Rprd1a (regulation of nuclear pre-mRNA domain containing 1A) - Rat Genome Database

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Gene: Rprd1a (regulation of nuclear pre-mRNA domain containing 1A) Mus musculus
Analyze
Symbol: Rprd1a
Name: regulation of nuclear pre-mRNA domain containing 1A
RGD ID: 1316538
MGI Page MGI
Description: Predicted to enable RNA polymerase II complex binding activity and identical protein binding activity. Predicted to be involved in RNA polymerase II promoter clearance and mRNA 3'-end processing. Predicted to be located in nucleus. Predicted to be part of transcription preinitiation complex. Is expressed in dorsal root ganglion; renal calyx; and submandibular gland primordium. Orthologous to human RPRD1A (regulation of nuclear pre-mRNA domain containing 1A).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C77387; cyclin-dependent kinase inhibitor 2B-related protein; expressed sequence C77387; KIAA4077; MGC29396; MGC36325; mKIAA4077; p15INK4B-related protein; regulation of nuclear pre-mRNA domain-containing protein 1A
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Lt1  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391824,618,017 - 24,663,306 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1824,618,017 - 24,663,261 (-)EnsemblGRCm39 Ensembl
GRCm381824,484,960 - 24,530,235 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1824,484,960 - 24,530,204 (-)EnsemblGRCm38mm10GRCm38
MGSCv371824,643,463 - 24,688,705 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361824,627,972 - 24,673,214 (-)NCBIMGSCv36mm8
Celera1824,973,427 - 25,018,811 (-)NCBICelera
Cytogenetic Map18A2NCBI
cM Map1813.18NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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
Additional References at PubMed
PMID:8889548   PMID:9253602   PMID:10349636   PMID:10725249   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12520002   PMID:12904583  
PMID:14610273   PMID:16141072   PMID:16141073   PMID:17967808   PMID:18799693   PMID:21267068   PMID:21873635   PMID:32325033   PMID:36108743   PMID:38355793  


