RGD1559459 (similar to Expressed sequence AI788959) - Rat Genome Database

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Gene: RGD1559459 (similar to Expressed sequence AI788959) Rattus norvegicus
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Symbol: RGD1559459
Name: similar to Expressed sequence AI788959
RGD ID: 1559459
Description: Predicted to enable glucuronosyltransferase activity. Predicted to be involved in estrogen metabolic process and xenobiotic glucuronidation. Predicted to be located in endoplasmic reticulum and nuclear outer membrane. Orthologous to human UGT2B28 (UDP glucuronosyltransferase family 2 member B28); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC501907; UDP-glucuronosyltransferase 2B31-like
RGD Orthologs
Human
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21421,146,140 - 21,167,706 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1421,145,827 - 21,167,704 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01422,932,454 - 22,955,663 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1422,937,421 - 22,952,822 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01422,830,157 - 22,852,941 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41422,768,551 - 22,786,094 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1420,639,284 - 20,662,598 (+)NCBICelera
Cytogenetic Map14p21NCBI
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11300766  


Genomics

Comparative Map Data
RGD1559459
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21421,146,140 - 21,167,706 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1421,145,827 - 21,167,704 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01422,932,454 - 22,955,663 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1422,937,421 - 22,952,822 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01422,830,157 - 22,852,941 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41422,768,551 - 22,786,094 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1420,639,284 - 20,662,598 (+)NCBICelera
Cytogenetic Map14p21NCBI
UGT2B28
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38469,280,475 - 69,295,050 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl469,280,475 - 69,295,050 (+)EnsemblGRCh38hg38GRCh38
GRCh37470,146,193 - 70,160,768 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36470,180,806 - 70,195,357 (+)NCBINCBI36Build 36hg18NCBI36
Build 34470,326,976 - 70,341,527NCBI
Celera467,489,536 - 67,504,128 (+)NCBICelera
Cytogenetic Map4q13.2NCBI
HuRef465,944,695 - 65,959,246 (+)NCBIHuRef
LOC100516628
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1866,377,171 - 66,395,323 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2870,821,924 - 70,840,082 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in RGD1559459
61 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:38
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000065079
Prediction methods: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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat

Markers in Region
RH134619  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21421,167,278 - 21,167,471 (+)MAPPERmRatBN7.2
Rnor_6.01422,953,675 - 22,953,867NCBIRnor6.0
Rnor_5.01422,850,958 - 22,851,150UniSTSRnor5.0
RGSC_v3.41422,786,947 - 22,787,139UniSTSRGSC3.4
Celera1420,660,610 - 20,660,802UniSTS
RH 3.4 Map14309.9UniSTS
Cytogenetic Map14p21UniSTS


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 29 29 29
Low 2 22 12 8 12 2 9 8 3
Below cutoff 3 4 3 4 4 12 17 21 8 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065079   ⟹   ENSRNOP00000058927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1421,145,827 - 21,167,704 (+)Ensembl
Rnor_6.0 Ensembl1422,937,421 - 22,952,822 (+)Ensembl
RefSeq Acc Id: XM_003751344   ⟹   XP_003751392
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21421,146,147 - 21,167,706 (+)NCBI
Rnor_6.01422,932,496 - 22,955,663 (+)NCBI
Rnor_5.01422,830,157 - 22,852,941 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250809   ⟹   XP_006250871
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21421,146,148 - 21,167,706 (+)NCBI
Rnor_6.01422,932,550 - 22,955,663 (+)NCBI
Rnor_5.01422,830,157 - 22,852,941 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008770101   ⟹   XP_008768323
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21421,146,140 - 21,167,706 (+)NCBI
Rnor_6.01422,932,454 - 22,955,663 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003751392 (Get FASTA)   NCBI Sequence Viewer  
  XP_006250871 (Get FASTA)   NCBI Sequence Viewer  
  XP_008768323 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_003751392   ⟸   XM_003751344
- Peptide Label: isoform X1
- UniProtKB: F1LTB8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250871   ⟸   XM_006250809
- Peptide Label: isoform X1
- UniProtKB: F1LTB8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768323   ⟸   XM_008770101
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000058927   ⟸   ENSRNOT00000065079
Protein Domains
UDPGT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LTB8-F1-model_v2 AlphaFold F1LTB8 1-530 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:1559459 AgrOrtholog
BioCyc Gene G2FUF-16089 BioCyc
Ensembl Genes ENSRNOG00000042714 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000058927 ENTREZGENE
  ENSRNOP00000058927.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065079 ENTREZGENE
  ENSRNOT00000065079.3 UniProtKB/TrEMBL
InterPro UDP_glucos_trans UniProtKB/TrEMBL
  UDP_glycos_trans_CS UniProtKB/TrEMBL
KEGG Report rno:501907 UniProtKB/TrEMBL
NCBI Gene 501907 ENTREZGENE
Pfam UDPGT UniProtKB/TrEMBL
PhenoGen RGD1559459 PhenoGen
PROSITE UDPGT UniProtKB/TrEMBL
UniProt F1LTB8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 RGD1559459  similar to Expressed sequence AI788959   RGD1559459_predicted  similar to Expressed sequence AI788959 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1559459_predicted  similar to Expressed sequence AI788959 (predicted)  LOC501907  similar to Expressed sequence AI788959  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501907  similar to Expressed sequence AI788959      Symbol and Name status set to provisional 70820 PROVISIONAL