Prpf40a (pre-mRNA processing factor 40 homolog A) - Rat Genome Database

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Gene: Prpf40a (pre-mRNA processing factor 40 homolog A) Rattus norvegicus
Analyze
Symbol: Prpf40a
Name: pre-mRNA processing factor 40 homolog A
RGD ID: 1311401
Description: Predicted to enable RNA binding activity and proline-rich region binding activity. Predicted to be involved in several processes, including mRNA splicing, via spliceosome; regulation of cell shape; and regulation of cytokinesis. Predicted to be located in nuclear matrix and nuclear speck. Predicted to be part of U1 snRNP and U2-type prespliceosome. Orthologous to human PRPF40A (pre-mRNA processing factor 40 homolog A); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Fnbp3; formin binding protein 3; LOC295607; pre-mRNA processing factor 40 homolog A (yeast); pre-mRNA-processing factor 40 homolog A; PRP40 pre-mRNA processing factor 40 homolog A; PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)
RGD Orthologs
Human
Mouse
Chinchilla
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
GRCr8358,036,779 - 58,098,996 (-)NCBIGRCr8
mRatBN7.2337,625,585 - 37,689,859 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl337,627,690 - 37,690,886 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx341,001,890 - 41,062,025 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0349,586,708 - 49,646,842 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0347,371,550 - 47,431,684 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0338,680,583 - 38,741,570 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl338,682,146 - 38,741,113 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0343,778,141 - 43,839,268 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4334,661,461 - 34,721,438 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1334,557,496 - 34,618,041 (-)NCBI
Celera335,768,130 - 35,827,799 (-)NCBICelera
Cytogenetic Map3q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
aristolochic acid A  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
chloroprene  (EXP)
chlorpyrifos  (ISO)
coumarin  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
daidzein  (ISO)
daidzein 7-O-beta-D-glucoside  (ISO)
diarsenic trioxide  (ISO)
Dibutyl phosphate  (ISO)
dicrotophos  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
elemental selenium  (ISO)
enzyme inhibitor  (ISO)
flutamide  (EXP)
FR900359  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
genistein 7-O-beta-D-glucoside  (ISO)
glucose  (ISO)
glycitein  (ISO)
glycitin  (ISO)
hexadecanoic acid  (ISO)
hinokiflavone  (ISO)
ivermectin  (ISO)
kojic acid  (ISO)
lead(0)  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
miconazole  (ISO)
N-nitrosodiethylamine  (EXP)
paracetamol  (EXP)
phenobarbital  (ISO)
progesterone  (ISO)
rimonabant  (ISO)
selenium atom  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
succimer  (ISO)
sulfadimethoxine  (EXP)
tamibarotene  (ISO)
tamoxifen  (ISO)
thioacetamide  (EXP)
trichloroethene  (EXP)
triptonide  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11092755   PMID:16391387   PMID:17915251   PMID:19946888   PMID:21834987   PMID:22082260   PMID:22206666   PMID:22681889   PMID:31505169  


Genomics

Comparative Map Data
Prpf40a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8358,036,779 - 58,098,996 (-)NCBIGRCr8
mRatBN7.2337,625,585 - 37,689,859 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl337,627,690 - 37,690,886 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx341,001,890 - 41,062,025 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0349,586,708 - 49,646,842 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0347,371,550 - 47,431,684 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0338,680,583 - 38,741,570 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl338,682,146 - 38,741,113 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0343,778,141 - 43,839,268 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4334,661,461 - 34,721,438 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1334,557,496 - 34,618,041 (-)NCBI
Celera335,768,130 - 35,827,799 (-)NCBICelera
Cytogenetic Map3q12NCBI
PRPF40A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382152,651,732 - 152,718,019 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2152,651,593 - 152,718,012 (-)EnsemblGRCh38hg38GRCh38
GRCh372153,508,246 - 153,574,533 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362153,216,353 - 153,282,221 (-)NCBINCBI36Build 36hg18NCBI36
Celera2147,122,555 - 147,188,431 (-)NCBICelera
Cytogenetic Map2q23.3NCBI
HuRef2145,394,474 - 145,460,345 (-)NCBIHuRef
CHM1_12153,514,130 - 153,580,008 (-)NCBICHM1_1
T2T-CHM13v2.02153,104,294 - 153,170,565 (-)NCBIT2T-CHM13v2.0
Prpf40a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39253,024,714 - 53,081,450 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl253,024,716 - 53,081,714 (-)EnsemblGRCm39 Ensembl
GRCm38253,134,702 - 53,191,438 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl253,134,704 - 53,191,284 (-)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl253,134,704 - 53,191,702 (-)EnsemblGRCm38mm10GRCm38
MGSCv37252,997,509 - 53,050,221 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36252,960,484 - 53,013,196 (-)NCBIMGSCv36mm8
Celera254,880,090 - 54,932,591 (-)NCBICelera
Cytogenetic Map2C1.1NCBI
cM Map230.69NCBI
Prpf40a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544018,083,838 - 18,128,701 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544018,083,838 - 18,128,701 (-)NCBIChiLan1.0ChiLan1.0
PRPF40A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21355,339,652 - 55,401,915 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B55,354,632 - 55,417,571 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B39,955,290 - 40,017,636 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B157,189,945 - 157,256,184 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B157,194,506 - 157,254,983 (-)Ensemblpanpan1.1panPan2
PRPF40A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11953,649,424 - 53,710,095 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1953,651,453 - 53,710,633 (-)NCBICanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1953,651,453 - 53,710,633 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2627,948,940 - 28,009,892 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01955,161,297 - 55,222,274 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1955,163,918 - 55,222,155 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11953,877,024 - 53,937,982 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01953,947,078 - 54,007,975 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01955,412,012 - 55,472,975 (-)NCBIUU_Cfam_GSD_1.0
Prpf40a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303116,596,815 - 116,654,368 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493646924,963,905 - 25,018,961 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493646924,963,691 - 25,019,961 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRPF40A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1560,386,596 - 60,439,807 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11560,388,582 - 60,440,478 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21567,034,695 - 67,085,766 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PRPF40A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11038,086,971 - 38,151,726 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1038,088,281 - 38,151,371 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040161,416,070 - 161,480,948 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prpf40a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248664,369,605 - 4,430,816 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Prpf40a
145 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:520
Count of miRNA genes:250
Interacting mature miRNAs:315
Transcripts:ENSRNOT00000006549
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1298073Cm13Cardiac mass QTL 132.5heart mass (VT:0007028)heart wet weight (CMO:0000069)32501391138192233Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
631832Sach1Saccharin preference QTL 12.70.02consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)32749462144188411Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
2313079Bss73Bone structure and strength QTL 731.5tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)32749462150302886Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
2313076Bss74Bone structure and strength QTL 7420.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)32749462150302886Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33370334761017857Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
2313093Bmd77Bone mineral density QTL 772.20.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)32749462150302886Rat
12879852Cm93Cardiac mass QTL 930.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)31831145447233430Rat
12879853Am5Aortic mass QTL 50.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)31831145447233430Rat
12879854Kidm63Kidney mass QTL 630.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)31831145447233430Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
12879849Bw180Body weight QTL 1800.037body mass (VT:0001259)body weight (CMO:0000012)31831145447233430Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
12879850Cm91Cardiac mass QTL 910.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)31831145447233430Rat
2313101Bmd76Bone mineral density QTL 763.60.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)32749462150302886Rat
731172Bp151Blood pressure QTL 1510.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31831145447233430Rat
12879851Cm92Cardiac mass QTL 920.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)31831145447233430Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)32824968773249687Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
2313049Bss72Bone structure and strength QTL 722.60.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)32749462150302886Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat

Markers in Region
RH133617  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2337,629,710 - 37,629,894 (+)MAPPERmRatBN7.2
Rnor_6.0338,682,601 - 38,682,784NCBIRnor6.0
Rnor_5.0343,779,767 - 43,779,950UniSTSRnor5.0
RGSC_v3.4334,661,916 - 34,662,099UniSTSRGSC3.4
Celera335,768,585 - 35,768,768UniSTS
RH 3.4 Map3465.8UniSTS
Cytogenetic Map3q12UniSTS
AI461736  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2337,627,871 - 37,627,999 (+)MAPPERmRatBN7.2
Rnor_6.0338,680,762 - 38,680,889NCBIRnor6.0
Rnor_5.0343,777,928 - 43,778,055UniSTSRnor5.0
RGSC_v3.4334,660,077 - 34,660,204UniSTSRGSC3.4
Celera335,766,746 - 35,766,873UniSTS
Cytogenetic Map3q12UniSTS
RH140784  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2337,629,196 - 37,629,381 (+)MAPPERmRatBN7.2
Rnor_6.0338,682,087 - 38,682,271NCBIRnor6.0
Rnor_5.0343,779,253 - 43,779,437UniSTSRnor5.0
RGSC_v3.4334,661,402 - 34,661,586UniSTSRGSC3.4
Celera335,768,071 - 35,768,255UniSTS
RH 3.4 Map3465.8UniSTS
Cytogenetic Map3q12UniSTS
UniSTS:234392  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2337,690,623 - 37,690,770 (+)MAPPERmRatBN7.2
Rnor_6.0338,742,308 - 38,742,454NCBIRnor6.0
Rnor_5.0343,840,147 - 43,840,293UniSTSRnor5.0
RGSC_v3.4334,722,634 - 34,722,780UniSTSRGSC3.4
Celera335,828,995 - 35,829,141UniSTS
Cytogenetic Map3q12UniSTS
Prpf40a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2337,629,254 - 37,629,984 (+)MAPPERmRatBN7.2
Rnor_6.0338,682,145 - 38,682,874NCBIRnor6.0
Rnor_5.0343,779,311 - 43,780,040UniSTSRnor5.0
RGSC_v3.4334,661,460 - 34,662,189UniSTSRGSC3.4
Celera335,768,129 - 35,768,858UniSTS
Cytogenetic Map3q12UniSTS


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 41 57 41 19 41 8 10 74 35 41 11 8
Low 2 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001106480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761709 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761711 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210557 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211946 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000006549   ⟹   ENSRNOP00000006549
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl337,629,259 - 37,689,473 (-)Ensembl
Rnor_6.0 Ensembl338,682,146 - 38,741,113 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095713   ⟹   ENSRNOP00000083490
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl337,629,259 - 37,689,592 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104801   ⟹   ENSRNOP00000083163
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl337,627,690 - 37,690,886 (-)Ensembl
RefSeq Acc Id: NM_001106480   ⟹   NP_001099950
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,038,341 - 58,098,509 (-)NCBI
mRatBN7.2337,629,256 - 37,689,428 (-)NCBI
Rnor_6.0338,682,146 - 38,741,113 (-)NCBI
Rnor_5.0343,778,141 - 43,839,268 (-)NCBI
RGSC_v3.4334,661,461 - 34,721,438 (-)RGD
Celera335,768,130 - 35,827,799 (-)RGD
Sequence:
RefSeq Acc Id: XM_006234164   ⟹   XP_006234226
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,037,170 - 58,098,740 (-)NCBI
mRatBN7.2337,627,693 - 37,689,859 (-)NCBI
Rnor_6.0338,680,583 - 38,741,569 (-)NCBI
Rnor_5.0343,778,141 - 43,839,268 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761709   ⟹   XP_008759931
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,036,779 - 58,098,740 (-)NCBI
mRatBN7.2337,627,693 - 37,689,859 (-)NCBI
Rnor_6.0338,680,583 - 38,741,570 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761710   ⟹   XP_008759932
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,036,779 - 58,098,740 (-)NCBI
mRatBN7.2337,627,693 - 37,689,859 (-)NCBI
Rnor_6.0338,680,583 - 38,741,570 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761711   ⟹   XP_008759933
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,036,779 - 58,098,740 (-)NCBI
mRatBN7.2337,627,693 - 37,689,859 (-)NCBI
Rnor_6.0338,680,583 - 38,741,569 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761712   ⟹   XP_008759934
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,036,779 - 58,098,740 (-)NCBI
mRatBN7.2337,627,693 - 37,689,859 (-)NCBI
Rnor_6.0338,680,583 - 38,741,569 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761713   ⟹   XP_008759935
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,037,170 - 58,097,417 (-)NCBI
mRatBN7.2337,625,585 - 37,688,333 (-)NCBI
Rnor_6.0338,680,583 - 38,738,457 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039104475   ⟹   XP_038960403
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,036,779 - 58,098,740 (-)NCBI
mRatBN7.2337,627,693 - 37,689,859 (-)NCBI
RefSeq Acc Id: XM_039104476   ⟹   XP_038960404
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,036,779 - 58,098,740 (-)NCBI
mRatBN7.2337,627,693 - 37,689,859 (-)NCBI
RefSeq Acc Id: XM_063283248   ⟹   XP_063139318
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,037,170 - 58,098,996 (-)NCBI
RefSeq Acc Id: XM_063283249   ⟹   XP_063139319
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8358,045,988 - 58,098,740 (-)NCBI
RefSeq Acc Id: NP_001099950   ⟸   NM_001106480
- UniProtKB: A6JF33 (UniProtKB/TrEMBL),   A0A8I5ZVY5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006234226   ⟸   XM_006234164
- Peptide Label: isoform X4
- UniProtKB: A0A8I5ZVY5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759932   ⟸   XM_008761710
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZVY5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759934   ⟸   XM_008761712
- Peptide Label: isoform X5
- UniProtKB: A0A8I5ZVY5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759931   ⟸   XM_008761709
- Peptide Label: isoform X8
- UniProtKB: A0A8I5ZVY5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759933   ⟸   XM_008761711
- Peptide Label: isoform X3
- UniProtKB: A0A8I5ZVI3 (UniProtKB/TrEMBL),   A0A8I5ZVY5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759935   ⟸   XM_008761713
- Peptide Label: isoform X9
- UniProtKB: A0A8I5ZVY5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006549   ⟸   ENSRNOT00000006549
RefSeq Acc Id: XP_038960404   ⟸   XM_039104476
- Peptide Label: isoform X6
- UniProtKB: A0A8I5ZVY5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038960403   ⟸   XM_039104475
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZVY5 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000083163   ⟸   ENSRNOT00000104801
RefSeq Acc Id: ENSRNOP00000083490   ⟸   ENSRNOT00000095713
RefSeq Acc Id: XP_063139318   ⟸   XM_063283248
- Peptide Label: isoform X7
- UniProtKB: A0A8I5ZVY5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139319   ⟸   XM_063283249
- Peptide Label: isoform X10
Protein Domains
FF   WW

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZJ92-F1-model_v2 AlphaFold D3ZJ92 1-953 view protein structure

Transcriptome

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

Promoters
RGD ID:13692078
Promoter ID:EPDNEW_R2603
Type:initiation region
Name:Prpf40a_1
Description:pre-mRNA processing factor 40 homolog A
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_6.0338,741,154 - 38,741,214EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311401 AgrOrtholog
BioCyc Gene G2FUF-49719 BioCyc
Ensembl Genes ENSRNOG00000004864 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006549 ENTREZGENE
  ENSRNOT00000006549.6 UniProtKB/TrEMBL
  ENSRNOT00000095713.1 UniProtKB/TrEMBL
  ENSRNOT00000104801.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.440 UniProtKB/TrEMBL
  2.20.70.10 UniProtKB/TrEMBL
InterPro FF_domain UniProtKB/TrEMBL
  FF_domain_sf UniProtKB/TrEMBL
  Prp40/Urn1 UniProtKB/TrEMBL
  WW_dom_sf UniProtKB/TrEMBL
  WW_Rsp5_WWP UniProtKB/TrEMBL
KEGG Report rno:295607 UniProtKB/TrEMBL
NCBI Gene 295607 ENTREZGENE
PANTHER PRE-MRNA-PROCESSING FACTOR 40 HOMOLOG A UniProtKB/TrEMBL
  PTHR11864 UniProtKB/TrEMBL
Pfam PF00397 UniProtKB/TrEMBL
  PF01846 UniProtKB/TrEMBL
PhenoGen Prpf40a PhenoGen
PROSITE PS51676 UniProtKB/TrEMBL
  WW_DOMAIN_1 UniProtKB/TrEMBL
  WW_DOMAIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004864 RatGTEx
SMART SM00441 UniProtKB/TrEMBL
  SM00456 UniProtKB/TrEMBL
Superfamily-SCOP 81698 UniProtKB/TrEMBL
  WW_Rsp5_WWP UniProtKB/TrEMBL
UniProt A0A8I5ZVI3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZVY5 ENTREZGENE, UniProtKB/TrEMBL
  A6JF33 ENTREZGENE, UniProtKB/TrEMBL
  D3ZJ92_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-02 Prpf40a  pre-mRNA processing factor 40 homolog A  Prpf40a  PRP40 pre-mRNA processing factor 40 homolog A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-17 Prpf40a  PRP40 pre-mRNA processing factor 40 homolog A  Prpf40a  PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Prpf40a  PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)  Prpf40a_predicted  pre-mRNA processing factor 40 homolog A (yeast) (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Prpf40a_predicted  pre-mRNA processing factor 40 homolog A (yeast) (predicted)  Fnbp3_predicted  formin binding protein 3 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Fnbp3_predicted  formin binding protein 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED