Gnpda2 (glucosamine-6-phosphate deaminase 2) - Rat Genome Database

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Gene: Gnpda2 (glucosamine-6-phosphate deaminase 2) Rattus norvegicus
Analyze
Symbol: Gnpda2
Name: glucosamine-6-phosphate deaminase 2
RGD ID: 1305521
Description: Predicted to enable glucosamine-6-phosphate deaminase activity and identical protein binding activity. Predicted to be involved in UDP-N-acetylglucosamine biosynthetic process and amino sugar catabolic process. Predicted to be active in cytoplasm. Orthologous to human GNPDA2 (glucosamine-6-phosphate deaminase 2); PARTICIPATES IN amino sugar metabolic pathway; nucleotide sugar metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: glucosamine-6-phosphate isomerase 2; LOC289608
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81438,874,611 - 38,892,688 (+)NCBIGRCr8
mRatBN7.21438,520,663 - 38,538,713 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1438,520,705 - 38,538,713 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1438,896,548 - 38,914,550 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01440,196,580 - 40,214,582 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01438,677,427 - 38,695,429 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01462,628,102 - 62,646,158 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1462,628,111 - 62,646,110 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01462,730,787 - 62,749,053 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41441,048,839 - 41,067,584 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11441,051,193 - 41,069,954 (+)NCBI
Celera1437,719,177 - 37,737,184 (+)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Body Weight  (ISO)
obesity  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA)

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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:12477932   PMID:21630459   PMID:21779089   PMID:22871113  


Genomics

Comparative Map Data
Gnpda2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81438,874,611 - 38,892,688 (+)NCBIGRCr8
mRatBN7.21438,520,663 - 38,538,713 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1438,520,705 - 38,538,713 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1438,896,548 - 38,914,550 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01440,196,580 - 40,214,582 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01438,677,427 - 38,695,429 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01462,628,102 - 62,646,158 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1462,628,111 - 62,646,110 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01462,730,787 - 62,749,053 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41441,048,839 - 41,067,584 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11441,051,193 - 41,069,954 (+)NCBI
Celera1437,719,177 - 37,737,184 (+)NCBICelera
Cytogenetic Map14p11NCBI
GNPDA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38444,701,795 - 44,726,556 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl444,682,200 - 44,726,588 (-)EnsemblGRCh38hg38GRCh38
GRCh37444,703,812 - 44,728,573 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36444,398,925 - 44,423,369 (-)NCBINCBI36Build 36hg18NCBI36
Build 34444,545,096 - 44,569,540NCBI
Celera445,152,192 - 45,176,638 (-)NCBICelera
Cytogenetic Map4p12NCBI
HuRef444,025,436 - 44,050,279 (-)NCBIHuRef
CHM1_1444,702,923 - 44,727,736 (-)NCBICHM1_1
T2T-CHM13v2.0444,668,716 - 44,693,480 (-)NCBIT2T-CHM13v2.0
Gnpda2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39569,732,344 - 69,749,684 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl569,730,451 - 69,749,683 (-)EnsemblGRCm39 Ensembl
GRCm38569,574,998 - 69,592,332 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl569,573,108 - 69,592,340 (-)EnsemblGRCm38mm10GRCm38
MGSCv37569,966,240 - 69,983,524 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36569,852,245 - 69,871,420 (-)NCBIMGSCv36mm8
Celera566,858,645 - 66,875,974 (-)NCBICelera
Cytogenetic Map5C3.1NCBI
cM Map537.13NCBI
Gnpda2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554433,338,300 - 3,360,561 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554433,338,300 - 3,360,561 (+)NCBIChiLan1.0ChiLan1.0
GNPDA2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2344,878,721 - 44,923,195 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1445,065,371 - 45,109,845 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0439,011,732 - 39,056,234 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1444,861,252 - 44,905,733 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl444,881,220 - 44,905,733 (-)Ensemblpanpan1.1panPan2
GNPDA2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11341,207,192 - 41,228,573 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1341,207,897 - 41,232,404 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1341,160,250 - 41,185,478 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01341,814,500 - 41,839,486 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1341,801,109 - 41,839,600 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11341,494,001 - 41,518,794 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01341,538,927 - 41,563,984 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01341,931,427 - 41,956,525 (-)NCBIUU_Cfam_GSD_1.0
LOC101968793
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528534,874,360 - 34,958,967 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648211,339,682 - 11,362,150 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0 EnsemblNW_00493648211,397,322 - 11,423,885 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648211,382,358 - 11,423,823 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GNPDA2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl835,193,659 - 35,216,206 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1835,192,509 - 35,219,527 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2836,899,569 - 36,925,403 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GNPDA2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1275,562,894 - 5,587,459 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl275,562,916 - 5,586,543 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604751,710,663 - 51,735,473 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Gnpda2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476122,261,869 - 22,286,147 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476122,261,838 - 22,286,180 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Gnpda2
67 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:78
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000002992
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
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
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
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
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143076702539153750Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat

Markers in Region
RH129612  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21438,538,452 - 38,538,665 (-)MAPPERmRatBN7.2
Rnor_6.01462,628,150 - 62,628,362NCBIRnor6.0
Rnor_5.01462,731,054 - 62,731,266UniSTSRnor5.0
RGSC_v3.41441,067,324 - 41,067,536UniSTSRGSC3.4
Celera1437,736,924 - 37,737,136UniSTS
Cytogenetic Map14p11UniSTS
RH142376  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21438,538,298 - 38,538,474 (-)MAPPERmRatBN7.2
Rnor_6.01462,628,341 - 62,628,516NCBIRnor6.0
Rnor_5.01462,731,245 - 62,731,420UniSTSRnor5.0
RGSC_v3.41441,067,170 - 41,067,345UniSTSRGSC3.4
Celera1437,736,770 - 37,736,945UniSTS
Cytogenetic Map14p11UniSTS


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 14 16 4 19 4 68 20 31 11
Low 2 29 41 37 37 8 10 6 15 10 8
Below cutoff 1

Sequence


RefSeq Acc Id: ENSRNOT00000002992   ⟹   ENSRNOP00000002992
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1438,520,705 - 38,538,713 (+)Ensembl
Rnor_6.0 Ensembl1462,628,111 - 62,646,110 (-)Ensembl
RefSeq Acc Id: NM_001106005   ⟹   NP_001099475
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81438,874,657 - 38,892,665 (+)NCBI
mRatBN7.21438,520,705 - 38,538,713 (+)NCBI
Rnor_6.01462,628,102 - 62,646,110 (-)NCBI
Rnor_5.01462,730,787 - 62,749,053 (-)NCBI
RGSC_v3.41441,048,839 - 41,067,584 (+)RGD
Celera1437,719,177 - 37,737,184 (+)RGD
Sequence:
RefSeq Acc Id: XM_006251036   ⟹   XP_006251098
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81438,874,611 - 38,892,688 (+)NCBI
mRatBN7.21438,520,663 - 38,538,711 (+)NCBI
Rnor_6.01462,628,104 - 62,646,158 (-)NCBI
Rnor_5.01462,730,787 - 62,749,053 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005492912
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81438,874,611 - 38,887,307 (+)NCBI
mRatBN7.21438,520,663 - 38,535,906 (+)NCBI
RefSeq Acc Id: XR_010057351
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81438,874,611 - 38,887,887 (+)NCBI
RefSeq Acc Id: XR_010057352
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81438,874,611 - 38,887,307 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001099475 (Get FASTA)   NCBI Sequence Viewer  
  XP_006251098 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68866 (Get FASTA)   NCBI Sequence Viewer  
  EDL90011 (Get FASTA)   NCBI Sequence Viewer  
  EDL90012 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002992
  ENSRNOP00000002992.4
RefSeq Acc Id: NP_001099475   ⟸   NM_001106005
- UniProtKB: B5DEZ6 (UniProtKB/TrEMBL),   F7FL82 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251098   ⟸   XM_006251036
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000002992   ⟸   ENSRNOT00000002992
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5DEZ6-F1-model_v2 AlphaFold B5DEZ6 1-276 view protein structure

Transcriptome

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

Promoters
RGD ID:13699341
Promoter ID:EPDNEW_R9865
Type:initiation region
Name:Gnpda2_1
Description:glucosamine-6-phosphate deaminase 2
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_6.01462,646,110 - 62,646,170EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305521 AgrOrtholog
BioCyc Gene G2FUF-15817 BioCyc
BioCyc Pathway GLUAMCAT-PWY [N-acetylglucosamine degradation I] BioCyc
BioCyc Pathway Image GLUAMCAT-PWY BioCyc
Ensembl Genes ENSRNOG00000002177 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002992 ENTREZGENE
  ENSRNOT00000002992.7 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1360 UniProtKB/TrEMBL
InterPro Glc/Gal-6P_isomerase UniProtKB/TrEMBL
  Glucosamine6P_isomerase UniProtKB/TrEMBL
  Glucosamine6P_isomerase_CS UniProtKB/TrEMBL
  NagB/RpiA_transferase-like UniProtKB/TrEMBL
KEGG Report rno:289608 UniProtKB/TrEMBL
NCBI Gene 289608 ENTREZGENE
PANTHER GLUCOSAMINE-6-PHOSPHATE ISOMERASE 2 UniProtKB/TrEMBL
  NagB UniProtKB/TrEMBL
Pfam Glucosamine_iso UniProtKB/TrEMBL
PhenoGen Gnpda2 PhenoGen
PROSITE GLC_GALNAC_ISOMERASE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002177 RatGTEx
Superfamily-SCOP SSF100950 UniProtKB/TrEMBL
UniProt B5DEZ6 ENTREZGENE, UniProtKB/TrEMBL
  F7FL82 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Gnpda2  glucosamine-6-phosphate deaminase 2   Gnpda2_predicted  glucosamine-6-phosphate deaminase 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Gnpda2_predicted  glucosamine-6-phosphate deaminase 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED