,109,782 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,707,876 - 178,772,145 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03177,098,137 - 177,162,937 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,098,073 - 177,162,916 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,807,600 - 180,871,661 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,740,406 - 170,804,674 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,646,458 - 170,710,709 (+)NCBI
Celera3163,816,537 - 163,880,658 (-)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, etal., Cell. 2009 Feb 20;136(4):701-18. doi: 10.1016/j.cell.2009.02.009.
Additional References at PubMed
PMID:10788320   PMID:11991638   PMID:12477932   PMID:15257298   PMID:16414017   PMID:19946888   PMID:20797886   PMID:21549338   PMID:22658674   PMID:25931508   PMID:28781166   PMID:31505169  


Genomics

Comparative Map Data
Prpf6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83189,084,465 - 189,148,705 (+)NCBIGRCr8
mRatBN7.23168,706,952 - 168,771,191 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,704,299 - 168,774,991 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3173,086,155 - 173,150,690 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03182,045,248 - 182,109,782 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,707,876 - 178,772,145 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03177,098,137 - 177,162,937 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,098,073 - 177,162,916 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,807,600 - 180,871,661 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,740,406 - 170,804,674 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13170,646,458 - 170,710,709 (+)NCBI
Celera3163,816,537 - 163,880,658 (-)NCBICelera
Cytogenetic Map3q43NCBI
PRPF6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382063,981,132 - 64,033,100 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2063,981,132 - 64,033,100 (+)EnsemblGRCh38hg38GRCh38
GRCh372062,612,485 - 62,664,453 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362062,082,875 - 62,134,897 (+)NCBINCBI36Build 36hg18NCBI36
Build 342062,082,900 - 62,134,895NCBI
Celera2059,299,064 - 59,350,558 (+)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2059,347,184 - 59,398,551 (+)NCBIHuRef
CHM1_12062,513,489 - 62,564,783 (+)NCBICHM1_1
T2T-CHM13v2.02065,800,894 - 65,853,046 (+)NCBIT2T-CHM13v2.0
Prpf6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392181,243,112 - 181,297,454 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2181,233,661 - 181,297,453 (+)EnsemblGRCm39 Ensembl
GRCm382181,601,319 - 181,655,661 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2181,591,868 - 181,655,660 (+)EnsemblGRCm38mm10GRCm38
MGSCv372181,336,024 - 181,390,366 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362181,530,799 - 181,585,067 (+)NCBIMGSCv36mm8
Celera2185,682,918 - 185,737,812 (+)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2103.67NCBI
PRPF6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22169,800,307 - 69,850,708 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12069,792,317 - 69,842,719 (+)NCBINHGRI_mPanPan1
PanPan1.12061,899,076 - 61,948,088 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2061,899,076 - 61,948,088 (+)Ensemblpanpan1.1panPan2
PRPF6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12447,439,210 - 47,483,531 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2447,433,130 - 47,483,522 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2446,572,911 - 46,617,337 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02448,578,493 - 48,622,460 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2448,581,925 - 48,622,458 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12447,422,699 - 47,467,056 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02447,547,594 - 47,591,550 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02448,286,014 - 48,330,440 (+)NCBIUU_Cfam_GSD_1.0
Prpf6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640195,721,774 - 195,767,285 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651411,175,526 - 11,220,241 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651411,175,410 - 11,220,928 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRPF6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1762,815,085 - 62,858,382 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11762,815,509 - 62,857,795 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PRPF6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12211,482 - 259,590 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2211,604 - 259,447 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605047,645,668 - 47,789,609 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prpf6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474129,601,047 - 29,664,054 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474129,601,050 - 29,664,054 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Prpf6
174 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:94
Interacting mature miRNAs:99
Transcripts:ENSRNOT00000021722
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 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000066837   ⟹   ENSRNOP00000062368
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,772,613 - 168,774,991 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000083423   ⟹   ENSRNOP00000073536
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,706,935 - 168,771,190 (+)Ensembl
Rnor_6.0 Ensembl3177,098,073 - 177,162,916 (+)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_001079766   ⟹   NP_001073234
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83189,084,465 - 189,148,705 (+)NCBI
mRatBN7.23168,706,952 - 168,771,191 (+)NCBI
Rnor_6.03177,098,137 - 177,162,937 (+)NCBI
Rnor_5.03180,807,600 - 180,871,661 (+)NCBI
RGSC_v3.43170,740,406 - 170,804,674 (+)RGD
Celera3163,816,537 - 163,880,658 (-)RGD
Sequence:
RefSeq Acc Id: NP_001073234   ⟸   NM_001079766
- UniProtKB: A1A5S1 (UniProtKB/Swiss-Prot),   A0A8I6AVE4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000073536   ⟸   ENSRNOT00000083423
Ensembl Acc Id: ENSRNOP00000096663   ⟸   ENSRNOT00000117191
Ensembl Acc Id: ENSRNOP00000062368   ⟸   ENSRNOT00000066837
Ensembl Acc Id: ENSRNOP00000097317   ⟸   ENSRNOT00000110479
Protein Domains
PRP1 splicing factor N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A1A5S1-F1-model_v2 AlphaFold A1A5S1 1-941 view protein structure

Transcriptome

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

Promoters
RGD ID:13692763
Promoter ID:EPDNEW_R3285
Type:initiation region
Name:Prpf6_1
Description:pre-mRNA processing factor 6
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_6.03177,098,134 - 177,098,194EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307103 AgrOrtholog
BioCyc Gene G2FUF-46270 BioCyc
Ensembl Genes ENSRNOG00000051498 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055001387 UniProtKB/Swiss-Prot
  ENSRNOG00060001630 UniProtKB/Swiss-Prot
  ENSRNOG00065014637 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000083423.2 UniProtKB/Swiss-Prot
  ENSRNOT00000110479.1 UniProtKB/TrEMBL
  ENSRNOT00000117191.1 UniProtKB/TrEMBL
  ENSRNOT00055002264 UniProtKB/Swiss-Prot
  ENSRNOT00060002475 UniProtKB/Swiss-Prot
  ENSRNOT00065024191 UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7191091 IMAGE-MGC_LOAD
InterPro HAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PRP1_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syf1-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:366276 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156816 IMAGE-MGC_LOAD
NCBI Gene 366276 ENTREZGENE
PANTHER PTHR11246 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11246:SF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PRP1_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR_16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR_19 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Prpf6 PhenoGen
PROSITE TPR_REGION UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000051498 RatGTEx
  ENSRNOG00055001387 RatGTEx
  ENSRNOG00060001630 RatGTEx
  ENSRNOG00065014637 RatGTEx
SMART HAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AVE4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AW80_RAT UniProtKB/TrEMBL
  A1A5S1 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-07-09 Prpf6  pre-mRNA processing factor 6  Prpf6  PRP6 pre-mRNA processing factor 6 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-10-22 Prpf6  PRP6 pre-mRNA processing factor 6 homolog (S. cerevisiae)  Prpf6  PRP6 pre-mRNA splicing factor 6 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Prpf6  PRP6 pre-mRNA splicing factor 6 homolog (S. cerevisiae)  RGD1307103_predicted  similar to RIKEN cDNA 1190003A07 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1307103_predicted  similar to RIKEN cDNA 1190003A07 (predicted)  LOC366276_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC366276_predicted  similar to RIKEN cDNA 1190003A07 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL