Rbm39 (RNA binding motif protein 39) - Rat Genome Database

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Gene: Rbm39 (RNA binding motif protein 39) Rattus norvegicus
Analyze
Symbol: Rbm39
Name: RNA binding motif protein 39
RGD ID: 1310071
Description: Predicted to enable RS domain binding activity; U1 snRNP binding activity; and transcription coactivator activity. Predicted to be involved in regulation of mRNA splicing, via spliceosome. Predicted to act upstream of or within regulation of transcription by RNA polymerase II. Predicted to be located in centriolar satellite and nuclear speck. Predicted to be part of protein-containing complex. Orthologous to human RBM39 (RNA binding motif protein 39); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100910882; LOC362251; MGC109490; RNA-binding protein 39; RNA-binding protein 39-like; RNA-binding region (RNP1, RRM) containing 2; RNA-binding region-containing 2; Rnp1; Rnpc2; Rrm
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83165,123,087 - 165,156,453 (-)NCBIGRCr8
mRatBN7.23144,662,998 - 144,696,222 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3144,663,001 - 144,696,213 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3148,528,781 - 148,561,928 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03157,146,051 - 157,179,198 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03154,885,576 - 154,918,724 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03151,691,498 - 151,724,723 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3151,691,514 - 151,724,654 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl3152,226,710 - 152,259,156 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03158,056,123 - 158,089,351 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43146,555,202 - 146,587,650 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13146,461,112 - 146,493,559 (-)NCBI
Celera3143,385,461 - 143,417,910 (-)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,6-tribromophenol  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-butoxyethanol  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
6-propyl-2-thiouracil  (EXP)
acetazolamide  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (ISO)
alpha-pinene  (ISO)
amitrole  (EXP)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (ISO)
bilirubin IXalpha  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
cadmium dichloride  (EXP)
caffeine  (ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
chlorpyrifos  (EXP)
chrysene  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
diuron  (EXP,ISO)
endosulfan  (EXP)
ethanol  (ISO)
ferroheme b  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
FR900359  (ISO)
gentamycin  (EXP)
heme b  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
mercury dichloride  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
ozone  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
phenobarbital  (ISO)
pirinixic acid  (EXP,ISO)
propiconazole  (EXP,ISO)
quercitrin  (ISO)
quinomethionate  (ISO)
resveratrol  (EXP,ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
streptozocin  (EXP)
succimer  (ISO)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrahydropalmatine  (ISO)
tetraphene  (ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
torcetrapib  (ISO)
Tributyltin oxide  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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 GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. 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:15453907   PMID:15694343   PMID:22658674   PMID:22681889   PMID:28302793   PMID:28437394  


Genomics

Comparative Map Data
Rbm39
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83165,123,087 - 165,156,453 (-)NCBIGRCr8
mRatBN7.23144,662,998 - 144,696,222 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3144,663,001 - 144,696,213 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3148,528,781 - 148,561,928 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03157,146,051 - 157,179,198 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03154,885,576 - 154,918,724 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03151,691,498 - 151,724,723 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3151,691,514 - 151,724,654 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl3152,226,710 - 152,259,156 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03158,056,123 - 158,089,351 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43146,555,202 - 146,587,650 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13146,461,112 - 146,493,559 (-)NCBI
Celera3143,385,461 - 143,417,910 (-)NCBICelera
Cytogenetic Map3q42NCBI
RBM39
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382035,701,347 - 35,742,260 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2035,701,347 - 35,742,312 (-)EnsemblGRCh38hg38GRCh38
GRCh372034,289,269 - 34,330,182 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362033,754,945 - 33,793,607 (-)NCBINCBI36Build 36hg18NCBI36
Build 342033,754,944 - 33,793,607NCBI
Celera2031,039,826 - 31,078,484 (-)NCBICelera
Cytogenetic Map20q11.22NCBI
HuRef2031,068,914 - 31,107,649 (-)NCBIHuRef
CHM1_12034,193,463 - 34,232,187 (-)NCBICHM1_1
T2T-CHM13v2.02037,422,322 - 37,463,242 (-)NCBIT2T-CHM13v2.0
Rbm39
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392155,989,159 - 156,022,649 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2155,989,159 - 156,022,158 (-)EnsemblGRCm39 Ensembl
GRCm382156,147,239 - 156,180,238 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2156,147,239 - 156,180,238 (-)EnsemblGRCm38mm10GRCm38
MGSCv372155,972,975 - 156,005,976 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362155,839,078 - 155,871,581 (-)NCBIMGSCv36mm8
Celera2162,082,815 - 162,115,677 (-)NCBICelera
Cytogenetic Map2H1NCBI
cM Map277.36NCBI
Rbm39
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542225,719,771 - 25,755,757 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542225,719,771 - 25,755,757 (+)NCBIChiLan1.0ChiLan1.0
RBM39
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22141,436,065 - 41,474,664 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12041,429,168 - 41,467,767 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02032,030,938 - 32,069,442 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12033,151,973 - 33,191,072 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2033,151,973 - 33,191,072 (-)Ensemblpanpan1.1panPan2
RBM39
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12424,618,966 - 24,648,384 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2424,619,691 - 24,648,474 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2424,263,987 - 24,293,214 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02425,311,461 - 25,340,682 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2425,311,465 - 25,340,769 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12424,597,750 - 24,627,188 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02424,692,832 - 24,722,288 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02425,132,248 - 25,161,470 (-)NCBIUU_Cfam_GSD_1.0
Rbm39
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640173,618,812 - 173,650,017 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365615,099,580 - 5,128,134 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365615,099,052 - 5,149,947 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RBM39
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1739,031,957 - 39,063,699 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11739,032,141 - 39,064,803 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21744,382,747 - 44,415,404 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RBM39
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1256,621,692 - 56,645,028 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl256,622,562 - 56,644,921 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660872,964,723 - 3,004,111 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rbm39
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248423,698,632 - 3,733,221 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248423,698,630 - 3,733,221 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rbm39
152 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:417
Count of miRNA genes:208
Interacting mature miRNAs:237
Transcripts:ENSRNOT00000026964, ENSRNOT00000065729
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3140069424146976080Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141339236155617360Rat

Markers in Region
RH129887  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23144,663,028 - 144,663,245 (+)MAPPERmRatBN7.2
Rnor_6.03152,226,045 - 152,226,261NCBIRnor6.0
Rnor_6.03151,691,532 - 151,691,748NCBIRnor6.0
Rnor_5.03159,464,520 - 159,464,736UniSTSRnor5.0
Rnor_5.03158,056,150 - 158,056,366UniSTSRnor5.0
RGSC_v3.43146,554,539 - 146,554,755UniSTSRGSC3.4
Celera3143,384,798 - 143,385,014UniSTS
RH 3.4 Map81000.39UniSTS
Cytogenetic Map3q42UniSTS
AI578416  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23144,672,419 - 144,672,545 (+)MAPPERmRatBN7.2
Rnor_6.03152,235,436 - 152,235,561NCBIRnor6.0
Rnor_6.03151,700,923 - 151,701,048NCBIRnor6.0
Rnor_5.03159,455,220 - 159,455,345UniSTSRnor5.0
Rnor_5.03158,065,541 - 158,065,666UniSTSRnor5.0
RGSC_v3.43146,563,930 - 146,564,055UniSTSRGSC3.4
Celera3143,394,189 - 143,394,314UniSTS
RH 3.4 Map31293.9UniSTS
Cytogenetic Map3q42UniSTS
BM388276  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23144,687,968 - 144,688,122 (+)MAPPERmRatBN7.2
Rnor_6.03152,250,985 - 152,251,138NCBIRnor6.0
Rnor_6.03151,716,472 - 151,716,625NCBIRnor6.0
Rnor_5.03159,439,643 - 159,439,796UniSTSRnor5.0
Rnor_5.03158,081,090 - 158,081,243UniSTSRnor5.0
RGSC_v3.43146,579,479 - 146,579,632UniSTSRGSC3.4
Celera3143,409,739 - 143,409,892UniSTS
RH 3.4 Map31294.1UniSTS
Cytogenetic Map3q42UniSTS
stSG636839  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23144,693,891 - 144,695,020 (+)MAPPERmRatBN7.2
Rnor_6.03152,256,908 - 152,258,036NCBIRnor6.0
Rnor_6.03151,722,395 - 151,723,523NCBIRnor6.0
Rnor_5.03158,087,013 - 158,088,141UniSTSRnor5.0
Rnor_5.03159,432,745 - 159,433,873UniSTSRnor5.0
RGSC_v3.43146,585,402 - 146,586,530UniSTSRGSC3.4
Celera3143,415,662 - 143,416,790UniSTS
Cytogenetic Map3q42UniSTS
MARC_17207-17208:1023890900:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23144,693,476 - 144,693,979 (+)MAPPERmRatBN7.2
Rnor_6.03152,256,493 - 152,256,995NCBIRnor6.0
Rnor_6.03151,721,980 - 151,722,482NCBIRnor6.0
Rnor_5.03158,086,598 - 158,087,100UniSTSRnor5.0
Rnor_5.03159,433,786 - 159,434,288UniSTSRnor5.0
RGSC_v3.43146,584,987 - 146,585,489UniSTSRGSC3.4
Celera3143,415,247 - 143,415,749UniSTS
Cytogenetic Map3q42UniSTS
G64285  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23144,695,213 - 144,695,975 (+)MAPPERmRatBN7.2
Rnor_6.03152,258,230 - 152,258,991NCBIRnor6.0
Rnor_6.03151,723,717 - 151,724,478NCBIRnor6.0
Rnor_5.03158,088,335 - 158,089,096UniSTSRnor5.0
Rnor_5.03159,431,790 - 159,432,551UniSTSRnor5.0
RGSC_v3.43146,586,724 - 146,587,485UniSTSRGSC3.4
Celera3143,416,984 - 143,417,745UniSTS
Cytogenetic Map3q42UniSTS
ECD08795  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23144,664,056 - 144,665,030 (+)MAPPERmRatBN7.2
Rnor_6.03152,227,073 - 152,228,046NCBIRnor6.0
Rnor_6.03151,692,560 - 151,693,533NCBIRnor6.0
Rnor_5.03158,057,178 - 158,058,151UniSTSRnor5.0
Rnor_5.03159,462,735 - 159,463,708UniSTSRnor5.0
RGSC_v3.43146,555,567 - 146,556,540UniSTSRGSC3.4
Celera3143,385,826 - 143,386,799UniSTS
Cytogenetic Map3q42UniSTS
REN58939  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23144,694,875 - 144,695,122 (+)MAPPERmRatBN7.2
Rnor_6.03152,257,892 - 152,258,138NCBIRnor6.0
Rnor_6.03151,723,379 - 151,723,625NCBIRnor6.0
Rnor_5.03158,087,997 - 158,088,243UniSTSRnor5.0
RGSC_v3.43146,586,386 - 146,586,632UniSTSRGSC3.4
Celera3143,416,646 - 143,416,892UniSTS
Cytogenetic Map3q42UniSTS


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001013207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235335 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591925 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105498 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284182 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC118414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY769432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC078917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC091394 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226699 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227690 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227784 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231143 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232143 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000026964   ⟹   ENSRNOP00000026964
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3144,663,003 - 144,696,197 (-)Ensembl
Rnor_6.0 Ensembl3151,691,514 - 151,724,654 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000065729   ⟹   ENSRNOP00000060273
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3144,663,005 - 144,696,193 (-)Ensembl
Rnor_6.0 Ensembl3152,226,710 - 152,259,156 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111677   ⟹   ENSRNOP00000094754
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3144,691,061 - 144,696,213 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112953   ⟹   ENSRNOP00000089286
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3144,663,005 - 144,696,193 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117296   ⟹   ENSRNOP00000090119
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3144,663,001 - 144,696,169 (-)Ensembl
RefSeq Acc Id: NM_001013207   ⟹   NP_001013225
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,089 - 165,156,235 (-)NCBI
mRatBN7.23144,663,005 - 144,696,151 (-)NCBI
Rnor_6.03151,691,508 - 151,724,654 (-)NCBI
Rnor_5.03158,056,123 - 158,089,351 (-)NCBI
RGSC_v3.43146,555,202 - 146,587,650 (-)RGD
Celera3143,384,774 - 143,417,921 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235331   ⟹   XP_006235393
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,156,453 (-)NCBI
mRatBN7.23144,662,998 - 144,696,217 (-)NCBI
Rnor_6.03151,691,498 - 151,724,720 (-)NCBI
Rnor_5.03158,056,123 - 158,089,351 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235332   ⟹   XP_006235394
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,156,453 (-)NCBI
mRatBN7.23144,663,004 - 144,696,218 (-)NCBI
Rnor_6.03151,691,498 - 151,724,721 (-)NCBI
Rnor_5.03158,056,123 - 158,089,351 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762349   ⟹   XP_008760571
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,156,453 (-)NCBI
mRatBN7.23144,662,998 - 144,696,221 (-)NCBI
Rnor_6.03151,691,498 - 151,724,723 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762350   ⟹   XP_008760572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,156,453 (-)NCBI
mRatBN7.23144,662,998 - 144,696,222 (-)NCBI
Rnor_6.03151,691,498 - 151,724,723 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008762356   ⟹   XP_008760578
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,156,453 (-)NCBI
mRatBN7.23144,663,004 - 144,696,222 (-)NCBI
Rnor_6.03151,691,498 - 151,724,723 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105498   ⟹   XP_038961426
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,156,453 (-)NCBI
mRatBN7.23144,662,998 - 144,696,217 (-)NCBI
RefSeq Acc Id: XM_063284180   ⟹   XP_063140250
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,156,453 (-)NCBI
RefSeq Acc Id: XM_063284181   ⟹   XP_063140251
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,155,349 (-)NCBI
RefSeq Acc Id: XM_063284182   ⟹   XP_063140252
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,156,453 (-)NCBI
RefSeq Acc Id: XM_063284183   ⟹   XP_063140253
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,152,608 (-)NCBI
RefSeq Acc Id: XM_063284184   ⟹   XP_063140254
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83165,123,087 - 165,155,349 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001013225   ⟸   NM_001013207
- UniProtKB: Q5BJP4 (UniProtKB/TrEMBL),   F1MA64 (UniProtKB/TrEMBL),   D3ZR20 (UniProtKB/TrEMBL),   A0A8J8XIU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235393   ⟸   XM_006235331
- Peptide Label: isoform X1
- UniProtKB: A0A8J8XIU8 (UniProtKB/TrEMBL),   A0A8J8XIU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235394   ⟸   XM_006235332
