Prpf38b (pre-mRNA processing factor 38B) - Rat Genome Database

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Gene: Prpf38b (pre-mRNA processing factor 38B) Rattus norvegicus
Analyze
Symbol: Prpf38b
Name: pre-mRNA processing factor 38B
RGD ID: 1562940
Description: Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be part of precatalytic spliceosome. Orthologous to human PRPF38B (pre-mRNA processing factor 38B); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC499691; pre-mRNA-splicing factor 38B; PRP38 pre-mRNA processing factor 38 (yeast) domain containing B; PRP38 pre-mRNA processing factor 38 domain containing B; similar to sarcoma antigen NY-SAR-27
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
GRCr82199,241,312 - 199,250,342 (-)NCBIGRCr8
mRatBN7.22196,553,224 - 196,562,271 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2196,553,225 - 196,562,250 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2204,196,221 - 204,205,249 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02202,077,695 - 202,086,719 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02196,894,754 - 196,903,778 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02211,706,245 - 211,715,271 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2211,706,228 - 211,715,311 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02231,180,383 - 231,189,409 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42204,509,110 - 204,518,135 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2189,201,471 - 189,210,495 (-)NCBICelera
Cytogenetic Map2q34NCBI
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 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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:22658674  


Genomics

Comparative Map Data
Prpf38b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82199,241,312 - 199,250,342 (-)NCBIGRCr8
mRatBN7.22196,553,224 - 196,562,271 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2196,553,225 - 196,562,250 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2204,196,221 - 204,205,249 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02202,077,695 - 202,086,719 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02196,894,754 - 196,903,778 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02211,706,245 - 211,715,271 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2211,706,228 - 211,715,311 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02231,180,383 - 231,189,409 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42204,509,110 - 204,518,135 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2189,201,471 - 189,210,495 (-)NCBICelera
Cytogenetic Map2q34NCBI
PRPF38B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381108,692,310 - 108,702,928 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1108,692,310 - 108,702,928 (+)EnsemblGRCh38hg38GRCh38
GRCh371109,234,932 - 109,245,550 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361109,036,661 - 109,045,686 (+)NCBINCBI36Build 36hg18NCBI36
Celera1107,504,760 - 107,514,241 (+)NCBICelera
Cytogenetic Map1p13.3NCBI
HuRef1107,127,792 - 107,137,273 (+)NCBIHuRef
CHM1_11109,349,793 - 109,359,274 (+)NCBICHM1_1
T2T-CHM13v2.01108,725,575 - 108,736,181 (+)NCBIT2T-CHM13v2.0
Prpf38b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393108,810,121 - 108,819,055 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3108,810,121 - 108,819,043 (-)EnsemblGRCm39 Ensembl
GRCm383108,902,805 - 108,911,729 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3108,902,805 - 108,911,727 (-)EnsemblGRCm38mm10GRCm38
MGSCv373108,705,725 - 108,714,622 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363109,030,863 - 109,039,760 (-)NCBIMGSCv36mm8
Celera3111,237,740 - 111,246,664 (-)NCBICelera
Cytogenetic Map3F3NCBI
cM Map347.92NCBI
Prpf38b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543512,162,730 - 12,172,136 (+)NCBIChiLan1.0ChiLan1.0
PRPF38B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21118,606,080 - 118,617,799 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11117,765,944 - 117,774,828 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01111,066,210 - 111,075,076 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11110,232,851 - 110,242,511 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1110,233,031 - 110,242,506 (+)Ensemblpanpan1.1panPan2
PRPF38B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1643,044,322 - 43,052,622 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl642,948,236 - 43,053,027 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha645,820,463 - 45,828,975 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0643,378,039 - 43,386,561 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl643,351,764 - 43,386,746 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1643,108,363 - 43,116,878 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0643,066,832 - 43,075,350 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0643,509,602 - 43,518,117 (-)NCBIUU_Cfam_GSD_1.0
Prpf38b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505819,831,957 - 19,841,149 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936704273,282 - 281,010 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936704272,998 - 282,189 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRPF38B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4111,233,281 - 111,347,501 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14111,338,988 - 111,347,505 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24121,836,910 - 121,846,047 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PRPF38B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12024,884,889 - 24,893,818 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2024,882,780 - 24,893,535 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603833,452,535 - 33,462,771 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prpf38b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247724,480,463 - 4,491,189 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247724,480,464 - 4,490,017 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Prpf38b
19 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:138
Count of miRNA genes:101
Interacting mature miRNAs:124
Transcripts:ENSRNOT00000027738
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat
4889834Pur24Proteinuria QTL 245.80.014urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2184114274202447032Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2184165752229165752Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2185876309219753474Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2185876309219753474Rat
61458Bp10Blood pressure QTL 103.42arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
1298083Bp158Blood pressure QTL 1582.62arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
1331745Bp203Blood pressure QTL 2034.377arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2189599258218414891Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2189599258226936289Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2189599258234599258Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189599258234599258Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2190613715226808892Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat

Markers in Region
AA925891  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22196,553,492 - 196,553,690 (+)MAPPERmRatBN7.2
Rnor_6.02211,706,514 - 211,706,711NCBIRnor6.0
Rnor_5.02231,180,652 - 231,180,849UniSTSRnor5.0
RGSC_v3.42204,509,378 - 204,509,575UniSTSRGSC3.4
Celera2189,201,739 - 189,201,936UniSTS
RH 3.4 Map21395.6UniSTS
Cytogenetic Map2q34UniSTS
RH131274  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22196,554,013 - 196,554,214 (+)MAPPERmRatBN7.2
Rnor_6.02211,707,035 - 211,707,235NCBIRnor6.0
Rnor_5.02231,181,173 - 231,181,373UniSTSRnor5.0
RGSC_v3.42204,509,899 - 204,510,099UniSTSRGSC3.4
Celera2189,202,260 - 189,202,460UniSTS
RH 3.4 Map7770.6UniSTS
Cytogenetic Map2q34UniSTS
RH125928  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22196,553,229 - 196,553,464 (+)MAPPERmRatBN7.2
Rnor_6.02211,706,251 - 211,706,485NCBIRnor6.0
Rnor_5.02231,180,389 - 231,180,623UniSTSRnor5.0
RGSC_v3.42204,509,115 - 204,509,349UniSTSRGSC3.4
Celera2189,201,476 - 189,201,710UniSTS
Cytogenetic Map2q34UniSTS
RH138818  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22196,554,701 - 196,554,826 (+)MAPPERmRatBN7.2
Rnor_6.02211,707,723 - 211,707,847NCBIRnor6.0
Rnor_5.02231,181,861 - 231,181,985UniSTSRnor5.0
RGSC_v3.42204,510,587 - 204,510,711UniSTSRGSC3.4
Celera2189,202,948 - 189,203,072UniSTS
RH 3.4 Map21394.6UniSTS
Cytogenetic Map2q34UniSTS
RH140563  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22196,557,544 - 196,557,734 (+)MAPPERmRatBN7.2
Rnor_6.02211,710,566 - 211,710,755NCBIRnor6.0
Rnor_5.02231,184,704 - 231,184,893UniSTSRnor5.0
RGSC_v3.42204,513,430 - 204,513,619UniSTSRGSC3.4
Celera2189,205,791 - 189,205,980UniSTS
RH 3.4 Map21395.3UniSTS
Cytogenetic Map2q34UniSTS
RH91206  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22196,553,376 - 196,553,510 (+)MAPPERmRatBN7.2
Rnor_6.02211,706,398 - 211,706,531NCBIRnor6.0
Rnor_5.02231,180,536 - 231,180,669UniSTSRnor5.0
RGSC_v3.42204,509,262 - 204,509,395UniSTSRGSC3.4
Celera2189,201,623 - 189,201,756UniSTS
Cytogenetic Map2q34UniSTS
RH136523  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22196,555,133 - 196,555,705 (+)MAPPERmRatBN7.2
Rnor_6.02211,708,155 - 211,708,726NCBIRnor6.0
Rnor_5.02231,182,293 - 231,182,864UniSTSRnor5.0
RGSC_v3.42204,511,019 - 204,511,590UniSTSRGSC3.4
Celera2189,203,380 - 189,203,951UniSTS
Cytogenetic Map2q34UniSTS


