Vpreb3 (V-set pre-B cell surrogate light chain 3) - Rat Genome Database

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Gene: Vpreb3 (V-set pre-B cell surrogate light chain 3) Rattus norvegicus
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Symbol: Vpreb3
Name: V-set pre-B cell surrogate light chain 3
RGD ID: 1306807
Description: Predicted to be involved in immune response. Predicted to be part of immunoglobulin complex. Orthologous to human VPREB3 (V-set pre-B cell surrogate light chain 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC103694871; LOC365550; pre-B lymphocyte 3; pre-B lymphocyte gene 3; pre-B lymphocyte protein 3; pre-B lymphocyte protein 3-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82012,716,862 - 12,720,108 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.22012,717,421 - 12,718,785 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2012,716,779 - 12,719,520 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2013,417,198 - 13,418,528 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02012,778,118 - 12,779,448 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02013,249,911 - 13,251,241 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02013,656,683 - 13,661,542 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2013,656,825 - 13,657,943 (-)Ensemblrn6Rnor6.0
Rnor_5.02015,812,246 - 15,817,063 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42013,116,299 - 13,117,609 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2014,208,786 - 14,210,096 (-)NCBICelera
RGSC_v3.12013,116,335 - 13,120,114 (-)NCBI
Cytogenetic Map20p12NCBI
JBrowse:




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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Vpreb3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82012,716,862 - 12,720,108 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.22012,717,421 - 12,718,785 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2012,716,779 - 12,719,520 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2013,417,198 - 13,418,528 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02012,778,118 - 12,779,448 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02013,249,911 - 13,251,241 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02013,656,683 - 13,661,542 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2013,656,825 - 13,657,943 (-)Ensemblrn6Rnor6.0
Rnor_5.02015,812,246 - 15,817,063 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42013,116,299 - 13,117,609 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2014,208,786 - 14,210,096 (-)NCBICelera
RGSC_v3.12013,116,335 - 13,120,114 (-)NCBI
Cytogenetic Map20p12NCBI
VPREB3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382223,752,743 - 23,754,425 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2223,752,743 - 23,754,425 (-)Ensemblhg38GRCh38
GRCh372224,094,930 - 24,096,612 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362222,424,932 - 22,426,592 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342222,419,487 - 22,421,146NCBI
Celera227,934,023 - 7,935,723 (-)NCBICelera
Cytogenetic Map22q11.23NCBI
HuRef227,083,000 - 7,084,700 (-)NCBIHuRef
CHM1_12224,107,172 - 24,108,872 (-)NCBICHM1_1
T2T-CHM13v2.02224,199,936 - 24,201,618 (-)NCBIT2T-CHM13v2.0
Vpreb3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391075,778,859 - 75,785,491 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1075,778,891 - 75,785,491 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381075,943,024 - 75,949,657 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1075,943,057 - 75,949,657 (+)Ensemblmm10GRCm38
MGSCv371075,411,057 - 75,412,391 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361075,392,028 - 75,393,362 (+)NCBIMGSCv36mm8
Celera1076,992,991 - 76,994,325 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1038.63NCBI
Vpreb3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554558,484,198 - 8,485,357 (+)Ensembl
ChiLan1.0NW_0049554558,483,685 - 8,485,514 (+)NCBIChiLan1.0ChiLan1.0
VPREB3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22333,484,482 - 33,489,144 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12236,220,869 - 36,222,702 (-)NCBINHGRI_mPanPan1
PanPan1.1 Ensembl2222,594,271 - 22,595,988 (-)EnsemblpanPan2panpan1.1
VPREB3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12628,750,702 - 28,751,928 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2628,750,742 - 28,751,792 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2627,822,823 - 27,825,262 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02630,154,663 - 30,157,100 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2630,155,921 - 30,156,971 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12628,235,770 - 28,238,213 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02627,853,744 - 27,856,185 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02628,841,578 - 28,844,021 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vpreb3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118141,419,880 - 141,421,304 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366191,332,863 - 1,334,046 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366191,332,863 - 1,334,135 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPREB3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1196,869,415 - 6,871,366 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl196,869,549 - 6,871,051 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666100503,742 - 505,707 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vpreb3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474710,424,262 - 10,425,438 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474710,422,747 - 10,425,633 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Vpreb3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11811,499,559 - 11,500,957 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vpreb3
48 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:90
Count of miRNA genes:78
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000032290
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804392029865039Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804392015089182Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)201224324249189476Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

Markers in Region
RH144147  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,717,496 - 12,717,648 (+)MAPPERmRatBN7.2
Rnor_6.02013,656,705 - 13,656,856NCBIRnor6.0
Rnor_5.02015,812,268 - 15,812,419UniSTSRnor5.0
RGSC_v3.42013,116,321 - 13,116,472UniSTSRGSC3.4
Celera2014,208,808 - 14,208,959UniSTS
Cytogenetic Map20p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
12 1 23 73 40 36 24 73 24 6 196 118 11 55 42 51 12 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000032290   ⟹   ENSRNOP00000028914
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2013,656,825 - 13,657,943 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000117970   ⟹   ENSRNOP00000094137
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2012,716,779 - 12,719,520 (-)Ensembl
RefSeq Acc Id: NM_001108930   ⟹   NP_001102400
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82012,716,916 - 12,718,226 (-)NCBI
mRatBN7.22012,717,475 - 12,718,785 (-)NCBI
Rnor_6.02013,656,683 - 13,657,993 (-)NCBI
Rnor_5.02015,812,246 - 15,817,063 (-)NCBI
RGSC_v3.42013,116,299 - 13,117,609 (-)RGD
Celera2014,208,786 - 14,210,096 (-)RGD
Sequence:
RefSeq Acc Id: NM_001413612   ⟹   NP_001400541
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82012,716,862 - 12,718,226 (-)NCBI
mRatBN7.22012,717,421 - 12,718,785 (-)NCBI
RefSeq Acc Id: XM_063279328   ⟹   XP_063135398
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82012,716,965 - 12,720,108 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001102400 (Get FASTA)   NCBI Sequence Viewer  
  NP_001400541 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135398 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97164 (Get FASTA)   NCBI Sequence Viewer  
  EDL97165 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000102169
  ENSRNOP00000102169.1
RefSeq Acc Id: NP_001102400   ⟸   NM_001108930
- Peptide Label: isoform 2
- UniProtKB: A6JKE8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000028914   ⟸   ENSRNOT00000032290
Ensembl Acc Id: ENSRNOP00000094137   ⟸   ENSRNOT00000117970
RefSeq Acc Id: NP_001400541   ⟸   NM_001413612
- Peptide Label: isoform 1 precursor
- UniProtKB: A0A8I6AKY6 (UniProtKB/TrEMBL),   A6JKE9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135398   ⟸   XM_063279328
- Peptide Label: isoform X1
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRL1-F1-model_v2 AlphaFold D3ZRL1 1-106 view protein structure

Transcriptome

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

Promoters
RGD ID:13701526
Promoter ID:EPDNEW_R12050
Type:multiple initiation site
Name:Vpreb3_1
Description:V-set pre-B cell surrogate light chain 3
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_6.02013,658,003 - 13,658,063EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306807 AgrOrtholog
BioCyc Gene G2FUF-4169 BioCyc
Ensembl Genes ENSRNOG00000028394 Ensembl
  ENSRNOG00000065441 Ensembl
  ENSRNOG00000075030 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000158074 ENTREZGENE
  ENSRNOT00000158074.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  IgV_Light_Chain UniProtKB/TrEMBL
NCBI Gene 365550 ENTREZGENE
PANTHER IMMUNOGLOBULIN LIGHT CHAIN UniProtKB/TrEMBL
Pfam V-set UniProtKB/TrEMBL
PhenoGen Vpreb3 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028394 RatGTEx
  ENSRNOG00000065441 RatGTEx
  ENSRNOG00000075030 RatGTEx
SMART IGv UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A8I6AKY6 ENTREZGENE
  A0ABK0L1D4_RAT UniProtKB/TrEMBL
  A6JKE8 ENTREZGENE, UniProtKB/TrEMBL
  A6JKE9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Vpreb3  V-set pre-B cell surrogate light chain 3  LOC103694871  pre-B lymphocyte protein 3-like  Data merged from RGD:9477019 737654 PROVISIONAL
2017-03-27 Vpreb3  V-set pre-B cell surrogate light chain 3  Vpreb3  pre-B lymphocyte 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103694871  pre-B lymphocyte protein 3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-10-23 Vpreb3  pre-B lymphocyte 3  Vpreb3  pre-B lymphocyte gene 3   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Vpreb3  pre-B lymphocyte gene 3   Vpreb3_predicted  pre-B lymphocyte gene 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Vpreb3_predicted  pre-B lymphocyte gene 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED