Mgat4d (MGAT4 family, member D) - Rat Genome Database

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Gene: Mgat4d (MGAT4 family, member D) Rattus norvegicus
Analyze
Symbol: Mgat4d
Name: MGAT4 family, member D
RGD ID: 1310572
Description: Predicted to enable acetylglucosaminyltransferase activity. Predicted to be involved in negative regulation of protein glycosylation and protein N-linked glycosylation. Predicted to be located in membrane. Predicted to be active in Golgi stack; endoplasmic reticulum; and endoplasmic reticulum-Golgi intermediate compartment. Orthologous to human MGAT4D (MGAT4 family member D); PARTICIPATES IN N-linked glycan biosynthetic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: PROVISIONAL
Previously known as: alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase-like protein MGAT4D; GL54D; glycosyltransferase 54 domain-containing protein; LOC304646; MGC114453; RGD1310572; similar to calmegin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81941,644,744 - 41,681,583 (-)NCBIGRCr8
mRatBN7.21924,740,068 - 24,777,012 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1924,740,078 - 24,777,012 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1931,559,553 - 31,596,164 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01932,213,949 - 32,250,568 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01934,431,626 - 34,468,527 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01924,494,366 - 24,534,039 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1924,496,569 - 24,532,772 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01935,474,577 - 35,510,796 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41926,447,874 - 26,495,782 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11926,452,699 - 26,500,608 (-)NCBI
Celera1924,280,376 - 24,316,664 (-)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:20805325  


Genomics

Comparative Map Data
Mgat4d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81941,644,744 - 41,681,583 (-)NCBIGRCr8
mRatBN7.21924,740,068 - 24,777,012 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1924,740,078 - 24,777,012 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1931,559,553 - 31,596,164 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01932,213,949 - 32,250,568 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01934,431,626 - 34,468,527 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01924,494,366 - 24,534,039 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1924,496,569 - 24,532,772 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01935,474,577 - 35,510,796 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41926,447,874 - 26,495,782 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11926,452,699 - 26,500,608 (-)NCBI
Celera1924,280,376 - 24,316,664 (-)NCBICelera
Cytogenetic Map19q11NCBI
MGAT4D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384140,442,262 - 140,498,293 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4140,442,262 - 140,498,377 (-)EnsemblGRCh38hg38GRCh38
GRCh374141,363,416 - 141,419,447 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364141,583,979 - 141,638,951 (-)NCBINCBI36Build 36hg18NCBI36
Celera4138,694,536 - 138,749,502 (-)NCBICelera
Cytogenetic Map4q31.1NCBI
HuRef4137,094,997 - 137,149,992 (-)NCBIHuRef
CHM1_14141,341,868 - 141,396,867 (-)NCBICHM1_1
T2T-CHM13v2.04143,762,026 - 143,818,003 (-)NCBIT2T-CHM13v2.0
Mgat4d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39884,075,101 - 84,106,031 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl884,075,100 - 84,108,949 (+)EnsemblGRCm39 Ensembl
GRCm38883,348,472 - 83,379,402 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl883,348,471 - 83,382,320 (+)EnsemblGRCm38mm10GRCm38
MGSCv37885,872,371 - 85,903,301 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36886,238,577 - 86,269,507 (+)NCBIMGSCv36mm8
Celera887,636,311 - 87,669,782 (+)NCBICelera
Cytogenetic Map8C2NCBI
cM Map839.84NCBI
Mgat4d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554283,328,352 - 3,348,542 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554283,316,031 - 3,352,945 (+)NCBIChiLan1.0ChiLan1.0
MGAT4D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23138,316,511 - 138,381,575 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14138,704,129 - 138,769,185 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04132,804,533 - 132,861,460 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14144,114,989 - 144,170,880 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4144,112,540 - 144,170,880 (-)Ensemblpanpan1.1panPan2
MGAT4D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1192,337,082 - 2,391,533 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl192,339,749 - 2,391,188 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha192,586,240 - 2,638,029 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0192,404,072 - 2,455,817 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl192,404,072 - 2,455,502 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1192,341,031 - 2,392,819 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0192,702,511 - 2,754,228 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0193,058,461 - 3,110,250 (+)NCBIUU_Cfam_GSD_1.0
Mgat4d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530149,874,094 - 49,919,082 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365357,311,511 - 7,349,167 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365357,311,511 - 7,347,756 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MGAT4D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl886,568,711 - 86,614,124 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1886,566,554 - 86,617,453 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2892,070,941 - 92,108,439 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MGAT4D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1787,389,476 - 87,439,358 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl787,398,249 - 87,438,739 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603766,913,163 - 66,983,549 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Mgat4d
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462500696,132 - 114,422 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Mgat4d
784 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:7
Count of miRNA genes:7
Interacting mature miRNAs:7
Transcripts:ENSRNOT00000004982
Prediction methods:Miranda, Rnahybrid
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
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat


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
nervous system
renal system
reproductive system
respiratory system
1 3 1 77 17 12 6 8 6 1 28 13 72 5 36 6

Sequence


Ensembl Acc Id: ENSRNOT00000004982   ⟹   ENSRNOP00000004982
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1924,740,078 - 24,777,012 (-)Ensembl
Rnor_6.0 Ensembl1924,496,569 - 24,532,772 (+)Ensembl
RefSeq Acc Id: NM_001025666   ⟹   NP_001020837
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81941,644,744 - 41,681,583 (-)NCBI
mRatBN7.21924,740,068 - 24,777,012 (-)NCBI
Rnor_6.01924,496,573 - 24,532,767 (+)NCBI
Rnor_5.01935,474,577 - 35,510,796 (+)NCBI
RGSC_v3.41926,447,874 - 26,495,782 (-)RGD
Celera1924,280,376 - 24,316,664 (-)RGD
Sequence:
RefSeq Acc Id: XM_063277959   ⟹   XP_063134029
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81941,644,744 - 41,681,142 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001020837 (Get FASTA)   NCBI Sequence Viewer  
  XP_063134029 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH97408 (Get FASTA)   NCBI Sequence Viewer  
  EDL92281 (Get FASTA)   NCBI Sequence Viewer  
  Q4V8F8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001020837   ⟸   NM_001025666
- Peptide Label: precursor
- UniProtKB: Q4V8F8 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000004982   ⟸   ENSRNOT00000004982
RefSeq Acc Id: XP_063134029   ⟸   XM_063277959
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4V8F8-F1-model_v2 AlphaFold Q4V8F8 1-372 view protein structure

Transcriptome

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

Promoters
RGD ID:13700997
Promoter ID:EPDNEW_R11520
Type:initiation region
Name:Mgat4d_1
Description:MGAT4 family, member D
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_6.01924,496,579 - 24,496,639EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310572 AgrOrtholog
BioCyc Gene G2FUF-6007 BioCyc
Ensembl Genes ENSRNOG00000003695 Ensembl
IMAGE_CLONE IMAGE:7454086 IMAGE-MGC_LOAD
InterPro Glyco_transf_54 UniProtKB/Swiss-Prot
KEGG Report rno:304646 UniProtKB/Swiss-Prot
MGC_CLONE MGC:114453 IMAGE-MGC_LOAD
NCBI Gene 304646 ENTREZGENE
PANTHER ALPHA-1,3-MANNOSYL-GLYCOPROTEIN 4-BETA-N-ACETYLGLUCOSAMINYLTRANSFERASE-LIKE PROTEIN MGAT4D UniProtKB/Swiss-Prot
  PTHR12062 UniProtKB/Swiss-Prot
Pfam Glyco_transf_54 UniProtKB/Swiss-Prot
PhenoGen Mgat4d PhenoGen
RatGTEx ENSRNOG00000003695 RatGTEx
  ENSRNOG00055007527 RatGTEx
  ENSRNOG00060013551 RatGTEx
  ENSRNOG00065010166 RatGTEx
UniProt MGT4D_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-29 Mgat4d  MGAT4 family, member D  RGD1310572  similar to calmegin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1310572  similar to calmegin  RGD1310572_predicted  similar to calmegin (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1310572_predicted  similar to calmegin (predicted)  LOC304646_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC304646_predicted  similar to calmegin (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL