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) Rattus norvegicus
Analyze
Symbol: Rprd1a
Name: regulation of nuclear pre-mRNA domain containing 1A
RGD ID: 1307374
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. Orthologous to human RPRD1A (regulation of nuclear pre-mRNA domain containing 1A); INTERACTS WITH 6-propyl-2-thiouracil; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cyclin-dependent kinase 2B-inhibitor-related protein; LOC291736; P15rs; regulation of nuclear pre-mRNA domain-containing protein 1A; RGD1307374; similar to hypothetical protein MGC36325
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Rprd1aTn(sb-T2/Bart3)2.247Mcwi  
Genetic Models: F344-Rprd1aTn(sb-T2/Bart3)2.247Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
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

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:22231121   PMID:24997600  


Genomics

Comparative Map Data
Rprd1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
(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
(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
(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_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 (+)EnsemblSpeTri2.0
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
182 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:88
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000021624
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18125758124Rat
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125758124Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor surface area measurement (CMO:0002078)18224947722066430Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)18224947722066430Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181179151863636873Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194179131393320Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181194179131393320Rat
12904690Cm129Cardiac mass QTL 1290.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)181194427326548295Rat
12904689Cm128Cardiac mass QTL 1280.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)181194427326548295Rat
12904693Am20Aortic mass QTL 200.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)181194427326548295Rat
12904695Kidm73Kidney mass QTL 730.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)181194427326548295Rat
12904691Cm130Cardiac mass QTL 1300.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)181194427326548295Rat
12904680Bw189Body weight QTL 1890.019body mass (VT:0001259)body weight (CMO:0000012)181194427326548295Rat
2301410Bp317Blood pressure QTL 3170.004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194427326548295Rat
1331781Scl28Serum cholesterol level QTL 283.995blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)181194429924797117Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194429931359530Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)181194429941122201Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194429952293055Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat

Markers in Region
RH137088  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21815,812,912 - 15,813,095 (+)MAPPERmRatBN7.2
Rnor_6.01816,471,654 - 16,471,836NCBIRnor6.0
Rnor_5.01816,230,626 - 16,230,808UniSTSRnor5.0
RGSC_v3.41816,301,767 - 16,301,949UniSTSRGSC3.4
Celera1815,742,942 - 15,743,124UniSTS
RH 3.4 Map18192.6UniSTS
Cytogenetic Map18p12UniSTS


Genetic Models
This gene Rprd1a is modified in the following models/strains

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 40 44 28 19 28 3 4 74 35 37 11 3
Low 3 13 13 13 5 7 4 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021624   ⟹   ENSRNOP00000021624
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1815,791,418 - 15,839,338 (-)Ensembl
Rnor_6.0 Ensembl1816,453,369 - 16,497,886 (-)Ensembl
RefSeq Acc Id: NM_001305179   ⟹   NP_001292108
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21815,791,418 - 15,839,338 (-)NCBI
Rnor_6.01816,450,160 - 16,497,913 (-)NCBI
Celera1815,721,452 - 15,768,465 (-)NCBI
Sequence:
RefSeq Acc Id: XM_214609   ⟹   XP_214609
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21815,791,421 - 15,839,335 (-)NCBI
Rnor_6.01816,450,163 - 16,497,910 (-)NCBI
Rnor_5.01816,209,135 - 16,256,883 (-)NCBI
RGSC_v3.41816,283,291 - 16,328,357 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001292108 (Get FASTA)   NCBI Sequence Viewer  
  XP_214609 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76138 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_214609   ⟸   XM_214609
- Peptide Label: isoform X1
- UniProtKB: D4AAU4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001292108   ⟸   NM_001305179
- UniProtKB: D4AAU4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021624   ⟸   ENSRNOT00000021624
Protein Domains
CID

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AAU4-F1-model_v2 AlphaFold D4AAU4 1-312 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:1307374 AgrOrtholog
BioCyc Gene G2FUF-8150 BioCyc
Ensembl Genes ENSRNOG00000016036 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021624 ENTREZGENE
  ENSRNOP00000021624.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021624 ENTREZGENE
  ENSRNOT00000021624.8 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.90 UniProtKB/TrEMBL
  6.10.250.2560 UniProtKB/TrEMBL
InterPro CREPT UniProtKB/TrEMBL
  ENTH_VHS UniProtKB/TrEMBL
  RNA_polymerase_II_lsu_CTD UniProtKB/TrEMBL
KEGG Report rno:291736 UniProtKB/TrEMBL
NCBI Gene 291736 ENTREZGENE
PANTHER CYCLIN-DEPENDENT KINASE INHIBITOR-RELATED PROTEIN UniProtKB/TrEMBL
  REGULATION OF NUCLEAR PRE-MRNA DOMAIN-CONTAINING PROTEIN 1A UniProtKB/TrEMBL
Pfam CREPT UniProtKB/TrEMBL
  DUF618 UniProtKB/TrEMBL
PhenoGen Rprd1a PhenoGen
PROSITE CID UniProtKB/TrEMBL
SMART RPR UniProtKB/TrEMBL
Superfamily-SCOP ENTH_VHS UniProtKB/TrEMBL
UniProt D4AAU4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-24 Rprd1a  regulation of nuclear pre-mRNA domain containing 1A  P15rs  cyclin-dependent kinase 2B-inhibitor-related protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-18 P15rs  cyclin-dependent kinase 2B-inhibitor-related protein  RGD1307374_predicted  similar to hypothetical protein MGC36325 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1307374_predicted  similar to hypothetical protein MGC36325 (predicted)  LOC291736_predicted  similar to hypothetical protein MGC36325 (predicted)  Symbol and Name status set to approved 1331353 APPROVED