Ginm1 (glycosylated integral membrane protein 1) - Rat Genome Database

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Gene: Ginm1 (glycosylated integral membrane protein 1) Rattus norvegicus
Analyze
Symbol: Ginm1
Name: glycosylated integral membrane protein 1
RGD ID: 1309759
Description: Predicted to be located in membrane. Orthologous to human GINM1 (glycosylated integral membrane protein 1); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: glycoprotein integral membrane 1; glycoprotein integral membrane protein 1; LOC361448; RGD1309759; similar to cDNA sequence BC013529
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
GRCr814,066,766 - 4,082,640 (-)NCBIGRCr8
mRatBN7.212,246,384 - 2,262,260 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl12,246,394 - 2,262,217 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx11,896,216 - 1,912,079 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.017,896,618 - 7,912,483 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.012,178,323 - 2,194,190 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.011,870,039 - 1,885,976 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl11,870,388 - 1,885,981 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013,566,597 - 3,582,594 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.412,438,830 - 2,455,290 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.112,438,995 - 2,455,285 (-)NCBI
Celera1795,143 - 810,978 (-)NCBICelera
Cytogenetic Map1p13NCBI
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
membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23376485  


Genomics

Comparative Map Data
Ginm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814,066,766 - 4,082,640 (-)NCBIGRCr8
mRatBN7.212,246,384 - 2,262,260 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl12,246,394 - 2,262,217 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx11,896,216 - 1,912,079 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.017,896,618 - 7,912,483 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.012,178,323 - 2,194,190 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.011,870,039 - 1,885,976 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl11,870,388 - 1,885,981 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013,566,597 - 3,582,594 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.412,438,830 - 2,455,290 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.112,438,995 - 2,455,285 (-)NCBI
Celera1795,143 - 810,978 (-)NCBICelera
Cytogenetic Map1p13NCBI
GINM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386149,566,375 - 149,591,748 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6149,566,294 - 149,591,748 (+)EnsemblGRCh38hg38GRCh38
GRCh376149,887,511 - 149,912,884 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366149,929,217 - 149,953,760 (+)NCBINCBI36Build 36hg18NCBI36
Build 346149,929,220 - 149,953,760NCBI
Celera6150,622,574 - 150,647,109 (+)NCBICelera
Cytogenetic Map6q25.1NCBI
HuRef6147,454,156 - 147,478,695 (+)NCBIHuRef
CHM1_16150,152,232 - 150,176,773 (+)NCBICHM1_1
T2T-CHM13v2.06150,766,116 - 150,791,484 (+)NCBIT2T-CHM13v2.0
Ginm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39107,643,711 - 7,656,681 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl107,643,711 - 7,668,588 (-)EnsemblGRCm39 Ensembl
GRCm38107,767,947 - 7,780,950 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl107,767,947 - 7,792,824 (-)EnsemblGRCm38mm10GRCm38
MGSCv37107,487,745 - 7,500,715 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36107,458,140 - 7,471,107 (-)NCBIMGSCv36mm8
Celera107,646,399 - 7,659,429 (-)NCBICelera
Cytogenetic Map10A1NCBI
cM Map102.35NCBI
Ginm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543911,660,915 - 11,688,108 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543911,661,013 - 11,688,004 (-)NCBIChiLan1.0ChiLan1.0
GINM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25169,591,691 - 169,617,218 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16167,485,278 - 167,510,792 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06147,385,283 - 147,410,740 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16152,091,069 - 152,115,862 (+)NCBIpanpan1.1PanPan1.1panPan2
GINM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1140,349,325 - 40,374,268 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl140,349,141 - 40,374,199 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha141,186,520 - 41,212,163 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0140,529,405 - 40,556,488 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl140,522,091 - 40,554,488 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1140,405,570 - 40,430,875 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0140,270,570 - 40,297,633 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0140,611,438 - 40,638,518 (+)NCBIUU_Cfam_GSD_1.0
Ginm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946135,289,506 - 135,304,222 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364892,541,449 - 2,556,721 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364892,541,507 - 2,556,942 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GINM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl116,360,370 - 16,381,864 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1116,362,777 - 16,381,897 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2118,690,574 - 18,702,882 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GINM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11322,042,159 - 22,069,569 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040198,065,368 - 198,092,817 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ginm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247858,467,443 - 8,502,699 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247858,467,142 - 8,502,790 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ginm1
19 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:59
Interacting mature miRNAs:63
Transcripts:ENSRNOT00000020810
Prediction methods:Miranda
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
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124744506Rat
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128736750Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat


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 64 35 39 11 8
Low 10 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020810   ⟹   ENSRNOP00000020811
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12,246,394 - 2,262,217 (-)Ensembl
Rnor_6.0 Ensembl11,870,388 - 1,885,981 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112697   ⟹   ENSRNOP00000080985
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl12,246,394 - 2,258,003 (-)Ensembl
RefSeq Acc Id: NM_001400838   ⟹   NP_001387767
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814,066,766 - 4,082,617 (-)NCBI
mRatBN7.212,246,387 - 2,262,238 (-)NCBI
RefSeq Acc Id: XM_006227627   ⟹   XP_006227689
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814,066,766 - 4,078,527 (-)NCBI
mRatBN7.212,246,384 - 2,258,157 (-)NCBI
Rnor_6.011,870,039 - 1,881,858 (-)NCBI
Rnor_5.013,566,597 - 3,582,594 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098446   ⟹   XP_038954374
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814,066,766 - 4,082,596 (-)NCBI
mRatBN7.212,246,384 - 2,262,012 (-)NCBI
RefSeq Acc Id: XM_063265953   ⟹   XP_063122023
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814,066,766 - 4,082,560 (-)NCBI
RefSeq Acc Id: XM_063265954   ⟹   XP_063122024
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814,066,766 - 4,078,555 (-)NCBI
RefSeq Acc Id: XM_341726   ⟹   XP_341727
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814,066,766 - 4,082,640 (-)NCBI
mRatBN7.212,246,384 - 2,262,260 (-)NCBI
Rnor_6.011,870,039 - 1,885,976 (-)NCBI
Rnor_5.013,566,597 - 3,582,594 (-)NCBI
RGSC_v3.412,438,830 - 2,455,290 (-)RGD
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_341727   ⟸   XM_341726
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZQP9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006227689   ⟸   XM_006227627
- Peptide Label: isoform X4
- UniProtKB: A0A8I5ZQP9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000020811   ⟸   ENSRNOT00000020810
RefSeq Acc Id: XP_038954374   ⟸   XM_039098446
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZQP9 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000080985   ⟸   ENSRNOT00000112697
RefSeq Acc Id: NP_001387767   ⟸   NM_001400838
- Peptide Label: precursor
- UniProtKB: D3ZJB2 (UniProtKB/TrEMBL),   A6JP18 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063122023   ⟸   XM_063265953
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063122024   ⟸   XM_063265954
- Peptide Label: isoform X5

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZJB2-F1-model_v2 AlphaFold D3ZJB2 1-329 view protein structure

Transcriptome

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

Promoters
RGD ID:13689485
Promoter ID:EPDNEW_R6
Type:initiation region
Name:Ginm1_1
Description:glycoprotein integral membrane 1
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_6.011,885,948 - 1,886,008EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309759 AgrOrtholog
BioCyc Gene G2FUF-62447 BioCyc
Ensembl Genes ENSRNOG00000015239 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020810 ENTREZGENE
  ENSRNOT00000020810.8 UniProtKB/TrEMBL
  ENSRNOT00000112697.1 UniProtKB/TrEMBL
InterPro GINM1 UniProtKB/TrEMBL
KEGG Report rno:361448 UniProtKB/TrEMBL
NCBI Gene 361448 ENTREZGENE
PANTHER GLYCOPROTEIN INTEGRAL MEMBRANE PROTEIN 1 UniProtKB/TrEMBL
  PTHR28549 UniProtKB/TrEMBL
PhenoGen Ginm1 PhenoGen
RatGTEx ENSRNOG00000015239 RatGTEx
UniProt A0A8I5ZQP9 ENTREZGENE, UniProtKB/TrEMBL
  A6JP18 ENTREZGENE, UniProtKB/TrEMBL
  D3ZJB2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-04-21 Ginm1  glycosylated integral membrane protein 1  Ginm1  glycoprotein integral membrane 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 Ginm1  glycoprotein integral membrane 1  RGD1309759  similar to cDNA sequence BC013529  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1309759  similar to cDNA sequence BC013529   RGD1309759_predicted  similar to cDNA sequence BC013529 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1309759_predicted  similar to cDNA sequence BC013529 (predicted)  LOC361448_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361448_predicted  similar to cDNA sequence BC013529 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL