Glra4 (glycine receptor alpha 4) - Rat Genome Database

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Gene: Glra4 (glycine receptor alpha 4) Rattus norvegicus
Analyze
Symbol: Glra4
Name: glycine receptor alpha 4
RGD ID: 1564103
Description: Predicted to enable extracellularly glycine-gated chloride channel activity and neurotransmitter receptor activity. Predicted to contribute to chloride channel activity. Predicted to be involved in several processes, including chemical synaptic transmission; chloride transmembrane transport; and response to amino acid. Predicted to be part of transmembrane transporter complex. Predicted to be active in glycinergic synapse; neuron projection; and postsynaptic specialization membrane. Orthologous to human GLRA4 (glycine receptor alpha 4 (pseudogene)); INTERACTS WITH bisphenol A; trichloroethene; 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: glycine receptor subunit alpha-4; glycine receptor, alpha 4; glycine receptor, alpha 4 subunit; LOC367912; RGD1564103; similar to Glycine receptor alpha-4 chain precursor
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
GRCr8X104,899,449 - 104,923,328 (-)NCBIGRCr8
mRatBN7.2X100,110,517 - 100,131,042 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX100,110,517 - 100,131,042 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX102,240,701 - 102,261,223 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X105,739,380 - 105,759,902 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X103,308,550 - 103,329,073 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X107,416,019 - 107,447,253 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX107,422,357 - 107,442,878 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X107,306,116 - 107,326,637 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X124,410,009 - 124,430,532 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX100,945,585 - 100,966,108 (-)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10762330   PMID:17154252  


Genomics

Comparative Map Data
Glra4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X104,899,449 - 104,923,328 (-)NCBIGRCr8
mRatBN7.2X100,110,517 - 100,131,042 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX100,110,517 - 100,131,042 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX102,240,701 - 102,261,223 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X105,739,380 - 105,759,902 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X103,308,550 - 103,329,073 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X107,416,019 - 107,447,253 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX107,422,357 - 107,442,878 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X107,306,116 - 107,326,637 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X124,410,009 - 124,430,532 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX100,945,585 - 100,966,108 (-)NCBICelera
Cytogenetic MapXq32NCBI
GLRA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X103,705,494 - 103,728,495 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX103,707,224 - 103,728,203 (-)EnsemblGRCh38hg38GRCh38
GRCh37X102,960,422 - 102,983,423 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X102,848,928 - 102,866,560 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX103,401,274 - 103,422,554 (-)NCBICelera
Cytogenetic MapXq22.2NCBI
HuRefX92,619,349 - 92,640,430 (-)NCBIHuRef
CHM1_1X102,855,289 - 102,876,568 (-)NCBICHM1_1
T2T-CHM13v2.0X102,152,460 - 102,175,469 (-)NCBIT2T-CHM13v2.0
Glra4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X135,655,107 - 135,680,935 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX135,658,423 - 135,680,890 (-)EnsemblGRCm39 Ensembl
GRCm38X136,754,515 - 136,780,141 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX136,757,674 - 136,780,141 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X133,292,213 - 133,314,260 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X132,104,060 - 132,122,275 (-)NCBIMGSCv36mm8
CeleraX120,041,251 - 120,061,763 (-)NCBICelera
Cytogenetic MapXF1NCBI
cM MapX59.1NCBI
Glra4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955548712,257 - 736,327 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955548712,257 - 736,279 (-)NCBIChiLan1.0ChiLan1.0
GLRA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X103,317,432 - 103,340,251 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X103,319,883 - 103,343,856 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X92,933,694 - 92,957,714 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X103,316,810 - 103,338,910 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX103,317,486 - 103,338,910 (-)Ensemblpanpan1.1panPan2
GLRA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X77,115,962 - 77,142,381 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX77,119,072 - 77,194,726 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX63,345,343 - 63,371,619 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X78,735,140 - 78,761,415 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX78,737,813 - 78,761,133 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X76,212,496 - 76,238,770 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X77,899,243 - 77,925,515 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X77,666,343 - 77,692,622 (-)NCBIUU_Cfam_GSD_1.0
LOC101969868
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X77,035,389 - 77,060,252 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493649910,597,673 - 10,622,868 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GLRA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX84,584,907 - 84,612,860 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X84,584,907 - 84,612,860 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X98,373,709 - 98,401,678 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103232415
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X91,593,838 - 91,619,885 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX91,597,324 - 91,618,542 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606516,461,522 - 16,483,355 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Glra4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624954205,888 - 229,894 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Glra4
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:51
Count of miRNA genes:46
Interacting mature miRNAs:49
Transcripts:ENSRNOT00000052302
Prediction methods:Miranda, Pita, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat

Markers in Region
AU049455  
Rat AssemblyChrPosition (strand)SourceJBrowse
CeleraX100,956,882 - 100,957,043UniSTS
CeleraX126,729,638 - 126,729,759UniSTS
Cytogenetic MapXq35UniSTS


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 7 24 8 16 8 7 7 21 8 8 8 7
Below cutoff 2 1 1 1 1 1 1 1 10 1 12 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000052302   ⟹   ENSRNOP00000042161
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX100,110,517 - 100,131,042 (-)Ensembl
Rnor_6.0 EnsemblX107,422,357 - 107,442,878 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077452   ⟹   ENSRNOP00000069714
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX100,110,517 - 100,127,659 (-)Ensembl
RefSeq Acc Id: NM_001191914   ⟹   NP_001178843
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X104,902,805 - 104,923,328 (-)NCBI
mRatBN7.2X100,110,517 - 100,131,042 (-)NCBI
Rnor_6.0X107,422,357 - 107,442,878 (-)NCBI
Rnor_5.0X107,306,116 - 107,326,637 (-)NCBI
CeleraX100,945,585 - 100,966,108 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063280183   ⟹   XP_063136253
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X104,899,449 - 104,919,653 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001178843 (Get FASTA)   NCBI Sequence Viewer  
  XP_063136253 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87985 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000042161
  ENSRNOP00000042161.3
  ENSRNOP00000069714.2
Reference Protein Sequences
RefSeq Acc Id: NP_001178843   ⟸   NM_001191914
- Peptide Label: precursor
- UniProtKB: D4A4R5 (UniProtKB/TrEMBL),   A0A0G2JW26 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000042161   ⟸   ENSRNOT00000052302
RefSeq Acc Id: ENSRNOP00000069714   ⟸   ENSRNOT00000077452
RefSeq Acc Id: XP_063136253   ⟸   XM_063280183
- Peptide Label: isoform X1
Protein Domains
Neurotransmitter-gated ion-channel ligand-binding   Neurotransmitter-gated ion-channel transmembrane

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A4R5-F1-model_v2 AlphaFold D4A4R5 1-456 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:1564103 AgrOrtholog
BioCyc Gene G2FUF-1609 BioCyc
Ensembl Genes ENSRNOG00000002391 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000052302 ENTREZGENE
  ENSRNOT00000052302.5 UniProtKB/TrEMBL
  ENSRNOT00000077452.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.390 UniProtKB/TrEMBL
  2.70.170.10 UniProtKB/TrEMBL
InterPro GABAA_rcpt UniProtKB/TrEMBL
  Glycine_rcpt_A UniProtKB/TrEMBL
  Neur_chan_lig-bd UniProtKB/TrEMBL
  Neur_chan_lig-bd_sf UniProtKB/TrEMBL
  Neur_channel UniProtKB/TrEMBL
  Neuro-gated_channel_TM_sf UniProtKB/TrEMBL
  Neuro_actylchol_rec UniProtKB/TrEMBL
  Neurotrans-gated_channel_TM UniProtKB/TrEMBL
  Neurotransmitter_ion_chnl_CS UniProtKB/TrEMBL
KEGG Report rno:367912 UniProtKB/TrEMBL
NCBI Gene 367912 ENTREZGENE
PANTHER GLYCINE RECEPTOR SUBUNIT ALPHA-4 UniProtKB/TrEMBL
  Neur_channel UniProtKB/TrEMBL
Pfam Neur_chan_LBD UniProtKB/TrEMBL
  Neur_chan_memb UniProtKB/TrEMBL
PhenoGen Glra4 PhenoGen
PRINTS GABAARECEPTR UniProtKB/TrEMBL
  GLYRALPHA UniProtKB/TrEMBL
  NRIONCHANNEL UniProtKB/TrEMBL
PROSITE NEUROTR_ION_CHANNEL UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002391 RatGTEx
Superfamily-SCOP Neu_channel_TM UniProtKB/TrEMBL
  Neur_chan_LBD UniProtKB/TrEMBL
UniProt A0A0G2JW26 ENTREZGENE, UniProtKB/TrEMBL
  D4A4R5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-11-28 Glra4  glycine receptor alpha 4  Glra4  glycine receptor, alpha 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-02-26 Glra4  glycine receptor, alpha 4  Glra4  glycine receptor, alpha 4 subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Glra4  glycine receptor, alpha 4 subunit  RGD1564103_predicted  similar to Glycine receptor alpha-4 chain precursor (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564103_predicted  similar to Glycine receptor alpha-4 chain precursor (predicted)  LOC367912  similar to Glycine receptor alpha-4 chain precursor  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367912  similar to Glycine receptor alpha-4 chain precursor      Symbol and Name status set to provisional 70820 PROVISIONAL