- Peptide Label: isoform X1
- UniProtKB: A0A8J8XIU8 (UniProtKB/TrEMBL),   A0A8J8XIU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760578   ⟸   XM_008762356
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008760571   ⟸   XM_008762349
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008760572   ⟸   XM_008762350
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_038961426   ⟸   XM_039105498
- Peptide Label: isoform X4
- UniProtKB: A0A8I6A8P3 (UniProtKB/TrEMBL),   A0A8J8XIU1 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000026964   ⟸   ENSRNOT00000026964
RefSeq Acc Id: ENSRNOP00000060273   ⟸   ENSRNOT00000065729
RefSeq Acc Id: ENSRNOP00000089286   ⟸   ENSRNOT00000112953
RefSeq Acc Id: ENSRNOP00000094754   ⟸   ENSRNOT00000111677
RefSeq Acc Id: ENSRNOP00000090119   ⟸   ENSRNOT00000117296
RefSeq Acc Id: XP_063140252   ⟸   XM_063284182
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063140250   ⟸   XM_063284180
- Peptide Label: isoform X2
- UniProtKB: D3ZR20 (UniProtKB/TrEMBL),   F1MA64 (UniProtKB/TrEMBL),   Q5BJP4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140254   ⟸   XM_063284184
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063140251   ⟸   XM_063284181
- Peptide Label: isoform X4
- UniProtKB: A0A8I6A8P3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140253   ⟸   XM_063284183
- Peptide Label: isoform X6
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BJP4-F1-model_v2 AlphaFold Q5BJP4 1-524 view protein structure

Transcriptome

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

Promoters
RGD ID:13692595
Promoter ID:EPDNEW_R3120
Type:initiation region
Name:LOC100910882_1
Description:RNA-binding protein 39-like
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_6.03151,724,661 - 151,724,721EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310071 AgrOrtholog
BioCyc Gene G2FUF-47102 BioCyc
Ensembl Genes ENSRNOG00000019848 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000049814 Ensembl
Ensembl Transcript ENSRNOT00000026964.8 UniProtKB/TrEMBL
  ENSRNOT00000065729.4 UniProtKB/TrEMBL
  ENSRNOT00000111677.1 UniProtKB/TrEMBL
  ENSRNOT00000112953.1 UniProtKB/TrEMBL
  ENSRNOT00000117296.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7096440 IMAGE-MGC_LOAD
  IMAGE:7322533 IMAGE-MGC_LOAD
InterPro CC1_SF UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RBM39_linker UniProtKB/TrEMBL
  RRM_dom UniProtKB/TrEMBL
  RRM_dom_euk UniProtKB/TrEMBL
KEGG Report rno:362251 UniProtKB/TrEMBL
MGC_CLONE MGC:109490 IMAGE-MGC_LOAD
  MGC:93693 IMAGE-MGC_LOAD
NCBI Gene 362251 ENTREZGENE
PANTHER INNER NUCLEAR MEMBRANE PROTEIN MAN1-RELATED UniProtKB/TrEMBL
  SPLICING FACTOR (PAD-1), PUTATIVE (AFU_ORTHOLOGUE AFUA_1G15810)-RELATED UniProtKB/TrEMBL
Pfam RBM39linker UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
PhenoGen Rbm39 PhenoGen
PROSITE RRM UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019848 RatGTEx
  ENSRNOG00000049814 RatGTEx
SMART RRM UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A8I6A8P3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A9I1_RAT UniProtKB/TrEMBL
  A0A8I6B1G7_RAT UniProtKB/TrEMBL
  A0A8J8XIU1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8J8XIU8 ENTREZGENE, UniProtKB/TrEMBL
  A6KI94_RAT UniProtKB/TrEMBL
  D3ZR20 ENTREZGENE
  F1MA64 ENTREZGENE
  Q5BJP4 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary D3ZR20 UniProtKB/TrEMBL
  F1MA64 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Rbm39  RNA binding motif protein 39  LOC100910882  RNA-binding protein 39-like  Data merged from RGD:6496028 737654 PROVISIONAL
2012-07-05 LOC100910882  RNA-binding protein 39-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-07 Rbm39  RNA binding motif protein 39  Rnpc2  RNA-binding region (RNP1, RRM) containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Rnpc2  RNA-binding region (RNP1, RRM) containing 2  Rnpc2_predicted  RNA-binding region (RNP1, RRM) containing 2 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Rnpc2_predicted  RNA-binding region (RNP1, RRM) containing 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED