Rpap3 (RNA polymerase II associated protein 3) - Rat Genome Database

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Gene: Rpap3 (RNA polymerase II associated protein 3) Mus musculus
Analyze
Symbol: Rpap3
Name: RNA polymerase II associated protein 3
RGD ID: 1620772
MGI Page MGI
Description: Predicted to be located in cytosol. Predicted to be part of R2TP complex; RPAP3/R2TP/prefoldin-like complex; and protein folding chaperone complex. Orthologous to human RPAP3 (RNA polymerase II associated protein 3).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 2310042P20Rik; D15Ertd682; D15Ertd682e; RNA polymerase II-associated protein 3
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Gm18803   Gm5697   Rpap3-ps2  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391597,572,978 - 97,603,746 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1597,572,978 - 97,603,706 (-)EnsemblGRCm39 Ensembl
GRCm381597,675,097 - 97,705,822 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1597,675,097 - 97,705,825 (-)EnsemblGRCm38mm10GRCm38
MGSCv371597,505,536 - 97,536,253 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361597,503,139 - 97,533,856 (-)NCBIMGSCv36mm8
Celera1599,802,797 - 99,833,872 (-)NCBICelera
Cytogenetic Map15F1NCBI
cM Map1553.54NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10725249   PMID:11042159   PMID:11076861   PMID:11125038   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12520002   PMID:14610273   PMID:16141072  
PMID:16141073   PMID:18799693   PMID:21677750   PMID:21873635   PMID:32325033   PMID:32554809   PMID:34376666   PMID:38355793  


Genomics

Comparative Map Data
Rpap3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391597,572,978 - 97,603,746 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1597,572,978 - 97,603,706 (-)EnsemblGRCm39 Ensembl
GRCm381597,675,097 - 97,705,822 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1597,675,097 - 97,705,825 (-)EnsemblGRCm38mm10GRCm38
MGSCv371597,505,536 - 97,536,253 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361597,503,139 - 97,533,856 (-)NCBIMGSCv36mm8
Celera1599,802,797 - 99,833,872 (-)NCBICelera
Cytogenetic Map15F1NCBI
cM Map1553.54NCBI
RPAP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381247,661,249 - 47,706,030 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1247,661,249 - 47,706,030 (-)EnsemblGRCh38hg38GRCh38
GRCh371248,055,032 - 48,099,813 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361246,343,341 - 46,386,041 (-)NCBINCBI36Build 36hg18NCBI36
Celera1246,853,186 - 46,897,316 (-)NCBICelera
Cytogenetic Map12q13.11NCBI
HuRef1245,086,823 - 45,130,955 (-)NCBIHuRef
CHM1_11248,021,629 - 48,065,751 (-)NCBICHM1_1
T2T-CHM13v2.01247,622,569 - 47,667,355 (-)NCBIT2T-CHM13v2.0
Rpap3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87130,689,923 - 130,719,411 (-)NCBIGRCr8
mRatBN7.27128,810,820 - 128,840,006 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7128,810,827 - 128,839,950 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7130,607,902 - 130,635,622 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07132,833,436 - 132,861,156 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07132,745,891 - 132,773,611 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07139,167,302 - 139,196,468 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7139,167,303 - 139,196,416 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,359,664 - 139,386,634 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,382,843 - 136,415,654 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17136,459,279 - 136,492,091 (-)NCBI
Celera7125,302,242 - 125,329,913 (-)NCBICelera
Cytogenetic Map7q36NCBI
Rpap3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555006,585,969 - 6,595,219 (-)NCBIChiLan1.0ChiLan1.0
RPAP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21046,462,129 - 46,508,651 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11246,458,886 - 46,505,093 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01241,027,791 - 41,074,925 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11241,901,843 - 41,947,756 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1241,901,843 - 41,947,756 (+)Ensemblpanpan1.1panPan2
RPAP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1277,060,179 - 7,097,417 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl277,059,154 - 7,097,233 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2739,209,667 - 39,251,044 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0277,124,127 - 7,165,693 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl277,124,155 - 7,167,544 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1277,060,569 - 7,102,121 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0277,095,929 - 7,137,295 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02739,491,245 - 39,539,227 (-)NCBIUU_Cfam_GSD_1.0
Rpap3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494567,561,159 - 67,596,324 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365125,568,500 - 5,603,654 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365125,568,500 - 5,603,613 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RPAP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl578,032,748 - 78,066,224 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1577,968,171 - 78,066,252 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RPAP3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11143,887,992 - 43,926,720 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1143,885,062 - 43,926,709 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037202,454,886 - 202,495,018 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rpap3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248164,578,769 - 4,611,647 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248164,578,749 - 4,620,038 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rpap3
1263 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:55
Count of miRNA genes:55
Interacting mature miRNAs:55
Transcripts:ENSMUST00000023104
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300627Sluc26_msusceptibility to lung cancer 26 (mouse)Not determined1570345653104073951Mouse
26884442Sklq6_mskull length QTL 6, 5 week (mouse)156129481100797881Mouse
1357526Hyplip2_mhyperlipidemia 2 (mouse)Not determined1512402203102896555Mouse
1301918Skull22_mskull morphology 22 (mouse)Not determined1585901546104073951Mouse
14928306Manh79_mmandible shape 79 (mouse)1578847557104073951Mouse
1357894Epfpq3_mepididymal fat percentage QTL 3 (mouse)Not determined1578601103102901704Mouse
4142060W3q6_mweight 3 weeks QTL 6 (mouse)Not determined78601103102901704Mouse
26884425Cvht2_mcranial vault height 2, 5 week (mouse)1528800146102008435Mouse
12791003Aath8_maortic arch atherosclerosis 8 (mouse)1573430144104073951Mouse
11530038Sluc34b_msusceptibility to lung cancer 34b (mouse)1585896437104073951Mouse
11530037Sluc34a_msusceptibility to lung cancer 34a (mouse)1585896437104073951Mouse
1558985Eae32_mexperimental allergic encephalomyelitis susceptibility 32 (mouse)Not determined1532578416103425899Mouse
4141921Pstc3_mperiosteal circumference 3 (mouse)Not determined1567270698101270847Mouse
12880411V125Dq11_mvitamin D active form serum level QTL 11 (mouse)1578897881104073951Mouse
1300851Heal4_mwound healing/regeneration 4 (mouse)Not determined1577527592104073951Mouse
1301171Brm2_mbrachyury modifier 2 (mouse)Not determined156552537699525499Mouse
14747011Mancz13_mmandible centroid size 13 (mouse)1572382669104073951Mouse
10402490Dipa5_mdrug induced psychomotor activation 5 (mouse)Not determined1579163411104073951Mouse
1300726Pitm4_mprion incubation time 4 (mouse)Not determined1570349271104073951Mouse
1302197Bhr2_mbronchial hyperresponsiveness 2 (mouse)Not determined1564306334103425899Mouse
1302074Bmd4_mbone mineral density 4 (mouse)Not determined1556186708103425899Mouse
1301119Drb7_mdopamine receptor binding 7 (mouse)Not determined156533657899341028Mouse
4141135Cia35_mcollagen induced arthritis 35 (mouse)Not determined156481182698811946Mouse
4141902Cia37_mcollagen induced arthritis 37 (mouse)Not determined1580884933104073951Mouse
4141581Dshv1_mdorsal hippocampal volume 1 (mouse)Not determined92788640103425899Mouse
26884399Humsd1_mhumerus midshaft diameter 1, 5 week (mouse)1548363396101708435Mouse
4141897Imrfq2_mimmune response to Factor IX QTL 2 (mouse)Not determined79908940104073951Mouse
1301284Cosz3_mcocaine seizure 3 (mouse)Not determined1580313634104073951Mouse
26884397Humsd5_mhumerus midshaft diameter 5, 10 week (mouse)154836339698397881Mouse
4141511Gdcr1_mglycerolphosphate dehydrogenase regulator 1 (mouse)Not determined82615474104073951Mouse
1357614Bmca_mbile mucin accumulation (mouse)Not determined1585896437104073951Mouse
1300648Dbsty4_mdiabesity 4 (mouse)Not determined1570349271104073951Mouse
1300974Pgia9_mproteoglycan induced arthritis 9 (mouse)Not determined1580884933104073951Mouse

Markers in Region
AU015612  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381597,675,165 - 97,675,317UniSTSGRCm38
MGSCv371597,505,596 - 97,505,748UniSTSGRCm37
Celera1599,802,857 - 99,803,009UniSTS
Celera128,586,776 - 28,586,928UniSTS
Cytogenetic Map15F2UniSTS
cM Map1555.8UniSTS
cM Map1555.8UniSTS
cM Map1555.8UniSTS
Whitehead/MRC_RH1477.88UniSTS
AU015612  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381597,675,155 - 97,675,376UniSTSGRCm38
MGSCv371597,505,586 - 97,505,807UniSTSGRCm37
Celera1599,802,847 - 99,803,068UniSTS
Cytogenetic Map15F2UniSTS
cM Map1555.8UniSTS
Whitehead/MRC_RH15972.85UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000023104   ⟹   ENSMUSP00000023104
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1597,572,978 - 97,603,706 (-)Ensembl
GRCm38.p6 Ensembl1597,675,097 - 97,705,825 (-)Ensembl
Ensembl Acc Id: ENSMUST00000229008
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1597,578,260 - 97,580,080 (-)Ensembl
GRCm38.p6 Ensembl1597,680,379 - 97,682,199 (-)Ensembl
Ensembl Acc Id: ENSMUST00000229109
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1597,575,674 - 97,578,234 (-)Ensembl
GRCm38.p6 Ensembl1597,677,793 - 97,680,353 (-)Ensembl
RefSeq Acc Id: NM_028003   ⟹   NP_082279
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391597,572,986 - 97,603,703 (-)NCBI
GRCm381597,675,105 - 97,705,822 (-)NCBI
MGSCv371597,505,536 - 97,536,253 (-)RGD
Celera1599,802,797 - 99,833,872 (-)RGD
cM Map15 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_011245735   ⟹   XP_011244037
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391597,572,978 - 97,603,723 (-)NCBI
GRCm381597,675,097 - 97,698,995 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030248782   ⟹   XP_030104642
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391597,572,978 - 97,601,250 (-)NCBI
GRCm381597,675,097 - 97,703,307 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030248783   ⟹   XP_030104643
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391597,572,978 - 97,599,026 (-)NCBI
GRCm381597,675,097 - 97,701,145 (-)NCBI
Sequence:
RefSeq Acc Id: XM_036159597   ⟹   XP_036015490
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391597,572,978 - 97,603,746 (-)NCBI
Sequence:
RefSeq Acc Id: XM_036159598   ⟹   XP_036015491
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391597,572,978 - 97,601,251 (-)NCBI
Sequence:
RefSeq Acc Id: NP_082279   ⟸   NM_028003
- UniProtKB: Q9D706 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011244037   ⟸   XM_011245735
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_030104642   ⟸   XM_030248782
- Peptide Label: isoform X3
RefSeq Acc Id: XP_030104643   ⟸   XM_030248783
- Peptide Label: isoform X3
Ensembl Acc Id: ENSMUSP00000023104   ⟸   ENSMUST00000023104
RefSeq Acc Id: XP_036015490   ⟸   XM_036159597
- Peptide Label: isoform X1
RefSeq Acc Id: XP_036015491   ⟸   XM_036159598
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9D706-F1-model_v2 AlphaFold Q9D706 1-660 view protein structure

Promoters
RGD ID:6826429
Promoter ID:MM_KWN:19563
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:ENSMUST00000023104
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361597,536,039 - 97,536,539 (-)MPROMDB
RGD ID:8684860
Promoter ID:EPDNEW_M20461
Type:initiation region
Name:Rpap3_1
Description:Mus musculus RNA polymerase II associated protein 3 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381597,705,822 - 97,705,882EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1277218 AgrOrtholog
Ensembl Genes ENSMUSG00000022466 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000023104 ENTREZGENE
  ENSMUST00000023104.7 UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot
InterPro RPAP3 UniProtKB/Swiss-Prot
  RPAP3-like_C UniProtKB/Swiss-Prot
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot
  TPR_repeat UniProtKB/Swiss-Prot
KEGG Report mmu:71919 UniProtKB/Swiss-Prot
MGD MGI:1277218 ENTREZGENE
NCBI Gene Rpap3 ENTREZGENE
PANTHER RNA POLYMERASE II-ASSOCIATED PROTEIN 3 UniProtKB/Swiss-Prot
  RNA POLYMERASE II-ASSOCIATED PROTEIN 3 UniProtKB/Swiss-Prot
Pfam RPAP3_C UniProtKB/Swiss-Prot
  TPR_1 UniProtKB/Swiss-Prot
  TPR_16 UniProtKB/Swiss-Prot
PhenoGen Rpap3 PhenoGen
PROSITE TPR UniProtKB/Swiss-Prot
  TPR_REGION UniProtKB/Swiss-Prot
SMART TPR UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48452 UniProtKB/Swiss-Prot
UniProt Q9D706 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-08-26 Rpap3  RNA polymerase II associated protein 3  D15Ertd682e  DNA segment, Chr 15, ERATO Doi 682, expressed  Symbol and/or name updated 27372883 PROVISIONAL
2024-08-21 D15Ertd682e  DNA segment, Chr 15, ERATO Doi 682, expressed  Rpap3  RNA polymerase II associated protein 3  Symbol and/or name change 5135510 APPROVED