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 42 57 41 19 41 3 5 74 35 39 11 3
Low 1 5 6 2 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001024305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102941 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063282405 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005500347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010063654 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC129843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC079264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF283777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB720005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DY314904 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000027738   ⟹   ENSRNOP00000027738
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2196,553,225 - 196,562,250 (-)Ensembl
Rnor_6.0 Ensembl2211,706,228 - 211,715,311 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094371   ⟹   ENSRNOP00000089820
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2196,559,930 - 196,561,973 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104883   ⟹   ENSRNOP00000083823
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2196,553,228 - 196,562,211 (-)Ensembl
RefSeq Acc Id: NM_001024305   ⟹   NP_001019476
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82199,241,313 - 199,250,338 (-)NCBI
mRatBN7.22196,553,225 - 196,562,250 (-)NCBI
Rnor_6.02211,706,246 - 211,715,271 (-)NCBI
Rnor_5.02231,180,383 - 231,189,409 (-)NCBI
RGSC_v3.42204,509,110 - 204,518,135 (-)RGD
Celera2189,201,471 - 189,210,495 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233172   ⟹   XP_006233234
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82199,241,312 - 199,249,914 (-)NCBI
mRatBN7.22196,553,224 - 196,561,835 (-)NCBI
Rnor_6.02211,706,245 - 211,714,809 (-)NCBI
Rnor_5.02231,180,383 - 231,189,409 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039102941   ⟹   XP_038958869
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82199,241,312 - 199,249,909 (-)NCBI
mRatBN7.22196,553,224 - 196,561,833 (-)NCBI
RefSeq Acc Id: XM_039102942   ⟹   XP_038958870
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82199,241,312 - 199,249,912 (-)NCBI
mRatBN7.22196,553,224 - 196,561,835 (-)NCBI
RefSeq Acc Id: XM_063282405   ⟹   XP_063138475
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82199,243,741 - 199,250,342 (-)NCBI
RefSeq Acc Id: XR_005500347
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82199,243,741 - 199,250,342 (-)NCBI
mRatBN7.22196,555,610 - 196,562,271 (-)NCBI
RefSeq Acc Id: XR_010063654
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82199,243,741 - 199,250,342 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001019476   ⟸   NM_001024305
- UniProtKB: Q6AXY7 (UniProtKB/Swiss-Prot),   A6HV34 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233234   ⟸   XM_006233172
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000027738   ⟸   ENSRNOT00000027738
RefSeq Acc Id: XP_038958870   ⟸   XM_039102942
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038958869   ⟸   XM_039102941
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000083823   ⟸   ENSRNOT00000104883
RefSeq Acc Id: ENSRNOP00000089820   ⟸   ENSRNOT00000094371
RefSeq Acc Id: XP_063138475   ⟸   XM_063282405
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AXY7-F1-model_v2 AlphaFold Q6AXY7 1-542 view protein structure

Transcriptome

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

Promoters
RGD ID:13691690
Promoter ID:EPDNEW_R2215
Type:initiation region
Name:Prpf38b_1
Description:pre-mRNA processing factor 38B
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_6.02211,715,268 - 211,715,328EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562940 AgrOrtholog
BioCyc Gene G2FUF-51586 BioCyc
Ensembl Genes ENSRNOG00000020438 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055021164 UniProtKB/Swiss-Prot
  ENSRNOG00060028843 UniProtKB/Swiss-Prot
  ENSRNOG00065022155 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027738 ENTREZGENE
  ENSRNOT00000027738.6 UniProtKB/Swiss-Prot
  ENSRNOT00000094371.1 UniProtKB/TrEMBL
  ENSRNOT00000104883.1 UniProtKB/TrEMBL
  ENSRNOT00055036163 UniProtKB/Swiss-Prot
  ENSRNOT00060050118 UniProtKB/Swiss-Prot
  ENSRNOT00065037755 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7133560 IMAGE-MGC_LOAD
InterPro PRP38 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:499691 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:94372 IMAGE-MGC_LOAD
NCBI Gene 499691 ENTREZGENE
PANTHER PRE-MRNA-SPLICING FACTOR 38B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR23142 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PRP38 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Prpf38b PhenoGen
RatGTEx ENSRNOG00000020438 RatGTEx
  ENSRNOG00055021164 RatGTEx
  ENSRNOG00060028843 RatGTEx
  ENSRNOG00065022155 RatGTEx
UniProt A0A8I6G9I2_RAT UniProtKB/TrEMBL
  A0A8I6GHP1_RAT UniProtKB/TrEMBL
  A6HV34 ENTREZGENE, UniProtKB/TrEMBL
  PR38B_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-19 Prpf38b  pre-mRNA processing factor 38B  Prpf38b  PRP38 pre-mRNA processing factor 38 (yeast) domain containing B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Prpf38b  PRP38 pre-mRNA processing factor 38 (yeast) domain containing B  LOC499691  similar to sarcoma antigen NY-SAR-27  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC499691  similar to sarcoma antigen NY-SAR-27      Symbol and Name status set to provisional 70820 PROVISIONAL