Gabarapl2 (GABA type A receptor associated protein like 2) - Rat Genome Database

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Gene: Gabarapl2 (GABA type A receptor associated protein like 2) Rattus norvegicus
Analyze
Symbol: Gabarapl2
Name: GABA type A receptor associated protein like 2
RGD ID: 620510
Description: Predicted to enable phosphatidylethanolamine binding activity and ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including cellular response to nitrogen starvation; macroautophagy; and negative regulation of proteasomal protein catabolic process. Predicted to be located in Golgi membrane and autophagosome. Predicted to be active in autophagosome membrane. Orthologous to human GABARAPL2 (GABA type A receptor associated protein like 2); PARTICIPATES IN autophagy pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: GABA(A) receptor-associated protein like 2; GABA(A) receptor-associated protein-like 2; gamma-aminobutyric acid receptor-associated protein-like 2; ganglioside expression factor 2; GATE-16; GEF-2; Gef2; golgi-associated ATPase enhancer of 16 kDa; MGC108686
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gabarapl3  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81956,819,826 - 56,830,662 (+)NCBIGRCr8
mRatBN7.21939,910,572 - 39,921,408 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl889,246,195 - 89,247,139 (+)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl1939,910,534 - 39,924,628 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1946,774,406 - 46,785,021 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01947,427,736 - 47,438,351 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01949,673,177 - 49,684,013 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01944,164,935 - 44,175,771 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1944,164,935 - 44,175,770 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01954,972,028 - 54,982,864 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41941,880,238 - 41,891,074 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11941,885,118 - 41,895,954 (+)NCBI
Celera1939,271,261 - 39,281,863 (+)NCBICelera
Cytogenetic Map19q12NCBI
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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
autophagy pathway  (IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Network organization of the human autophagy system. Behrends C, etal., Nature. 2010 Jul 1;466(7302):68-76. Epub 2010 Jun 20.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. GATE-16, a membrane transport modulator, interacts with NSF and the Golgi v-SNARE GOS-28. Sagiv Y, etal., EMBO J 2000 Apr 3;19(7):1494-504.
10. 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.
11. LC3 conjugation system in mammalian autophagy. Tanida I, etal., Int J Biochem Cell Biol. 2004 Dec;36(12):2503-18.
12. Cloning, expression patterns, and chromosome localization of three human and two mouse homologues of GABA(A) receptor-associated protein. Xin Y, etal., Genomics 2001 Jun 15;74(3):408-13.
Additional References at PubMed
PMID:15169837   PMID:15489334   PMID:19056683   PMID:21669198   PMID:25127057  


Genomics

Comparative Map Data
Gabarapl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81956,819,826 - 56,830,662 (+)NCBIGRCr8
mRatBN7.21939,910,572 - 39,921,408 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl889,246,195 - 89,247,139 (+)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl1939,910,534 - 39,924,628 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1946,774,406 - 46,785,021 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01947,427,736 - 47,438,351 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01949,673,177 - 49,684,013 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01944,164,935 - 44,175,771 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1944,164,935 - 44,175,770 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01954,972,028 - 54,982,864 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41941,880,238 - 41,891,074 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11941,885,118 - 41,895,954 (+)NCBI
Celera1939,271,261 - 39,281,863 (+)NCBICelera
Cytogenetic Map19q12NCBI
GABARAPL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381675,566,379 - 75,577,881 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1675,566,375 - 75,577,881 (+)EnsemblGRCh38hg38GRCh38
GRCh371675,600,277 - 75,611,779 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361674,157,750 - 74,169,280 (+)NCBINCBI36Build 36hg18NCBI36
Build 341674,157,749 - 74,169,279NCBI
Celera1659,894,551 - 59,906,124 (+)NCBICelera
Cytogenetic Map16q23.1NCBI
HuRef1661,353,919 - 61,365,449 (+)NCBIHuRef
CHM1_11677,012,617 - 77,024,147 (+)NCBICHM1_1
T2T-CHM13v2.01681,614,626 - 81,626,171 (+)NCBIT2T-CHM13v2.0
Gabarapl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398112,667,335 - 112,679,547 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8112,667,335 - 112,680,244 (+)EnsemblGRCm39 Ensembl
GRCm388111,940,703 - 111,952,915 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8111,940,703 - 111,953,612 (+)EnsemblGRCm38mm10GRCm38
MGSCv378114,464,618 - 114,476,480 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368114,827,395 - 114,842,055 (+)NCBIMGSCv36mm8
Celera8116,169,489 - 116,181,347 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map858.19NCBI
Gabarapl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554841,991,020 - 2,004,925 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554841,991,020 - 2,004,925 (-)NCBIChiLan1.0ChiLan1.0
GABARAPL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21885,284,079 - 85,295,639 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11691,206,742 - 91,218,301 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01656,135,482 - 56,147,046 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11675,483,459 - 75,495,019 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1675,483,459 - 75,495,019 (+)Ensemblpanpan1.1panPan2
GABARAPL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1575,230,214 - 75,240,724 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl575,230,243 - 75,240,730 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha575,207,568 - 75,218,596 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0575,544,321 - 75,555,339 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl575,544,322 - 75,554,830 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1575,480,287 - 75,491,305 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0575,315,531 - 75,326,538 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0575,806,854 - 75,817,870 (-)NCBIUU_Cfam_GSD_1.0
Gabarapl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934935,339,865 - 35,350,864 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647524,238,209 - 24,249,557 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647524,238,262 - 24,249,249 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GABARAPL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl612,107,422 - 12,132,991 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1612,122,219 - 12,132,986 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2611,963,183 - 11,973,930 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GABARAPL2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1561,053,283 - 61,078,675 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl561,053,262 - 61,066,083 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604714,980,713 - 15,005,010 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gabarapl2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474611,393,439 - 11,405,126 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474611,393,439 - 11,405,152 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gabarapl2
57 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:705
Count of miRNA genes:308
Interacting mature miRNAs:403
Transcripts:ENSRNOT00000048998
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat


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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000048998   ⟹   ENSRNOP00000040067
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1939,910,545 - 39,924,628 (+)Ensembl
Rnor_6.0 Ensembl1944,164,935 - 44,175,770 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106569   ⟹   ENSRNOP00000080839
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1939,910,546 - 39,920,740 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115254   ⟹   ENSRNOP00000097574
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1939,910,534 - 39,913,487 (+)Ensembl
RefSeq Acc Id: NM_022706   ⟹   NP_073197
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81956,819,826 - 56,830,662 (+)NCBI
mRatBN7.21939,910,572 - 39,921,408 (+)NCBI
Rnor_6.01944,164,935 - 44,175,771 (+)NCBI
Rnor_5.01954,972,028 - 54,982,864 (+)NCBI
RGSC_v3.41941,880,238 - 41,891,074 (+)RGD
Celera1939,271,261 - 39,281,863 (+)RGD
Sequence:
RefSeq Acc Id: NP_073197   ⟸   NM_022706
- UniProtKB: P60522 (UniProtKB/Swiss-Prot),   A6IZB7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000040067   ⟸   ENSRNOT00000048998
RefSeq Acc Id: ENSRNOP00000080839   ⟸   ENSRNOT00000106569
RefSeq Acc Id: ENSRNOP00000097574   ⟸   ENSRNOT00000115254

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P60522-F1-model_v2 AlphaFold P60522 1-117 view protein structure

Transcriptome

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

Promoters
RGD ID:13701156
Promoter ID:EPDNEW_R11680
Type:initiation region
Name:Gabarapl2_1
Description:GABA type A receptor associated protein like 2
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_6.01944,164,911 - 44,164,971EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620510 AgrOrtholog
BioCyc Gene G2FUF-5636 BioCyc
Ensembl Genes ENSRNOG00000019425 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00000051416 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00055018836 UniProtKB/Swiss-Prot
  ENSRNOG00060012752 UniProtKB/Swiss-Prot
  ENSRNOG00065011750 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000047078.5 UniProtKB/Swiss-Prot
  ENSRNOT00000048998 ENTREZGENE
  ENSRNOT00000048998.4 UniProtKB/Swiss-Prot
  ENSRNOT00000106569.1 UniProtKB/TrEMBL
  ENSRNOT00000115254.1 UniProtKB/TrEMBL
  ENSRNOT00055032105 UniProtKB/Swiss-Prot
  ENSRNOT00060021666 UniProtKB/Swiss-Prot
  ENSRNOT00065019096 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6921109 IMAGE-MGC_LOAD
  IMAGE:7323806 IMAGE-MGC_LOAD
InterPro Atg8-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:100359937 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  rno:64670 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:108686 IMAGE-MGC_LOAD
  MGC:72812 IMAGE-MGC_LOAD
NCBI Gene 64670 ENTREZGENE
PANTHER GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10969 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Atg8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gabarapl2 PhenoGen
RatGTEx ENSRNOG00000019425 RatGTEx
  ENSRNOG00000051416 RatGTEx
  ENSRNOG00055018836 RatGTEx
  ENSRNOG00060012752 RatGTEx
  ENSRNOG00065011750 RatGTEx
Superfamily-SCOP SSF54236 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6ASX5_RAT UniProtKB/TrEMBL
  A0A8I6G540_RAT UniProtKB/TrEMBL
  A6IZB7 ENTREZGENE, UniProtKB/TrEMBL
  GBRL2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O08765 UniProtKB/Swiss-Prot
  Q9DCP8 UniProtKB/Swiss-Prot
  Q9UQF7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-29 Gabarapl2  GABA type A receptor associated protein like 2  Gabarapl2  GABA(A) receptor-associated protein like 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Gabarapl2  GABA(A) receptor-associated protein like 2      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Gabarapl2  GABA(A) receptor-associated protein like 2      Symbol and Name status set to provisional 70820 PROVISIONAL