Pomgnt2 (protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)) - Rat Genome Database

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Gene: Pomgnt2 (protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)) Rattus norvegicus
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Symbol: Pomgnt2
Name: protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)
RGD ID: 1304827
Description: Predicted to enable protein O-acetylglucosaminyltransferase activity. Predicted to be involved in neuron migration and protein O-linked mannosylation. Predicted to be located in endoplasmic reticulum membrane. Predicted to be active in endoplasmic reticulum. Human ortholog(s) of this gene implicated in congenital muscular dystrophy-dystroglycanopathy type A8 and muscular dystrophy-dystroglycanopathy type C8. Orthologous to human POMGNT2 (protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Ago61; extracellular O-linked N-acetylglucosamine transferase-like; glycosyltransferase; glycosyltransferase-like domain containing 2; glycosyltransferase-like domain-containing protein 2; Gtdc2; hypothetical LOC316091; LOC316091; protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2; RGD1304827; uncharacterized glycosyltransferase AGO61
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
GRCr88130,522,607 - 130,538,273 (-)NCBIGRCr8
mRatBN7.28121,645,106 - 121,660,761 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,644,970 - 121,660,757 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8127,240,355 - 127,242,097 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,439,426 - 125,441,168 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,266,289 - 123,268,031 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,615,482 - 130,631,144 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,615,711 - 130,617,833 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,791,153 - 129,792,895 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48126,952,294 - 126,954,036 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18126,972,030 - 126,973,773 (+)NCBI
Celera8120,769,878 - 120,771,620 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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. Ectopic clustering of Cajal-Retzius and subplate cells is an initial pathological feature in Pomgnt2-knockout mice, a model of dystroglycanopathy. Nakagawa N, etal., Sci Rep. 2015 Jun 10;5:11163. doi: 10.1038/srep11163.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23929950   PMID:24256719   PMID:27066570  


Genomics

Comparative Map Data
Pomgnt2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88130,522,607 - 130,538,273 (-)NCBIGRCr8
mRatBN7.28121,645,106 - 121,660,761 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,644,970 - 121,660,757 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8127,240,355 - 127,242,097 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,439,426 - 125,441,168 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08123,266,289 - 123,268,031 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,615,482 - 130,631,144 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,615,711 - 130,617,833 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,791,153 - 129,792,895 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48126,952,294 - 126,954,036 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18126,972,030 - 126,973,773 (+)NCBI
Celera8120,769,878 - 120,771,620 (-)NCBICelera
Cytogenetic Map8q32NCBI
POMGNT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38343,079,234 - 43,106,079 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl343,079,229 - 43,106,085 (-)EnsemblGRCh38hg38GRCh38
GRCh37343,120,726 - 43,147,571 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36343,095,730 - 43,122,569 (-)NCBINCBI36Build 36hg18NCBI36
Celera343,058,234 - 43,085,072 (-)NCBICelera
Cytogenetic Map3p22.1NCBI
HuRef343,163,548 - 43,190,404 (-)NCBIHuRef
CHM1_1343,070,709 - 43,097,578 (-)NCBICHM1_1
T2T-CHM13v2.0343,094,564 - 43,121,424 (-)NCBIT2T-CHM13v2.0
Pomgnt2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399121,810,675 - 121,825,116 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9121,810,672 - 121,826,176 (-)EnsemblGRCm39 Ensembl
GRCm389121,981,606 - 121,996,053 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9121,981,606 - 121,997,110 (-)EnsemblGRCm38mm10GRCm38
MGSCv379121,890,724 - 121,905,144 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369121,830,307 - 121,844,673 (-)NCBIMGSCv36mm8
Celera9122,456,506 - 122,458,726 (-)NCBICelera
Cytogenetic Map9F4NCBI
cM Map972.78NCBI
Pomgnt2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542027,884,303 - 27,899,293 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542027,884,262 - 27,899,293 (+)NCBIChiLan1.0ChiLan1.0
POMGNT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2243,030,544 - 43,054,391 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1343,035,306 - 43,059,090 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0342,973,492 - 42,997,288 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1344,035,357 - 44,059,142 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl344,035,815 - 44,037,557 (-)Ensemblpanpan1.1panPan2
POMGNT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12312,094,306 - 12,235,491 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2312,094,778 - 12,143,214 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2312,070,388 - 12,072,130 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02312,385,758 - 12,514,160 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2312,385,759 - 12,490,593 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12312,188,508 - 12,190,250 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02312,330,417 - 12,332,159 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02312,334,318 - 12,336,060 (-)NCBIUU_Cfam_GSD_1.0
Pomgnt2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118199,765,155 - 199,789,524 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366952,139,661 - 2,141,403 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366952,117,506 - 2,141,859 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
POMGNT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1326,523,983 - 26,526,133 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11326,503,610 - 26,526,185 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21329,115,735 - 29,138,369 (-)NCBISscrofa10.2Sscrofa10.2susScr3
POMGNT2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1224,521,925 - 4,548,431 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041162,650,289 - 162,676,794 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pomgnt2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473076,818,751 - 76,832,291 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473076,811,200 - 76,832,299 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pomgnt2
79 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:156
Count of miRNA genes:119
Interacting mature miRNAs:131
Transcripts:ENSRNOT00000026363
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
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat

Markers in Region
RH129890  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28121,645,136 - 121,645,316 (+)MAPPERmRatBN7.2
Rnor_6.08130,615,513 - 130,615,692NCBIRnor6.0
Rnor_5.08129,790,756 - 129,790,935UniSTSRnor5.0
RGSC_v3.48126,954,254 - 126,954,433UniSTSRGSC3.4
Celera8120,769,481 - 120,769,660UniSTS
RH 3.4 Map81259.09UniSTS
Cytogenetic Map8q32UniSTS


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 64 9
Low 3 43 57 41 19 41 8 8 10 35 32 11 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000026363   ⟹   ENSRNOP00000063923
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8121,644,970 - 121,660,757 (-)Ensembl
Rnor_6.0 Ensembl8130,615,711 - 130,617,833 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100933   ⟹   ENSRNOP00000079681
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8121,645,085 - 121,660,757 (-)Ensembl
RefSeq Acc Id: NM_001009437   ⟹   NP_001009437
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,523,034 - 130,524,776 (-)NCBI
mRatBN7.28121,645,534 - 121,647,276 (-)NCBI
Rnor_6.08130,615,910 - 130,617,652 (-)NCBI
Rnor_5.08129,791,153 - 129,792,895 (-)NCBI
RGSC_v3.48126,952,294 - 126,954,036 (+)RGD
Celera8120,769,878 - 120,771,620 (-)RGD
Sequence:
RefSeq Acc Id: XM_008766681   ⟹   XP_008764903
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,522,607 - 130,538,273 (-)NCBI
mRatBN7.28121,645,106 - 121,660,760 (-)NCBI
Rnor_6.08130,615,482 - 130,631,144 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766683   ⟹   XP_008764905
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,522,607 - 130,538,250 (-)NCBI
mRatBN7.28121,645,106 - 121,660,761 (-)NCBI
Rnor_6.08130,615,482 - 130,631,144 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081662   ⟹   XP_038937590
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,522,607 - 130,538,247 (-)NCBI
mRatBN7.28121,645,106 - 121,660,761 (-)NCBI
RefSeq Acc Id: NP_001009437   ⟸   NM_001009437
- UniProtKB: Q5NDF0 (UniProtKB/Swiss-Prot),   A6I471 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764903   ⟸   XM_008766681
- Peptide Label: isoform X1
- UniProtKB: Q5NDF0 (UniProtKB/Swiss-Prot),   A6I471 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764905   ⟸   XM_008766683
- Peptide Label: isoform X1
- UniProtKB: Q5NDF0 (UniProtKB/Swiss-Prot),   A6I471 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063923   ⟸   ENSRNOT00000026363
RefSeq Acc Id: XP_038937590   ⟸   XM_039081662
- Peptide Label: isoform X1
- UniProtKB: Q5NDF0 (UniProtKB/Swiss-Prot),   A6I471 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000079681   ⟸   ENSRNOT00000100933
Protein Domains
Fibronectin type-III

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5NDF0-F1-model_v2 AlphaFold Q5NDF0 1-580 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:1304827 AgrOrtholog
BioCyc Gene G2FUF-28670 BioCyc
BioCyc Pathway PWY-7979 [protein O-mannosylation III (mammals, core M3)] BioCyc
BioCyc Pathway Image PWY-7979 BioCyc
Ensembl Genes ENSRNOG00000019492 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055002168 UniProtKB/Swiss-Prot
  ENSRNOG00060017219 UniProtKB/Swiss-Prot
  ENSRNOG00065000505 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026363.7 UniProtKB/Swiss-Prot
  ENSRNOT00000100933.1 UniProtKB/Swiss-Prot
  ENSRNOT00055003441 UniProtKB/Swiss-Prot
  ENSRNOT00055003443 UniProtKB/Swiss-Prot
  ENSRNOT00060029394 UniProtKB/Swiss-Prot
  ENSRNOT00060029406 UniProtKB/Swiss-Prot
  ENSRNOT00065000728 UniProtKB/Swiss-Prot
  ENSRNOT00065000731 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glycosyltransferase_61 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:316091 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 316091 ENTREZGENE
PANTHER GLYCOSYLTRANSFERASE UniProtKB/TrEMBL
  PROTEIN O-LINKED-MANNOSE BETA-1,4-N-ACETYLGLUCOSAMINYLTRANSFERASE 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR20961 UniProtKB/Swiss-Prot
Pfam DUF563 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pomgnt2 PhenoGen
PROSITE FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000019492 RatGTEx
  ENSRNOG00055002168 RatGTEx
  ENSRNOG00060017219 RatGTEx
  ENSRNOG00065000505 RatGTEx
Superfamily-SCOP Fibronectin type III UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6I471 ENTREZGENE, UniProtKB/TrEMBL
  PMGT2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-09-16 Pomgnt2  protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)  Gtdc2  glycosyltransferase-like domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 Gtdc2  glycosyltransferase-like domain containing 2  RGD1304827  hypothetical LOC316091  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1304827  hypothetical LOC316091  RGD1304827_predicted  hypothetical LOC316091 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1304827_predicted  hypothetical LOC316091 (predicted)  LOC316091_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC316091_predicted  hypothetical LOC316091 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL