Pigm (phosphatidylinositol glycan anchor biosynthesis, class M) - Rat Genome Database

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Gene: Pigm (phosphatidylinositol glycan anchor biosynthesis, class M) Rattus norvegicus
Analyze
Symbol: Pigm
Name: phosphatidylinositol glycan anchor biosynthesis, class M
RGD ID: 71041
Description: Enables mannosyltransferase activity. Predicted to be located in endoplasmic reticulum membrane. Predicted to be part of glycosylphosphatidylinositol-mannosyltransferase I complex. Orthologous to human PIGM (phosphatidylinositol glycan anchor biosynthesis class M); PARTICIPATES IN glycosylphosphatidylinositol anchor biosynthetic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: GPI mannosyltransferase 1; GPI mannosyltransferase I; GPI-MT-I; LOC103694910; phosphatidylinositol glycan, class M; phosphatidylinositol-glycan biosynthesis class M protein; PIG-M mRNA for mannosyltransferase
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
mRatBN7.21384,838,329 - 84,842,026 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1384,838,175 - 84,843,381 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1387,341,646 - 87,345,343 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01388,741,920 - 88,745,617 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01385,926,307 - 85,930,006 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01390,759,260 - 90,762,957 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1390,759,260 - 90,762,957 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01395,281,187 - 95,284,884 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41388,377,212 - 88,380,909 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11388,566,095 - 88,569,793 (+)NCBI
Celera1384,448,384 - 84,452,081 (+)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. PIG-M transfers the first mannose to glycosylphosphatidylinositol on the lumenal side of the ER. Maeda Y, etal., EMBO J 2001 Jan 15;20(1-2):250-61.
3. Gene Data Set MGD Curation, June 12, 2002
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Pigm
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21384,838,329 - 84,842,026 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1384,838,175 - 84,843,381 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1387,341,646 - 87,345,343 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01388,741,920 - 88,745,617 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01385,926,307 - 85,930,006 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01390,759,260 - 90,762,957 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1390,759,260 - 90,762,957 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01395,281,187 - 95,284,884 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41388,377,212 - 88,380,909 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11388,566,095 - 88,569,793 (+)NCBI
Celera1384,448,384 - 84,452,081 (+)NCBICelera
Cytogenetic Map13q24NCBI
PIGM
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381160,024,953 - 160,031,990 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1160,024,953 - 160,031,990 (-)EnsemblGRCh38hg38GRCh38
GRCh371159,994,743 - 160,001,780 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361158,264,086 - 158,268,407 (-)NCBINCBI36Build 36hg18NCBI36
Build 341156,812,769 - 156,814,821NCBI
Celera1133,065,903 - 133,070,225 (-)NCBICelera
Cytogenetic Map1q23.2NCBI
HuRef1131,354,186 - 131,358,509 (-)NCBIHuRef
CHM1_11161,392,783 - 161,397,106 (-)NCBICHM1_1
T2T-CHM13v2.01159,162,027 - 159,169,067 (-)NCBIT2T-CHM13v2.0
Pigm
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391172,204,098 - 172,211,666 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1172,204,113 - 172,211,666 (+)EnsemblGRCm39 Ensembl
GRCm381172,376,531 - 172,384,099 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1172,376,546 - 172,384,099 (+)EnsemblGRCm38mm10GRCm38
MGSCv371174,306,662 - 174,314,230 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361174,213,231 - 174,217,208 (+)NCBIMGSCv36mm8
Celera1175,229,959 - 175,237,523 (+)NCBICelera
Cytogenetic Map1H3NCBI
cM Map179.73NCBI
Pigm
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546811,818,604 - 11,819,872 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546811,817,647 - 11,820,456 (-)NCBIChiLan1.0ChiLan1.0
PIGM
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1189,560,492 - 89,567,215 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01135,378,843 - 135,387,789 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11139,303,208 - 139,307,797 (-)NCBIpanpan1.1PanPan1.1panPan2
PIGM
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13822,150,006 - 22,151,589 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3822,225,395 - 22,230,629 (+)NCBIDog10K_Boxer_Tasha
Pigm
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244050586,156,494 - 6,158,603 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936740596,072 - 597,343 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936740595,932 - 597,964 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PIGM
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1490,461,507 - 90,464,500 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2498,432,754 - 98,434,851 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PIGM
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1203,913,163 - 3,914,853 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl203,913,336 - 3,914,607 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660382,969,696 - 2,972,124 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pigm
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247941,220,121 - 1,221,392 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247941,220,004 - 1,222,259 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pigm
14 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:206
Count of miRNA genes:151
Interacting mature miRNAs:172
Transcripts:ENSRNOT00000010551
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
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)137486211785581182Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat
1302791Stl29Serum triglyceride level QTL 293.30.0011blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)138473078886800898Rat

Markers in Region
AI644422  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21384,837,936 - 84,838,076 (+)MAPPERmRatBN7.2
Rnor_6.01390,758,868 - 90,759,007NCBIRnor6.0
Rnor_5.01395,280,795 - 95,280,934UniSTSRnor5.0
RGSC_v3.41388,376,820 - 88,376,959UniSTSRGSC3.4
Celera1384,447,992 - 84,448,131UniSTS
Cytogenetic Map13q24UniSTS
RH141295  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21384,840,451 - 84,840,642 (+)MAPPERmRatBN7.2
Rnor_6.01390,761,383 - 90,761,573NCBIRnor6.0
Rnor_5.01395,283,310 - 95,283,500UniSTSRnor5.0
RGSC_v3.41388,379,335 - 88,379,525UniSTSRGSC3.4
Celera1384,450,507 - 84,450,697UniSTS
RH 3.4 Map13556.9UniSTS
Cytogenetic Map13q24UniSTS


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 1 8 25 18 17 18 25 18 29 9
Low 2 35 32 23 2 23 8 11 49 17 12 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010551   ⟹   ENSRNOP00000010551
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1384,838,175 - 84,843,381 (+)Ensembl
Rnor_6.0 Ensembl1390,759,260 - 90,762,957 (+)Ensembl
RefSeq Acc Id: NM_024144   ⟹   NP_077058
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21384,838,329 - 84,842,026 (+)NCBI
Rnor_6.01390,759,260 - 90,762,957 (+)NCBI
Rnor_5.01395,281,187 - 95,284,884 (+)NCBI
RGSC_v3.41388,377,212 - 88,380,909 (+)RGD
Celera1384,448,384 - 84,452,081 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_077058 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAB18566 (Get FASTA)   NCBI Sequence Viewer  
  EDL94711 (Get FASTA)   NCBI Sequence Viewer  
  Q9EQY6 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_077058   ⟸   NM_024144
- UniProtKB: Q9EQY6 (UniProtKB/Swiss-Prot),   A6JG55 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010551   ⟸   ENSRNOT00000010551

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9EQY6-F1-model_v2 AlphaFold Q9EQY6 1-423 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:71041 AgrOrtholog
BioCyc Gene G2FUF-17322 BioCyc
Ensembl Genes ENSRNOG00000007735 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000010551 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000010551 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro PIG-M UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:79112 UniProtKB/Swiss-Prot
NCBI Gene 79112 ENTREZGENE
PANTHER GPI MANNOSYLTRANSFERASE 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PIG-M MANNOSYLTRANSFERASE UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
Pfam Mannosyl_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pigm PhenoGen
UniProt A6JG55 ENTREZGENE, UniProtKB/TrEMBL
  PIGM_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Pigm  phosphatidylinositol glycan anchor biosynthesis, class M  LOC103694910  GPI mannosyltransferase 1  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103694910  GPI mannosyltransferase 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-02-18 Pigm  phosphatidylinositol glycan anchor biosynthesis, class M  Pigm  phosphatidylinositol glycan, class M  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-07-09 Pigm  phosphatidylinositol glycan, class M      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference