C1galt1c1 (C1GALT1-specific chaperone 1) - Rat Genome Database

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Gene: C1galt1c1 (C1GALT1-specific chaperone 1) Rattus norvegicus
Analyze
Symbol: C1galt1c1
Name: C1GALT1-specific chaperone 1
RGD ID: 1311230
Description: Predicted to enable glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity. Predicted to be involved in protein O-linked glycosylation. Predicted to act upstream of or within platelet activation and platelet morphogenesis. Predicted to be located in membrane. Human ortholog(s) of this gene implicated in Tn polyagglutination syndrome and hemolytic-uremic syndrome. Orthologous to human C1GALT1C1 (C1GALT1 specific chaperone 1); PARTICIPATES IN O-linked glycan biosynthetic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: core 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase 2; LOC302499; MGC124680; RGD1311230; similar to contains transmembrane (TM) region and ATP binding region
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: C1galt1c1-ps1  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X122,243,736 - 122,248,217 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX122,234,454 - 122,248,422 (-)EnsemblGRCr8
mRatBN7.2X117,378,123 - 117,382,620 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX117,375,525 - 117,382,787 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX119,476,630 - 119,481,033 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X123,045,644 - 123,050,058 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X120,591,229 - 120,595,631 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X124,921,686 - 124,926,171 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX124,921,728 - 124,926,171 (-)Ensemblrn6Rnor6.0
Rnor_5.0X125,006,181 - 125,010,666 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X6,744,670 - 6,749,116 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX116,594,348 - 116,598,798 (-)NCBICelera
RGSC_v3.1X6,750,225 - 6,754,604 (+)NCBI
Cytogenetic MapXq35NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-methoxyethanol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
acetamide  (EXP)
aflatoxin M1  (ISO)
all-trans-retinoic acid  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
Azoxymethane  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calyculin A  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cypermethrin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
epoxiconazole  (ISO)
ethyl methanesulfonate  (ISO)
finasteride  (EXP)
folic acid  (ISO)
furan  (EXP)
indometacin  (ISO)
ketoconazole  (ISO)
lead(0)  (ISO)
menadione  (ISO)
methapyrilene  (ISO)
methyl methanesulfonate  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
potassium chromate  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sulindac  (EXP)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
tolcapone  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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:12477932   PMID:19199708   PMID:20439703   PMID:21383503   PMID:22988088  


Genomics

Comparative Map Data
C1galt1c1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X122,243,736 - 122,248,217 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX122,234,454 - 122,248,422 (-)EnsemblGRCr8
mRatBN7.2X117,378,123 - 117,382,620 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX117,375,525 - 117,382,787 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX119,476,630 - 119,481,033 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X123,045,644 - 123,050,058 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X120,591,229 - 120,595,631 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X124,921,686 - 124,926,171 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX124,921,728 - 124,926,171 (-)Ensemblrn6Rnor6.0
Rnor_5.0X125,006,181 - 125,010,666 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X6,744,670 - 6,749,116 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX116,594,348 - 116,598,798 (-)NCBICelera
RGSC_v3.1X6,750,225 - 6,754,604 (+)NCBI
Cytogenetic MapXq35NCBI
C1GALT1C1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X120,625,674 - 120,630,054 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX120,625,674 - 120,630,054 (-)Ensemblhg38GRCh38
GRCh37X119,759,529 - 119,763,909 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X119,643,559 - 119,647,969 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X119,541,415 - 119,545,823NCBI
CeleraX120,223,852 - 120,228,328 (-)NCBICelera
Cytogenetic MapXq24NCBI
HuRefX109,224,041 - 109,228,519 (-)NCBIHuRef
CHM1_1X119,671,176 - 119,675,652 (-)NCBICHM1_1
T2T-CHM13v2.0X119,001,127 - 119,005,507 (-)NCBIT2T-CHM13v2.0
C1galt1c1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X37,719,660 - 37,724,020 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX37,719,662 - 37,723,964 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X38,630,783 - 38,635,143 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX38,630,785 - 38,635,087 (-)Ensemblmm10GRCm38
MGSCv37X35,983,960 - 35,988,320 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X34,875,418 - 34,879,736 (-)NCBIMGSCv36mm8
CeleraX26,276,644 - 26,281,004 (-)NCBICelera
Cytogenetic MapXA3.3NCBI
cM MapX22.91NCBI
C1galt1c1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555721,254,289 - 1,258,561 (+)Ensembl
ChiLan1.0NW_0049555721,254,289 - 1,258,561 (+)NCBIChiLan1.0ChiLan1.0
C1GALT1C1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X120,180,679 - 120,185,307 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X120,184,283 - 120,188,593 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X109,905,468 - 109,909,826 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X120,091,635 - 120,095,990 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX120,092,052 - 120,093,008 (-)EnsemblpanPan2panpan1.1
C1GALT1C1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X92,581,124 - 92,584,701 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX92,581,488 - 92,582,444 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX78,611,498 - 78,616,224 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X94,326,291 - 94,331,017 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX94,325,944 - 94,330,930 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X91,775,518 - 91,780,244 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X93,538,078 - 93,542,803 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X93,312,953 - 93,317,669 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
C1galt1c1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X91,567,173 - 91,571,309 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364799,416,284 - 9,420,177 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364799,416,192 - 9,420,327 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C1GALT1C1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X98,752,711 - 98,758,428 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X112,640,591 - 112,646,306 (+)NCBISscrofa10.2Sscrofa10.2susScr3
C1GALT1C1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366606533,342,512 - 33,346,812 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
C1galt1c1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624931568,671 - 573,452 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624931568,636 - 573,452 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
C1galt1c1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X101,750,834 - 101,756,060 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in C1galt1c1
25 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:28
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000003449
Prediction methods:Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X120028026141353710Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X97528096142528096Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X120028026141353710Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX105359969157758123Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X105468858125434318Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118973754157758123Rat
2302047Pia34Pristane induced arthritis QTL 345.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1996916163141916163Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000003449   ⟹   ENSRNOP00000003449
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX124,921,728 - 124,926,171 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000105484   ⟹   ENSRNOP00000081816
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX122,234,454 - 122,248,422 (-)Ensembl
mRatBN7.2 EnsemblX117,375,525 - 117,382,787 (-)Ensembl
RefSeq Acc Id: NM_001030033   ⟹   NP_001025204
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X122,243,773 - 122,248,217 (-)NCBI
mRatBN7.2X117,378,176 - 117,382,620 (-)NCBI
Rnor_6.0X124,921,727 - 124,926,171 (-)NCBI
Rnor_5.0X125,006,181 - 125,010,666 (-)NCBI
RGSC_v3.4X6,744,670 - 6,749,116 (+)RGD
CeleraX116,594,348 - 116,598,798 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257487   ⟹   XP_006257549
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X122,243,736 - 122,248,172 (-)NCBI
mRatBN7.2X117,378,123 - 117,382,603 (-)NCBI
Rnor_6.0X124,921,686 - 124,926,153 (-)NCBI
Rnor_5.0X125,006,181 - 125,010,666 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001025204 (Get FASTA)   NCBI Sequence Viewer  
  XP_006257549 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99818 (Get FASTA)   NCBI Sequence Viewer  
  EDM10872 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000081816
  ENSRNOP00000081816.1
GenBank Protein Q499P3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001025204   ⟸   NM_001030033
- UniProtKB: Q499P3 (UniProtKB/Swiss-Prot),   A6JML0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257549   ⟸   XM_006257487
- Peptide Label: isoform X1
- UniProtKB: Q499P3 (UniProtKB/Swiss-Prot),   A6JML0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003449   ⟸   ENSRNOT00000003449
Ensembl Acc Id: ENSRNOP00000081816   ⟸   ENSRNOT00000105484

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q499P3-F1-model_v2 AlphaFold Q499P3 1-316 view protein structure

Transcriptome

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

Promoters
RGD ID:13702001
Promoter ID:EPDNEW_R12524
Type:initiation region
Name:C1galt1c1_1
Description:C1GALT1-specific chaperone 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_6.0X124,926,146 - 124,926,206EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311230 AgrOrtholog
BioCyc Gene G2FUF-1255 BioCyc
Ensembl Genes ENSRNOG00000002536 Ensembl
  ENSRNOG00000069353 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000105484 ENTREZGENE
  ENSRNOT00000105484.1 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.550.50 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7930810 IMAGE-MGC_LOAD
InterPro C1GALT1/C1GALT1_chp1 UniProtKB/Swiss-Prot
KEGG Report rno:302499 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124680 IMAGE-MGC_LOAD
NCBI Gene 302499 ENTREZGENE
PANTHER BETA1,3-GALACTOSYLTRANSFERASE UniProtKB/Swiss-Prot
  PTHR23033:SF2 UniProtKB/Swiss-Prot
PhenoGen C1galt1c1 PhenoGen
RatGTEx ENSRNOG00000002536 RatGTEx
  ENSRNOG00000069353 RatGTEx
UniProt A6JML0 ENTREZGENE, UniProtKB/TrEMBL
  C1GLC_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 C1galt1c1  C1GALT1-specific chaperone 1  RGD1311230  similar to contains transmembrane (TM) region and ATP binding region  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1311230  similar to contains transmembrane (TM) region and ATP binding region  RGD1311230_predicted  similar to contains transmembrane (TM) region and ATP binding region (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1311230_predicted  similar to contains transmembrane (TM) region and ATP binding region (predicted)  LOC302499_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC302499_predicted  similar to contains transmembrane (TM) region and ATP binding region (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL