Grin3b (glutamate ionotropic receptor NMDA type subunit 3B) - Rat Genome Database

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Gene: Grin3b (glutamate ionotropic receptor NMDA type subunit 3B) Rattus norvegicus
Analyze
Symbol: Grin3b
Name: glutamate ionotropic receptor NMDA type subunit 3B
RGD ID: 621705
Description: Enables several functions, including glycine binding activity; neurotransmitter binding activity; and neurotransmitter receptor activity. Involved in ionotropic glutamate receptor signaling pathway. Part of NMDA selective glutamate receptor complex. Is active in hippocampal mossy fiber to CA3 synapse; postsynaptic density membrane; and presynaptic active zone membrane. Orthologous to human GRIN3B (glutamate ionotropic receptor NMDA type subunit 3B); PARTICIPATES IN excitatory synaptic transmission pathway; glutamate signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: GluN3B; glutamate [NMDA] receptor subunit 3B; glutamate receptor ionotropic, NMDA 3B; glutamate receptor, ionotropic, N-methyl-D-aspartate 3B; glutamate receptor, ionotropic, NMDA3B; N-methyl-D-aspartate receptor subtype 3B; NMDAR3B; NR3B
RGD Orthologs
Human
Mouse
Chinchilla
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
mRatBN7.279,730,861 - 9,737,183 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,730,862 - 9,737,183 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx712,613,161 - 12,619,488 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0714,488,483 - 14,494,810 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0712,349,681 - 12,356,006 (-)NCBIRnor_WKY
Rnor_6.0712,764,993 - 12,771,310 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,764,993 - 12,771,310 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,934,715 - 12,941,032 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,243,973 - 11,250,311 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1711,243,973 - 11,250,304 (-)NCBI
Celera77,906,482 - 7,912,799 (-)NCBICelera
Cytogenetic Map7q11NCBI
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
Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Pre- and postsynaptic localization of NMDA receptor subunits at hippocampal mossy fibre synapses. Berg LK, etal., Neuroscience. 2013 Jan 29;230:139-50. doi: 10.1016/j.neuroscience.2012.10.061. Epub 2012 Nov 14.
2. Excitatory glycine receptors containing the NR3 family of NMDA receptor subunits. Chatterton JE, etal., Nature 2002 Feb 14;415(6873):793-8.
3. 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.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11717388   PMID:11735224   PMID:14602821   PMID:18425811   PMID:19361480   PMID:20813147   PMID:20887777  


Genomics

Comparative Map Data
Grin3b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.279,730,861 - 9,737,183 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl79,730,862 - 9,737,183 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx712,613,161 - 12,619,488 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0714,488,483 - 14,494,810 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0712,349,681 - 12,356,006 (-)NCBIRnor_WKY
Rnor_6.0712,764,993 - 12,771,310 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl712,764,993 - 12,771,310 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,934,715 - 12,941,032 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4711,243,973 - 11,250,311 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1711,243,973 - 11,250,304 (-)NCBI
Celera77,906,482 - 7,912,799 (-)NCBICelera
Cytogenetic Map7q11NCBI
GRIN3B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38191,000,419 - 1,009,732 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl191,000,419 - 1,009,732 (+)EnsemblGRCh38hg38GRCh38
GRCh37191,000,418 - 1,009,731 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3619951,437 - 960,723 (+)NCBINCBI36Build 36hg18NCBI36
Celera19932,775 - 942,061 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef19773,711 - 783,359 (+)NCBIHuRef
CHM1_119999,547 - 1,008,877 (+)NCBICHM1_1
T2T-CHM13v2.019963,087 - 972,401 (+)NCBIT2T-CHM13v2.0
Grin3b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391079,806,227 - 79,813,024 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1079,806,549 - 79,813,024 (+)EnsemblGRCm39 Ensembl
GRCm381079,970,397 - 79,977,190 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1079,970,715 - 79,977,190 (+)EnsemblGRCm38mm10GRCm38
MGSCv371079,433,469 - 79,439,935 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361079,373,853 - 79,380,319 (+)NCBIMGSCv36mm8
Celera1080,985,531 - 80,991,997 (+)NCBICelera
Cytogenetic Map10C1NCBI
Grin3b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554956,859,909 - 6,866,306 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554956,859,909 - 6,866,297 (-)NCBIChiLan1.0ChiLan1.0
GRIN3B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12057,703,569 - 57,710,119 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2057,505,626 - 57,512,392 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02058,445,553 - 58,452,550 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2058,445,603 - 58,452,334 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12057,500,871 - 57,509,457 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02057,980,403 - 57,987,181 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02058,183,413 - 58,190,220 (-)NCBIUU_Cfam_GSD_1.0
Grin3b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,394,254 - 217,401,759 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936588433,261 - 444,237 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936588433,544 - 440,534 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GRIN3B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl277,401,368 - 77,412,136 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1277,402,191 - 77,411,878 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2277,585,744 - 77,595,456 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GRIN3B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.16756,257 - 766,175 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl6756,618 - 766,048 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660818,153,737 - 8,163,435 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Grin3b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248287,614,672 - 7,622,111 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248287,614,656 - 7,622,111 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Grin3b
31 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:60
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000017064
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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat

Markers in Region
RH127486  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,712,644 - 9,712,846 (+)MAPPERmRatBN7.2
Rnor_6.0712,763,622 - 12,763,823NCBIRnor6.0
Rnor_5.0712,933,344 - 12,933,545UniSTSRnor5.0
RGSC_v3.4711,225,323 - 11,225,524UniSTSRGSC3.4
Celera77,888,321 - 7,888,522UniSTS
RH 3.4 Map725.2UniSTS
Cytogenetic Map7q11UniSTS
RH130604  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,730,674 - 9,730,885 (-)MAPPERmRatBN7.2
Rnor_6.0712,771,286 - 12,771,496NCBIRnor6.0
Rnor_5.0712,941,008 - 12,941,218UniSTSRnor5.0
RGSC_v3.4711,243,787 - 11,243,997UniSTSRGSC3.4
Celera77,906,296 - 7,906,506UniSTS
RH 3.4 Map749.1UniSTS
Cytogenetic Map7q11UniSTS
RH139166  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,713,029 - 9,713,169 (+)MAPPERmRatBN7.2
Rnor_6.0712,764,007 - 12,764,146NCBIRnor6.0
Rnor_5.0712,933,729 - 12,933,868UniSTSRnor5.0
RGSC_v3.4711,225,708 - 11,225,847UniSTSRGSC3.4
Celera77,888,706 - 7,888,845UniSTS
Cytogenetic Map7q11UniSTS


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
Low 3 11 17 1 19 1 7 10 17 11 21 11 7
Below cutoff 6 14 14 14 1 1 21 22 16 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017064   ⟹   ENSRNOP00000017064
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,730,862 - 9,737,183 (-)Ensembl
Rnor_6.0 Ensembl712,764,993 - 12,771,309 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093751
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl79,730,862 - 9,737,183 (-)Ensembl
Rnor_6.0 Ensembl712,764,993 - 12,771,310 (+)Ensembl
RefSeq Acc Id: NM_133308   ⟹   NP_579842
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.279,730,861 - 9,737,183 (-)NCBI
Rnor_6.0712,764,993 - 12,771,310 (+)NCBI
Rnor_5.0712,934,715 - 12,941,032 (+)NCBI
RGSC_v3.4711,243,973 - 11,250,311 (-)RGD
Celera77,906,482 - 7,912,799 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_579842 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAL69893 (Get FASTA)   NCBI Sequence Viewer  
  EDL89361 (Get FASTA)   NCBI Sequence Viewer  
  Q8VHN2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_579842   ⟸   NM_133308
- Peptide Label: precursor
- UniProtKB: Q8VHN2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017064   ⟸   ENSRNOT00000017064
Protein Domains
Lig_chan-Glu_bd   PBPe

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8VHN2-F1-model_v2 AlphaFold Q8VHN2 1-1002 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621705 AgrOrtholog
BioCyc Gene G2FUF-34904 BioCyc
Ensembl Genes ENSRNOG00000012562 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017064 ENTREZGENE
  ENSRNOP00000017064.5 UniProtKB/TrEMBL
  ENSRNOP00000076547.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017064 ENTREZGENE
  ENSRNOT00000017064.6 UniProtKB/TrEMBL
  ENSRNOT00000093751.2 UniProtKB/TrEMBL
InterPro Glu/Gly-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Iono_rcpt_met UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Iontro_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peripla_BP_I UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:170796 UniProtKB/Swiss-Prot
NCBI Gene 170796 ENTREZGENE
Pfam Lig_chan UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lig_chan-Glu_bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Grin3b PhenoGen
PRINTS NMDARECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Lig_chan-Glu_bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PBPe UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53822 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5YBD4_RAT UniProtKB/TrEMBL
  F1LPZ6_RAT UniProtKB/TrEMBL
  NMD3B_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Grin3b  glutamate ionotropic receptor NMDA type subunit 3B  Grin3b  glutamate receptor, ionotropic, N-methyl-D-aspartate 3B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Grin3b  glutamate receptor, ionotropic, N-methyl-D-aspartate 3B    glutamate receptor, ionotropic, NMDA3B  Name updated 1299863 APPROVED
2002-08-07 Grin3b  glutamate receptor, ionotropic, NMDA3B      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed predominantly in motor neurons 632842