Genomics

Comparative Map Data
Rprd1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391824,618,017 - 24,663,306 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1824,618,017 - 24,663,261 (-)EnsemblGRCm39 Ensembl
GRCm381824,484,960 - 24,530,235 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1824,484,960 - 24,530,204 (-)EnsemblGRCm38mm10GRCm38
MGSCv371824,643,463 - 24,688,705 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361824,627,972 - 24,673,214 (-)NCBIMGSCv36mm8
Celera1824,973,427 - 25,018,811 (-)NCBICelera
Cytogenetic Map18A2NCBI
cM Map1813.18NCBI
RPRD1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381835,989,824 - 36,067,559 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1835,984,387 - 36,067,576 (-)EnsemblGRCh38hg38GRCh38
GRCh371833,569,787 - 33,647,522 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361831,823,789 - 31,901,371 (-)NCBINCBI36Build 36hg18NCBI36
Celera1830,377,670 - 30,455,253 (-)NCBICelera
Cytogenetic Map18q12.2NCBI
HuRef1830,428,724 - 30,506,362 (-)NCBIHuRef
CHM1_11833,496,809 - 33,574,427 (-)NCBICHM1_1
T2T-CHM13v2.01836,181,320 - 36,259,091 (-)NCBIT2T-CHM13v2.0
Rprd1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81816,066,169 - 16,114,102 (-)NCBIGRCr8
mRatBN7.21815,791,418 - 15,839,338 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1815,791,418 - 15,839,338 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1815,978,782 - 16,026,350 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01816,761,496 - 16,809,063 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01816,050,053 - 16,097,579 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01816,450,160 - 16,497,913 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1816,453,369 - 16,497,886 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01816,209,135 - 16,256,883 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41816,283,291 - 16,328,357 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11816,309,731 - 16,356,467 (-)NCBI
Celera1815,721,452 - 15,768,465 (-)NCBICelera
Cytogenetic Map18p12NCBI
Rprd1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540222,584,600 - 22,646,046 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540222,584,600 - 22,646,046 (-)NCBIChiLan1.0ChiLan1.0
RPRD1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21753,385,357 - 53,463,623 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11839,077,946 - 39,156,211 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01829,242,080 - 29,320,372 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11832,800,352 - 32,878,544 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1832,800,352 - 32,878,544 (-)Ensemblpanpan1.1panPan2
RPRD1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1754,105,270 - 54,187,280 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl754,105,456 - 54,184,583 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha753,530,988 - 53,613,065 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0754,075,526 - 54,158,021 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl754,075,544 - 54,158,021 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1753,758,955 - 53,841,051 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0753,782,221 - 53,864,365 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0754,074,683 - 54,156,853 (+)NCBIUU_Cfam_GSD_1.0
Rprd1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494449,880,457 - 49,939,546 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365179,207,738 - 9,266,952 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365179,207,840 - 9,266,948 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RPRD1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6119,762,812 - 119,834,012 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16119,762,810 - 119,834,022 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26112,288,593 - 112,359,815 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RPRD1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11844,735,013 - 44,808,023 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1844,734,911 - 44,808,178 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605019,195,604 - 19,268,609 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rprd1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477910,301,878 - 10,371,184 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477910,299,378 - 10,371,213 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rprd1a
1494 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1129
Count of miRNA genes:580
Interacting mature miRNAs:732
Transcripts:ENSMUST00000046206
Prediction methods:Miranda, 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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558743Kcal1_mkilocalorie 1 (mouse)Not determined181901887453018992Mouse
11532716Sluc41c_msusceptibility to lung cancer 41c (mouse)182261991456620127Mouse
11532715Sluc41b_msusceptibility to lung cancer 41b (mouse)182261991456620127Mouse
12910787Pwbwq18_mpost-weaning body weight QTL 18 (mouse)181826552930570819Mouse
11532710Sluc41a_msusceptibility to lung cancer 41a (mouse)182261991456620127Mouse
11532709Sluc41_msusceptibility to lung cancer 41 (mouse)182095369457590708Mouse
1300638Im7_mimmunoregulatory 7 (mouse)Not determined181901887453018992Mouse
1558873Hrtfm7_mheart failure modifier 7 (mouse)Not determined18808696442087106Mouse
14928307Manh83_mmandible shape 83 (mouse)18126902168Mouse
12910805Pwbwq17_mpost-weaning body weight QTL 17 (mouse)181826552930570819Mouse
1300994Pvcan3_mprotection against vaginal candidiasis 3 (mouse)Not determined181619964050199776Mouse
1301570Sluc14_msusceptibility to lung cancer 14 (mouse)Not determined182261991456620127Mouse
13504732Cath6_mcarotid atherosclerosis 6 (mouse)181363712647637126Mouse
1558849W3q15_mweight 3 weeks QTL 15 (mouse)Not determined18504111961272643Mouse
1300877Adip8_madiposity 8 (mouse)Not determined182261991456620127Mouse
11354953Mom21_mmodifier of Min 21 (mouse)18128893823Mouse
12910819Ogrq6_moverall growth rate QTL 6 (mouse)181826552930570819Mouse
13207585Mwmlpt3_mMorris water maze latency to platform, training, 3 (mouse)18133547739Mouse
1301307Phospq1_mphospholipid QTL 1 (mouse)Not determined181813970452139859Mouse
13207589Mwmlpa3_mMorris water maze latency to platform, all, 3 (mouse)18133547739Mouse
1301950Otx2m1_morthodenticle homolog 2 (Drosophila) modifier 1 (mouse)Not determined182156868236187740Mouse
4142031Moen1_mmodifier of engrailed QTL 1 (mouse)Not determined182411556058115730Mouse
12801458Intmrm3_mintima/media ratio modifier 3 (mouse)18131720756Mouse
12801462Intim3_mintima modifier 3 (mouse)18131720756Mouse
1357603Mom3_mmodifier of Min 3 (mouse)Not determined181403002367098962Mouse
13463476Hctq8_mhematocrit QTL 8 (mouse)182121758055217727Mouse
27226723Tibw9_mtibia width 9, proximal, 16 week (mouse)18320000060933072Mouse

Markers in Region
UniSTS:237753  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381824,525,540 - 24,525,759UniSTSGRCm38
MGSCv371824,684,041 - 24,684,260UniSTSGRCm37
Celera1825,014,065 - 25,014,284UniSTS
Cytogenetic Map18A2UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000046206   ⟹   ENSMUSP00000043618
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1824,618,017 - 24,663,261 (-)Ensembl
GRCm38.p6 Ensembl1824,484,960 - 24,530,204 (-)Ensembl
Ensembl Acc Id: ENSMUST00000234403
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1824,638,484 - 24,663,115 (-)Ensembl
GRCm38.p6 Ensembl1824,505,427 - 24,530,058 (-)Ensembl
Ensembl Acc Id: ENSMUST00000234721
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1824,621,007 - 24,663,151 (-)Ensembl
GRCm38.p6 Ensembl1824,487,950 - 24,530,094 (-)Ensembl
RefSeq Acc Id: NM_001360807   ⟹   NP_001347736
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391824,618,019 - 24,663,261 (-)NCBI
GRCm381824,484,962 - 24,530,204 (-)NCBI
Sequence:
RefSeq Acc Id: NM_144861   ⟹   NP_659110
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391824,618,019 - 24,663,261 (-)NCBI
GRCm381824,484,962 - 24,530,204 (-)NCBI
MGSCv371824,643,463 - 24,688,705 (-)RGD
Celera1824,973,427 - 25,018,811 (-)RGD
cM Map18 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006525825   ⟹   XP_006525888
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391824,618,017 - 24,663,306 (-)NCBI
GRCm381824,484,960 - 24,530,235 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011246895   ⟹   XP_011245197
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391824,638,407 - 24,663,306 (-)NCBI
GRCm381824,505,349 - 24,530,235 (-)NCBI
Sequence:
RefSeq Acc Id: NP_659110   ⟸   NM_144861
- UniProtKB: Q5DTP5 (UniProtKB/Swiss-Prot),   Q8VDS4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006525888   ⟸   XM_006525825
- Peptide Label: isoform X1
- UniProtKB: Q5DTP5 (UniProtKB/Swiss-Prot),   Q8VDS4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011245197   ⟸   XM_011246895
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: NP_001347736   ⟸   NM_001360807
- UniProtKB: Q8VDS4 (UniProtKB/Swiss-Prot),   Q5DTP5 (UniProtKB/Swiss-Prot)
Ensembl Acc Id: ENSMUSP00000043618   ⟸   ENSMUST00000046206
Protein Domains
CID

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8VDS4-F1-model_v2 AlphaFold Q8VDS4 1-312 view protein structure

Promoters
RGD ID:13677266
Promoter ID:EPDNEW_M22782
Type:multiple initiation site
Name:Rprd1a_1
Description:Mus musculus regulation of nuclear pre-mRNA domain containing1A , transcript variant 1, 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
GRCm381824,530,213 - 24,530,273EPDNEW
RGD ID:6829511
Promoter ID:MM_KWN:24777
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6
Transcripts:NM_144861
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361824,688,486 - 24,689,007 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2385066 AgrOrtholog
Ensembl Genes ENSMUSG00000040446 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000046206 ENTREZGENE
  ENSMUST00000046206.5 UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.90 UniProtKB/Swiss-Prot
  6.10.250.2560 UniProtKB/Swiss-Prot
InterPro CID_dom UniProtKB/Swiss-Prot
  CREPT UniProtKB/Swiss-Prot
  ENTH_VHS UniProtKB/Swiss-Prot
  RPRD1A_CID UniProtKB/Swiss-Prot
KEGG Report mmu:225283 UniProtKB/Swiss-Prot
MGD MGI:2385066 ENTREZGENE
NCBI Gene 225283 ENTREZGENE
PANTHER CYCLIN-DEPENDENT KINASE INHIBITOR-RELATED PROTEIN UniProtKB/Swiss-Prot
  REGULATION OF NUCLEAR PRE-MRNA DOMAIN-CONTAINING PROTEIN 1A UniProtKB/Swiss-Prot
Pfam CREPT UniProtKB/Swiss-Prot
  CTD_bind UniProtKB/Swiss-Prot
PhenoGen Rprd1a PhenoGen
PROSITE CID UniProtKB/Swiss-Prot
SMART RPR UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48464 UniProtKB/Swiss-Prot
UniProt Q5DTP5 ENTREZGENE
  Q8VDS4 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5DTP5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-02 Rprd1a  regulation of nuclear pre-mRNA domain containing 1A  C77387  expressed sequence C77387  Data merged from RGD:1610614 737654 PROVISIONAL