Pbdc1 (polysaccharide biosynthesis domain containing 1) - Rat Genome Database

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Gene: Pbdc1 (polysaccharide biosynthesis domain containing 1) Rattus norvegicus
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Symbol: Pbdc1
Name: polysaccharide biosynthesis domain containing 1
RGD ID: 1562502
Description: Orthologous to human PBDC1 (polysaccharide biosynthesis domain containing 1); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC363485; LOC363485; RGD1562502; similar to RIKEN cDNA 2610029G23; uncharacterized protein LOC363485
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X74,219,713 - 74,275,954 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX74,219,713 - 74,227,418 (+)EnsemblGRCr8
mRatBN7.2X70,154,106 - 70,197,827 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX70,154,106 - 70,184,552 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX71,663,081 - 71,667,780 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X75,163,366 - 75,168,064 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X72,726,528 - 72,731,226 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X76,042,239 - 76,092,964 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX76,042,239 - 76,046,938 (+)Ensemblrn6Rnor6.0
Rnor_5.0X76,840,414 - 76,845,113 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X93,151,907 - 93,156,607 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX71,487,174 - 71,491,873 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
2. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Pbdc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X74,219,713 - 74,275,954 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX74,219,713 - 74,227,418 (+)EnsemblGRCr8
mRatBN7.2X70,154,106 - 70,197,827 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX70,154,106 - 70,184,552 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX71,663,081 - 71,667,780 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X75,163,366 - 75,168,064 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X72,726,528 - 72,731,226 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X76,042,239 - 76,092,964 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX76,042,239 - 76,046,938 (+)Ensemblrn6Rnor6.0
Rnor_5.0X76,840,414 - 76,845,113 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X93,151,907 - 93,156,607 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX71,487,174 - 71,491,873 (+)NCBICelera
Cytogenetic MapXq22NCBI
PBDC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X76,173,062 - 76,178,314 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX76,173,034 - 76,178,755 (+)Ensemblhg38GRCh38
GRCh37X75,392,897 - 75,398,149 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X75,309,173 - 75,314,436 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34X75,175,468 - 75,180,732NCBI
CeleraX75,672,493 - 75,677,756 (+)NCBICelera
Cytogenetic MapXq13.3NCBI
HuRefX69,025,570 - 69,030,833 (+)NCBIHuRef
CHM1_1X75,285,292 - 75,290,555 (+)NCBICHM1_1
T2T-CHM13v2.0X74,606,393 - 74,611,646 (+)NCBIT2T-CHM13v2.0
Pbdc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X104,123,337 - 104,160,696 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX104,123,362 - 104,160,696 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X105,079,731 - 105,117,094 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX105,079,756 - 105,117,090 (+)Ensemblmm10GRCm38
MGSCv37X102,275,114 - 102,280,525 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X101,282,494 - 101,287,905 (+)NCBIMGSCv36mm8
CeleraX91,943,752 - 91,949,163 (+)NCBICelera
Cytogenetic MapXDNCBI
cM MapX46.83NCBI
PBDC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X75,821,305 - 75,826,743 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X75,825,011 - 75,830,354 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X65,422,688 - 65,428,451 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X75,537,467 - 75,542,884 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX75,537,469 - 75,542,778 (+)EnsemblpanPan2panpan1.1
PBDC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X59,068,733 - 59,073,085 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX50,143,489 - 50,149,279 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X60,302,358 - 60,308,150 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX60,302,458 - 60,311,816 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X57,995,612 - 58,001,403 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X59,609,520 - 59,615,316 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X59,208,462 - 59,214,254 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pbdc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X43,019,270 - 43,025,160 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366831,922,346 - 1,930,163 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366831,922,633 - 1,928,510 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100515118
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX60,907,404 - 61,019,857 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X60,907,393 - 60,915,607 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X69,309,124 - 69,317,256 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PBDC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X65,511,974 - 65,517,238 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX65,512,044 - 65,517,211 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606716,069,799 - 16,075,037 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pbdc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248364,816,727 - 4,820,603 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248364,816,565 - 4,821,490 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pbdc1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X64,913,118 - 64,952,475 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pbdc1
121 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:264
Count of miRNA genes:182
Interacting mature miRNAs:199
Transcripts:ENSRNOT00000003667
Prediction methods:Microtar, Miranda, Pita
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
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
1598837Memor13Memory QTL 133.2exploratory 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)X4493088389930883Rat

Markers in Region
RH129657  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01130,900,584 - 30,900,764NCBIRnor5.0
Rnor_5.0X76,844,738 - 76,844,918NCBIRnor5.0
Rnor_5.01131,051,926 - 31,052,106NCBIRnor5.0
RGSC_v3.41127,383,989 - 27,384,168UniSTSRGSC3.4
RGSC_v3.4X93,156,233 - 93,156,412UniSTSRGSC3.4
Celera1126,602,670 - 26,602,849UniSTS
CeleraX71,491,499 - 71,491,678UniSTS
Cytogenetic MapXq31UniSTS


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: ENSRNOT00000003667   ⟹   ENSRNOP00000003667
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX74,219,713 - 74,224,133 (+)Ensembl
mRatBN7.2 EnsemblX70,154,106 - 70,184,552 (+)Ensembl
Rnor_6.0 EnsemblX76,042,239 - 76,046,938 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000105988   ⟹   ENSRNOP00000096521
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX70,154,743 - 70,161,810 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000107443   ⟹   ENSRNOP00000095875
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX74,220,325 - 74,227,418 (+)Ensembl
mRatBN7.2 EnsemblX70,154,743 - 70,161,810 (+)Ensembl
RefSeq Acc Id: NM_001108818   ⟹   NP_001102288
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X74,219,713 - 74,224,412 (+)NCBI
mRatBN7.2X70,154,106 - 70,158,805 (+)NCBI
Rnor_6.0X76,042,239 - 76,046,938 (+)NCBI
Rnor_5.0X76,840,414 - 76,845,113 (+)NCBI
RGSC_v3.4X93,151,907 - 93,156,607 (+)RGD
CeleraX71,487,174 - 71,491,873 (+)RGD
Sequence:
RefSeq Acc Id: XM_008773349   ⟹   XP_008771571
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X74,220,330 - 74,275,954 (+)NCBI
mRatBN7.2X70,154,650 - 70,197,827 (+)NCBI
Rnor_6.0X76,042,799 - 76,092,964 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063280150   ⟹   XP_063136220
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X74,220,330 - 74,250,598 (+)NCBI
RefSeq Acc Id: NP_001102288   ⟸   NM_001108818
- UniProtKB: A0A8I6GM43 (UniProtKB/TrEMBL),   A6IV25 (UniProtKB/TrEMBL),   A0A8I6AQ18 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771571   ⟸   XM_008773349
- Peptide Label: isoform X1
- UniProtKB: G3V6C3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003667   ⟸   ENSRNOT00000003667
Ensembl Acc Id: ENSRNOP00000095875   ⟸   ENSRNOT00000107443
Ensembl Acc Id: ENSRNOP00000096521   ⟸   ENSRNOT00000105988
RefSeq Acc Id: XP_063136220   ⟸   XM_063280150
- Peptide Label: isoform X2
- UniProtKB: G3V6C3 (UniProtKB/TrEMBL)
Protein Domains
Polysaccharide biosynthesis

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6C3-F1-model_v2 AlphaFold G3V6C3 1-198 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:1562502 AgrOrtholog
BioCyc Gene G2FUF-1966 BioCyc
Ensembl Genes ENSRNOG00000002662 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003667 ENTREZGENE
  ENSRNOT00000003667.7 UniProtKB/TrEMBL
  ENSRNOT00000107443.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.3560.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6918266 IMAGE-MGC_LOAD
InterPro Polysacc_synth_dom UniProtKB/TrEMBL
  UPF0368_met/fun UniProtKB/TrEMBL
  Yst0336-like_domain UniProtKB/TrEMBL
KEGG Report rno:363485 UniProtKB/TrEMBL
MGC_CLONE MGC:188906 IMAGE-MGC_LOAD
NCBI Gene 363485 ENTREZGENE
PANTHER DUF757 UniProtKB/TrEMBL
  PROTEIN PBDC1 UniProtKB/TrEMBL
Pfam DUF579 UniProtKB/TrEMBL
PhenoGen Pbdc1 PhenoGen
RatGTEx ENSRNOG00000002662 RatGTEx
UniProt A0A8I6AQ18 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GM43 ENTREZGENE
  A6IV25 ENTREZGENE, UniProtKB/TrEMBL
  G3V6C3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-12-10 Pbdc1  polysaccharide biosynthesis domain containing 1  RGD1562502  similar to RIKEN cDNA 2610029G23  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1562502  similar to RIKEN cDNA 2610029G23   RGD1562502_predicted  similar to RIKEN cDNA 2610029G23 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1562502_predicted  similar to RIKEN cDNA 2610029G23 (predicted)  LOC363485  similar to RIKEN cDNA 2610029G23  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363485  similar to RIKEN cDNA 2610029G23      Symbol and Name status set to provisional 70820 PROVISIONAL