Gcnt4 (glucosaminyl (N-acetyl) transferase 4) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Gcnt4 (glucosaminyl (N-acetyl) transferase 4) Rattus norvegicus
Analyze
Symbol: Gcnt4
Name: glucosaminyl (N-acetyl) transferase 4
RGD ID: 1563891
Description: Predicted to enable glycosyltransferase activity. Predicted to act upstream of or within several processes, including inter-male aggressive behavior; neutrophil homeostasis; and thyroid hormone metabolic process. Predicted to be located in Golgi membrane. Orthologous to human GCNT4 (glucosaminyl (N-acetyl) transferase 4); INTERACTS WITH 4,4'-diaminodiphenylmethane; bisphenol A; DDT.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4; glucosaminyl (N-acetyl) transferase 4, core 2; LOC310011; RGD1563891; similar to core 2 beta-1,6-N-acetylglucosaminyltransferase 3
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
mRatBN7.2228,253,311 - 28,329,381 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl228,252,860 - 28,283,082 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx235,300,997 - 35,331,013 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0233,401,074 - 33,431,089 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0228,215,443 - 28,246,105 (+)NCBIRnor_WKY
Rnor_6.0 Ensembl227,713,880 - 27,780,119 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0246,825,580 - 46,828,021 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4227,439,605 - 27,441,008 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera224,297,063 - 24,327,571 (+)NCBICelera
Cytogenetic Map2q12NCBI
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

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19349303  


Genomics

Comparative Map Data
Gcnt4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2228,253,311 - 28,329,381 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl228,252,860 - 28,283,082 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx235,300,997 - 35,331,013 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0233,401,074 - 33,431,089 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0228,215,443 - 28,246,105 (+)NCBIRnor_WKY
Rnor_6.0 Ensembl227,713,880 - 27,780,119 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0246,825,580 - 46,828,021 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4227,439,605 - 27,441,008 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera224,297,063 - 24,327,571 (+)NCBICelera
Cytogenetic Map2q12NCBI
GCNT4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38575,016,969 - 75,054,060 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl575,025,346 - 75,052,558 (-)EnsemblGRCh38hg38GRCh38
GRCh37574,321,171 - 74,348,383 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36574,359,045 - 74,362,480 (-)NCBINCBI36Build 36hg18NCBI36
Celera570,217,451 - 70,220,886 (-)NCBICelera
Cytogenetic Map5q13.3NCBI
HuRef569,528,134 - 69,531,569 (-)NCBIHuRef
CHM1_1573,756,061 - 73,759,496 (-)NCBICHM1_1
T2T-CHM13v2.0575,506,196 - 75,533,414 (-)NCBIT2T-CHM13v2.0
Gcnt4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391397,060,852 - 97,087,422 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1397,061,197 - 97,087,414 (+)EnsemblGRCm39 Ensembl
GRCm381396,924,344 - 96,950,914 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1396,924,689 - 96,950,906 (+)EnsemblGRCm38mm10GRCm38
MGSCv371397,694,644 - 97,720,869 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera13100,561,219 - 100,587,502 (+)NCBICelera
Cytogenetic Map13D1NCBI
Gcnt4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542525,662,036 - 25,681,948 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542525,661,648 - 25,681,948 (+)NCBIChiLan1.0ChiLan1.0
GCNT4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1540,863,275 - 40,889,919 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0540,249,346 - 40,279,559 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
GCNT4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1331,198,656 - 31,222,523 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl331,217,562 - 31,218,926 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha332,432,498 - 32,441,223 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0331,129,485 - 31,153,307 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1331,059,370 - 31,083,226 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0331,030,795 - 31,054,614 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0331,408,140 - 31,431,040 (+)NCBIUU_Cfam_GSD_1.0
Gcnt4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213189,211,120 - 189,234,616 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365491,645,256 - 1,647,307 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GCNT4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl284,105,655 - 84,134,721 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1284,105,652 - 84,135,122 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2285,693,080 - 85,722,498 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GCNT4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1469,392,170 - 69,421,082 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl469,393,958 - 69,395,319 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604918,168,983 - 18,198,423 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gcnt4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462495115,367 - 38,669 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gcnt4
672 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:9
Count of miRNA genes:9
Interacting mature miRNAs:9
Transcripts:ENSRNOT00000052189
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22699957143154682Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat


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
Low 2 2 51 41 16 41 7 7 54 33 32 11 7
Below cutoff 40 6 3 1 4 20 2 8 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000083143   ⟹   ENSRNOP00000070953
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl227,713,880 - 27,780,119 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107684   ⟹   ENSRNOP00000095630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl228,252,860 - 28,283,082 (+)Ensembl
RefSeq Acc Id: XM_039103466   ⟹   XP_038959394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2228,253,325 - 28,283,082 (+)NCBI
RefSeq Acc Id: XM_039103467   ⟹   XP_038959395
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2228,253,325 - 28,283,082 (+)NCBI
RefSeq Acc Id: XM_039103468   ⟹   XP_038959396
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2228,253,325 - 28,283,082 (+)NCBI
RefSeq Acc Id: XM_039103469   ⟹   XP_038959397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2228,253,325 - 28,283,082 (+)NCBI
RefSeq Acc Id: XR_005500517
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2228,253,311 - 28,313,585 (+)NCBI
RefSeq Acc Id: XR_005500518
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2228,253,314 - 28,329,381 (+)NCBI
RefSeq Acc Id: XR_005500519
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2228,253,311 - 28,329,381 (+)NCBI
Reference Sequences
RefSeq Acc Id: ENSRNOP00000070953   ⟸   ENSRNOT00000083143
RefSeq Acc Id: XP_038959395   ⟸   XM_039103467
- UniProtKB: A0A8I6ARU0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038959396   ⟸   XM_039103468
- UniProtKB: A0A8I6ARU0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038959394   ⟸   XM_039103466
RefSeq Acc Id: XP_038959397   ⟸   XM_039103469
- UniProtKB: A0A8I6ARU0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000095630   ⟸   ENSRNOT00000107684

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JZ89-F1-model_v2 AlphaFold A0A0G2JZ89 1-456 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:1563891 AgrOrtholog
BioCyc Gene G2FUF-54772 BioCyc
BioCyc Pathway PWY-7433 [mucin core 1 and core 2 O-glycosylation] BioCyc
Ensembl Genes ENSRNOG00000055451 Ensembl
  ENSRNOG00000064612 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000095630 ENTREZGENE
  ENSRNOP00000095630.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000107684 ENTREZGENE
  ENSRNOT00000107684.1 UniProtKB/TrEMBL
InterPro Glyco_trans_14 UniProtKB/TrEMBL
NCBI Gene Gcnt4 ENTREZGENE
Pfam Branch UniProtKB/TrEMBL
PhenoGen Gcnt4 PhenoGen
UniProt A0A8I6ARU0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Gcnt4  glucosaminyl (N-acetyl) transferase 4  Gcnt4  glucosaminyl (N-acetyl) transferase 4  Data Merged 737654 PROVISIONAL
2021-08-09 Gcnt4  glucosaminyl (N-acetyl) transferase 4      Symbol and Name status set to provisional 45752 PROVISIONAL
2018-10-30 Gcnt4  glucosaminyl (N-acetyl) transferase 4  Gcnt4  glucosaminyl (N-acetyl) transferase 4, core 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-12 Gcnt4  glucosaminyl (N-acetyl) transferase 4, core 2  RGD1563891  similar to core 2 beta-1,6-N-acetylglucosaminyltransferase 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563891  similar to core 2 beta-1,6-N-acetylglucosaminyltransferase 3   RGD1563891_predicted  similar to core 2 beta-1,6-N-acetylglucosaminyltransferase 3 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563891_predicted  similar to core 2 beta-1,6-N-acetylglucosaminyltransferase 3 (predicted)  LOC310011  similar to core 2 beta-1,6-N-acetylglucosaminyltransferase 3  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC310011  similar to core 2 beta-1,6-N-acetylglucosaminyltransferase 3      Symbol and Name status set to provisional 70820 PROVISIONAL