Amdhd2 (amidohydrolase domain containing 2) - Rat Genome Database

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Gene: Amdhd2 (amidohydrolase domain containing 2) Rattus norvegicus
Analyze
Symbol: Amdhd2
Name: amidohydrolase domain containing 2
RGD ID: 1304601
Description: Predicted to enable N-acetylglucosamine-6-phosphate deacetylase activity. Predicted to be involved in N-acetylglucosamine catabolic process. Orthologous to human AMDHD2 (amidohydrolase domain containing 2); PARTICIPATES IN amino sugar metabolic pathway; french type sialuria pathway; sialic acid storage disease pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: amidohydrolase domain-containing protein 2; glcNAc 6-P deacetylase; LOC302972; MGC109150; N-acetylglucosamine-6-phosphate deacetylase; putative N-acetylglucosamine-6-phosphate deacetylase; RGD1304601; similar to RIKEN cDNA 5730457F11
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
mRatBN7.21013,187,579 - 13,196,148 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1013,187,578 - 13,196,095 (-)Ensembl
Rnor_6.01013,528,400 - 13,536,949 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1013,528,413 - 13,536,899 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01013,344,252 - 13,352,913 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41013,407,051 - 13,415,537 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11013,407,050 - 13,415,527 (-)NCBI
Celera1012,873,632 - 12,882,118 (-)NCBICelera
Cytogenetic Map10q12NCBI
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

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:21630459   PMID:22692205  


Genomics

Comparative Map Data
Amdhd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21013,187,579 - 13,196,148 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1013,187,578 - 13,196,095 (-)Ensembl
Rnor_6.01013,528,400 - 13,536,949 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1013,528,413 - 13,536,899 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01013,344,252 - 13,352,913 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41013,407,051 - 13,415,537 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11013,407,050 - 13,415,527 (-)NCBI
Celera1012,873,632 - 12,882,118 (-)NCBICelera
Cytogenetic Map10q12NCBI
AMDHD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38162,520,371 - 2,531,417 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl162,520,357 - 2,531,422 (+)EnsemblGRCh38hg38GRCh38
GRCh37162,570,372 - 2,581,418 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36162,510,428 - 2,519,733 (+)NCBINCBI36hg18NCBI36
Celera162,785,299 - 2,795,891 (+)NCBI
Cytogenetic Map16p13.3NCBI
HuRef162,496,333 - 2,507,027 (+)NCBIHuRef
CHM1_1162,570,312 - 2,580,904 (+)NCBICHM1_1
T2T-CHM13v2.0162,542,493 - 2,553,539 (+)NCBI
Amdhd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391724,374,807 - 24,382,752 (-)NCBIGRCm39mm39
GRCm39 Ensembl1724,374,807 - 24,382,740 (-)Ensembl
GRCm381724,155,833 - 24,163,733 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1724,155,833 - 24,163,766 (-)EnsemblGRCm38mm10GRCm38
MGSCv371724,292,800 - 24,300,700 (-)NCBIGRCm37mm9NCBIm37
MGSCv361723,883,455 - 23,891,359 (-)NCBImm8
Celera1724,661,114 - 24,669,067 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
Amdhd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495544214,775,528 - 14,791,650 (-)NCBIChiLan1.0ChiLan1.0
AMDHD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1162,619,320 - 2,629,347 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl162,619,320 - 2,630,375 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0161,376,904 - 1,387,883 (+)NCBIMhudiblu_PPA_v0panPan3
AMDHD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1638,509,793 - 38,519,711 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha639,748,187 - 39,758,083 (-)NCBI
ROS_Cfam_1.0638,819,036 - 38,828,935 (-)NCBI
ROS_Cfam_1.0 Ensembl638,819,043 - 38,830,163 (-)Ensembl
UMICH_Zoey_3.1638,504,196 - 38,514,092 (-)NCBI
UNSW_CanFamBas_1.0638,476,804 - 38,486,701 (-)NCBI
UU_Cfam_GSD_1.0638,952,889 - 38,962,784 (-)NCBI
AMDHD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1339,523,076 - 39,532,590 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2342,706,973 - 42,716,475 (+)NCBISscrofa10.2Sscrofa10.2susScr3
AMDHD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.152,394,229 - 2,403,949 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl52,394,295 - 2,405,897 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606828,619,426 - 28,630,811 (-)NCBIVero_WHO_p1.0
Amdhd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624824273,036 - 282,866 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
Atp6l  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,196,216 - 13,196,379 (+)MAPPERmRatBN7.2
Rnor_6.01013,537,044 - 13,537,206NCBIRnor6.0
Rnor_5.01013,353,004 - 13,353,166UniSTSRnor5.0
RGSC_v3.41013,415,682 - 13,415,844UniSTSRGSC3.4
Celera1012,882,263 - 12,882,425UniSTS
Cytogenetic Map10q12UniSTS
RH135105  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,191,880 - 13,192,086 (+)MAPPERmRatBN7.2
Rnor_6.01013,532,705 - 13,532,910NCBIRnor6.0
Rnor_5.01013,348,544 - 13,348,870UniSTSRnor5.0
Rnor_5.01013,348,544 - 13,348,749UniSTSRnor5.0
RGSC_v3.41013,411,343 - 13,411,548UniSTSRGSC3.4
Celera1012,877,924 - 12,878,129UniSTS
RH 3.4 Map10191.3UniSTS
Cytogenetic Map10q12UniSTS
BI274660  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,187,668 - 13,187,818 (+)MAPPERmRatBN7.2
Rnor_6.01013,528,493 - 13,528,642NCBIRnor6.0
Rnor_5.01013,344,332 - 13,344,481UniSTSRnor5.0
RGSC_v3.41013,407,131 - 13,407,280UniSTSRGSC3.4
Celera1012,873,712 - 12,873,861UniSTS
Cytogenetic Map10q12UniSTS
Atp6c3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,196,216 - 13,196,405 (+)MAPPERmRatBN7.2
Rnor_6.01013,537,044 - 13,537,232NCBIRnor6.0
Rnor_5.01013,353,004 - 13,353,192UniSTSRnor5.0
RGSC_v3.41013,415,682 - 13,415,870UniSTSRGSC3.4
Celera1012,882,263 - 12,882,451UniSTS
Cytogenetic Map10q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:127
Count of miRNA genes:100
Interacting mature miRNAs:105
Transcripts:ENSRNOT00000008537
Prediction methods:Microtar, 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.


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 3 2 15 6 18 6 54 35 39 11
Low 41 42 35 1 35 8 11 20 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008537   ⟹   ENSRNOP00000008537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1013,187,587 - 13,196,095 (-)Ensembl
Rnor_6.0 Ensembl1013,528,413 - 13,536,899 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097046   ⟹   ENSRNOP00000085897
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1013,187,593 - 13,196,062 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101639   ⟹   ENSRNOP00000086057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1013,187,578 - 13,196,082 (-)Ensembl
RefSeq Acc Id: NM_001024990   ⟹   NP_001020161
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21013,187,589 - 13,196,072 (-)NCBI
Rnor_6.01013,528,413 - 13,536,899 (-)NCBI
Rnor_5.01013,344,252 - 13,352,913 (-)NCBI
RGSC_v3.41013,407,051 - 13,415,537 (-)RGD
Celera1012,873,632 - 12,882,118 (-)RGD
Sequence:
RefSeq Acc Id: XM_039085857   ⟹   XP_038941785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21013,187,579 - 13,196,148 (-)NCBI
RefSeq Acc Id: XR_005489794
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21013,187,834 - 13,196,148 (-)NCBI
RefSeq Acc Id: XR_357448
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21013,187,835 - 13,196,148 (-)NCBI
Rnor_6.01013,529,223 - 13,536,949 (-)NCBI
Rnor_5.01013,344,252 - 13,352,913 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001020161 (Get FASTA)   NCBI Sequence Viewer  
  XP_038941785 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM03807 (Get FASTA)   NCBI Sequence Viewer  
  EDM03808 (Get FASTA)   NCBI Sequence Viewer  
  Q5BJY6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001020161   ⟸   NM_001024990
- UniProtKB: Q5BJY6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008537   ⟸   ENSRNOT00000008537
RefSeq Acc Id: XP_038941785   ⟸   XM_039085857
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000085897   ⟸   ENSRNOT00000097046
RefSeq Acc Id: ENSRNOP00000086057   ⟸   ENSRNOT00000101639

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5BJY6-F1-model_v2 AlphaFold Q5BJY6 1-409 view protein structure

Transcriptome

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

Promoters
RGD ID:13697003
Promoter ID:EPDNEW_R7528
Type:initiation region
Name:Amdhd2_1
Description:amidohydrolase domain containing 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_6.01013,536,869 - 13,536,929EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 13530203 13530204 T C snv SHR/OlalpcvMcwi (2019)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 13346042 13346043 T C snv SHR/OlaIpcv (KNAW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 13408841 13408842 T C snv SHR/OlaIpcv (KNAW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 13189379 13189380 T C snv SHR/OlalpcvMcwi (2019)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304601 AgrOrtholog
BioCyc Gene G2FUF-25876 BioCyc
BioCyc Pathway GLUAMCAT-PWY [N-acetylglucosamine degradation I] BioCyc
Ensembl Genes ENSRNOG00000006460 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008537 ENTREZGENE
  ENSRNOP00000085897.1 UniProtKB/TrEMBL
  ENSRNOP00000086057 ENTREZGENE
  ENSRNOP00000086057.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008537 ENTREZGENE
  ENSRNOT00000097046 ENTREZGENE
  ENSRNOT00000097046.1 UniProtKB/TrEMBL
  ENSRNOT00000101639 ENTREZGENE
  ENSRNOT00000101639.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7384067 IMAGE-MGC_LOAD
InterPro Amidohydro-rel UniProtKB/Swiss-Prot
  GlcNAc_6-P_deAcase UniProtKB/Swiss-Prot
  Metal-dep_hydrolase_composite UniProtKB/Swiss-Prot
  Metal_Hydrolase UniProtKB/Swiss-Prot
KEGG Report rno:302972 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109150 IMAGE-MGC_LOAD
NCBI Gene 302972 ENTREZGENE
PANTHER PTHR11113:SF14 UniProtKB/Swiss-Prot
Pfam Amidohydro_1 UniProtKB/Swiss-Prot
PhenoGen Amdhd2 PhenoGen
PIRSF NagA UniProtKB/Swiss-Prot
Superfamily-SCOP SSF51338 UniProtKB/Swiss-Prot
  SSF51556 UniProtKB/Swiss-Prot
TIGRFAMs nagA UniProtKB/Swiss-Prot
UniProt A0A8I6A4U1_RAT UniProtKB/TrEMBL
  A0A8I6A5A8_RAT UniProtKB/TrEMBL
  NAGA_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Amdhd2  amidohydrolase domain containing 2  RGD1304601  similar to RIKEN cDNA 5730457F11  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1304601  similar to RIKEN cDNA 5730457F11  RGD1304601_predicted  similar to RIKEN cDNA 5730457F11 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1304601_predicted  similar to RIKEN cDNA 5730457F11 (predicted)  LOC302972_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC302972_predicted  similar to RIKEN cDNA 5730457F11 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL