Garin4 (golgi associated RAB2 interactor family member 4) - Rat Genome Database

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Gene: Garin4 (golgi associated RAB2 interactor family member 4) Rattus norvegicus
Analyze
Symbol: Garin4
Name: golgi associated RAB2 interactor family member 4
RGD ID: 1561646
Description: Predicted to be involved in Golgi organization. Predicted to act upstream of or within cell morphogenesis; penetration of zona pellucida; and spermatid development. Predicted to be located in Golgi apparatus. Predicted to be active in sperm head. Orthologous to human GARIN4 (golgi associated RAB2 interactor family member 4); INTERACTS WITH bisphenol A; cefaloridine; fenvalerate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Fam71a; family with sequence similarity 71, member A; Golgi-associated RAB2 interactor protein 4; hypothetical protein LOC498311; LOC498311; RGD1561646; similar to hypothetical protein; uncharacterized protein LOC498311
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813105,274,107 - 105,276,287 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl13105,274,106 - 105,276,286 (-)EnsemblGRCr8
mRatBN7.213102,742,988 - 102,745,168 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13102,742,988 - 102,745,168 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx13105,263,058 - 105,265,238 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013106,647,014 - 106,649,194 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013103,862,000 - 103,864,180 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.013109,768,019 - 109,770,199 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13109,768,019 - 109,770,199 (-)Ensemblrn6Rnor6.0
Rnor_5.013114,361,819 - 114,363,999 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.413107,182,184 - 107,184,364 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera13102,208,070 - 102,210,250 (-)NCBICelera
Cytogenetic Map13q27NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
Golgi apparatus  (IEA,ISO)
sperm head  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21630459  


Genomics

Comparative Map Data
Garin4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813105,274,107 - 105,276,287 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl13105,274,106 - 105,276,286 (-)EnsemblGRCr8
mRatBN7.213102,742,988 - 102,745,168 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13102,742,988 - 102,745,168 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx13105,263,058 - 105,265,238 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013106,647,014 - 106,649,194 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013103,862,000 - 103,864,180 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.013109,768,019 - 109,770,199 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13109,768,019 - 109,770,199 (-)Ensemblrn6Rnor6.0
Rnor_5.013114,361,819 - 114,363,999 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.413107,182,184 - 107,184,364 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera13102,208,070 - 102,210,250 (-)NCBICelera
Cytogenetic Map13q27NCBI
GARIN4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381212,624,474 - 212,626,775 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1212,624,474 - 212,626,775 (+)Ensemblhg38GRCh38
GRCh371212,797,816 - 212,800,117 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361210,864,439 - 210,866,740 (+)NCBIBuild 36Build 36hg18NCBI36
Celera1186,023,850 - 186,026,181 (+)NCBICelera
Cytogenetic Map1q32.3NCBI
HuRef1183,474,613 - 183,476,944 (+)NCBIHuRef
CHM1_11214,070,656 - 214,072,987 (+)NCBICHM1_1
T2T-CHM13v2.01211,869,409 - 211,871,710 (+)NCBIT2T-CHM13v2.0
Garin4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391190,894,781 - 190,897,014 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1190,894,781 - 190,897,014 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381191,162,584 - 191,164,817 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1191,162,584 - 191,164,817 (-)Ensemblmm10GRCm38
MGSCv371192,986,463 - 192,988,696 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361192,863,191 - 192,865,432 (-)NCBIMGSCv36mm8
Celera1198,088,115 - 198,090,348 (-)NCBICelera
Cytogenetic Map1H6NCBI
cM Map196.28NCBI
Garin4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554064,870,655 - 4,872,941 (-)NCBIChiLan1.0ChiLan1.0
GARIN4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2136,774,432 - 36,779,337 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1136,734,974 - 36,743,788 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01188,192,581 - 188,194,867 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11193,052,852 - 193,055,165 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1193,053,270 - 193,055,054 (+)EnsemblpanPan2panpan1.1
LOC102155437
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1710,795,915 - 10,799,134 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha710,370,752 - 10,374,149 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0710,501,332 - 10,504,734 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1710,424,101 - 10,427,502 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0710,525,354 - 10,528,760 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0710,649,170 - 10,652,576 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Garin4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934463,653,527 - 63,655,712 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936557893,923 - 895,602 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936557893,896 - 895,602 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GARIN4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9130,766,239 - 130,768,032 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.19130,766,150 - 130,768,044 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29143,647,159 - 143,649,172 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GARIN4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12516,904,350 - 16,907,934 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2516,904,461 - 16,906,245 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605517,401,118 - 17,406,930 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Garin4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11069,241,186 - 69,243,356 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Garin4
15 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:59
Count of miRNA genes:55
Interacting mature miRNAs:58
Transcripts:ENSRNOT00000043672
Prediction methods: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
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)1365613454109350286Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1321120177109350286Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1368983334109350286Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1367635937109350286Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1367635937109350286Rat
1576318Schws5Schwannoma susceptibility QTL 50.0351nervous system integrity trait (VT:0010566)post-insult time to trigeminal nerve neurilemmoma formation (CMO:0002019)1364497900109350286Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1364375743109350286Rat
8655951Rf63Renal function QTL 6312.2blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)1371610804109350286Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1383286150109350286Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1367635937109350286Rat


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
1 2 12 45 7 13 3 14 3 2 60 30 4 47 24 23 10 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000043672   ⟹   ENSRNOP00000051288
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl13105,274,106 - 105,276,286 (-)Ensembl
mRatBN7.2 Ensembl13102,742,988 - 102,745,168 (-)Ensembl
Rnor_6.0 Ensembl13109,768,019 - 109,770,199 (-)Ensembl
RefSeq Acc Id: NM_001109084   ⟹   NP_001102554
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813105,274,107 - 105,276,287 (-)NCBI
mRatBN7.213102,742,988 - 102,745,168 (-)NCBI
Rnor_6.013109,768,019 - 109,770,199 (-)NCBI
Rnor_5.013114,361,819 - 114,363,999 (-)NCBI
RGSC_v3.413107,182,184 - 107,184,364 (-)RGD
Celera13102,208,070 - 102,210,250 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102554 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94996 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000051288
  ENSRNOP00000051288.3
RefSeq Acc Id: NP_001102554   ⟸   NM_001109084
- UniProtKB: D3ZUI0 (UniProtKB/TrEMBL),   A6JGZ0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000051288   ⟸   ENSRNOT00000043672
Protein Domains
Golgi associated RAB2 interactor protein-like Rab2B-

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZUI0-F1-model_v2 AlphaFold D3ZUI0 1-572 view protein structure

Transcriptome

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

Promoters
RGD ID:13699113
Promoter ID:EPDNEW_R9638
Type:single initiation site
Name:Fam71a_1
Description:family with sequence similarity 71, member A
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_6.013109,770,198 - 109,770,258EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561646 AgrOrtholog
BioCyc Gene G2FUF-16861 BioCyc
Ensembl Genes ENSRNOG00000029371 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043672 ENTREZGENE
  ENSRNOT00000043672.6 UniProtKB/TrEMBL
InterPro DUF3699 UniProtKB/TrEMBL
KEGG Report rno:498311 UniProtKB/TrEMBL
NCBI Gene 498311 ENTREZGENE
PANTHER PROTEIN FAM71A UniProtKB/TrEMBL
  UNCHARACTERIZED UniProtKB/TrEMBL
Pfam DUF3699 UniProtKB/TrEMBL
PhenoGen Garin4 PhenoGen
RatGTEx ENSRNOG00000029371 RatGTEx
UniProt A6JGZ0 ENTREZGENE, UniProtKB/TrEMBL
  D3ZUI0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-12-02 Garin4  golgi associated RAB2 interactor family member 4  Fam71a  family with sequence similarity 71, member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Fam71a  family with sequence similarity 71, member A  RGD1561646_predicted  similar to hypothetical protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561646_predicted  similar to hypothetical protein (predicted)  LOC498311  similar to hypothetical protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498311  similar to hypothetical protein      Symbol and Name status set to provisional 70820 PROVISIONAL