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 have 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; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21013,187,579 - 13,196,148 (-)NCBI
Rnor_6.0 Ensembl1013,528,413 - 13,536,899 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01013,528,400 - 13,536,949 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

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 (-)NCBI
Rnor_6.0 Ensembl1013,528,413 - 13,536,899 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01013,528,400 - 13,536,949 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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
GRCh38.p13 Ensembl162,520,357 - 2,531,422 (+)EnsemblGRCh38hg38GRCh38
GRCh38162,520,362 - 2,531,422 (+)NCBIGRCh38GRCh38hg38GRCh38
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
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
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.152,394,229 - 2,403,949 (+)NCBI
ChlSab1.1 Ensembl52,394,295 - 2,405,897 (+)Ensembl
Vero_WHO_p1.0NW_02366606828,619,426 - 28,630,811 (-)NCBI
Amdhd2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624824273,036 - 282,866 (+)NCBI

Position Markers
Atp6l  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21013,196,216 - 13,196,379 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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 (+)MAPPER
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 (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129592136Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135538813Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138594330Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142669970Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)10144902893Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1076442166221621Rat
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)10483563820170031Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10521719917555534Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10521719919591669Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10546011921524070Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10546011921524070Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10546011921524070Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10546011921524070Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10546011921524070Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10587753664401490Rat
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)10622909575983805Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10622928936185929Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10752145052521450Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101263951357639513Rat

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
Rnor_6.0 Ensembl1013,528,413 - 13,536,899 (-)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_008767565   ⟹   XP_008765787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01013,528,400 - 13,536,949 (-)NCBI
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: XP_008765787   ⟸   XM_008767565
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000008537   ⟸   ENSRNOT00000008537
RefSeq Acc Id: XP_038941785   ⟸   XM_039085857
- Peptide Label: isoform X1

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 (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


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)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304601 AgrOrtholog
Ensembl Genes ENSRNOG00000006460 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000008537 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000008537 ENTREZGENE, UniProtKB/Swiss-Prot
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 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