Amelx (amelogenin, X-linked) - Rat Genome Database

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Gene: Amelx (amelogenin, X-linked) Rattus norvegicus
Analyze
Symbol: Amelx
Name: amelogenin, X-linked
RGD ID: 2107
Description: Enables identical protein binding activity. A structural constituent of tooth enamel. Involved in response to calcium ion; response to drug; and response to nutrient. Located in Golgi apparatus; endocytic vesicle; and extracellular matrix. Biomarker of autosomal dominant hypocalcemia. Human ortholog(s) of this gene implicated in amelogenesis imperfecta and amelogenesis imperfecta type 1E. Orthologous to several human genes including AMELX (amelogenin X-linked); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Amel; amelogenin; amelogenin X chromosome; amelogenin, X isoform; leucine-rich amelogenin peptide; LRAP
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
mRatBN7.2X25,076,362 - 25,087,660 (+)NCBImRatBN7.2
Rnor_6.0 EnsemblX26,439,197 - 26,450,495 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X26,439,197 - 26,450,495 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X26,843,989 - 26,855,287 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X45,763,451 - 45,769,374 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X45,816,919 - 45,822,842 (+)NCBI
CeleraX25,496,279 - 25,507,557 (+)NCBICelera
Cytogenetic MapXq13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:1483698   PMID:1734713   PMID:1916828   PMID:2509010   PMID:7948026   PMID:9041053   PMID:11852235   PMID:16293627   PMID:16674683   PMID:16674693   PMID:18281204   PMID:18757743  
PMID:19086270   PMID:20044581   PMID:20304108   PMID:20387077   PMID:20404336   PMID:21653221   PMID:23896516  


Genomics

Comparative Map Data
Amelx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X25,076,362 - 25,087,660 (+)NCBImRatBN7.2
Rnor_6.0 EnsemblX26,439,197 - 26,450,495 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X26,439,197 - 26,450,495 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X26,843,989 - 26,855,287 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X45,763,451 - 45,769,374 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X45,816,919 - 45,822,842 (+)NCBI
CeleraX25,496,279 - 25,507,557 (+)NCBICelera
Cytogenetic MapXq13NCBI
AMELX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX11,293,413 - 11,300,761 (+)EnsemblGRCh38hg38GRCh38
GRCh38X11,293,413 - 11,304,149 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X11,311,533 - 11,318,881 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X11,221,454 - 11,228,802 (+)NCBINCBI36hg18NCBI36
CeleraX15,438,990 - 15,446,338 (+)NCBI
Cytogenetic MapXp22.2NCBI
HuRefX9,091,155 - 9,098,355 (+)NCBIHuRef
CHM1_1X11,342,001 - 11,349,349 (+)NCBICHM1_1
Amelx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X167,959,110 - 167,970,205 (-)NCBIGRCm39mm39
GRCm39 EnsemblX167,959,110 - 167,970,196 (-)Ensembl
GRCm38X169,176,114 - 169,187,209 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX169,176,114 - 169,187,200 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X165,614,046 - 165,625,141 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X164,524,127 - 164,531,314 (-)NCBImm8
CeleraX152,339,918 - 152,351,218 (-)NCBICelera
Cytogenetic MapXF5NCBI
cM MapX78.95NCBI
Amelx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555441,969,216 - 1,979,063 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555441,974,889 - 1,979,063 (-)NCBIChiLan1.0ChiLan1.0
AMELX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X11,214,103 - 11,221,443 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX11,214,103 - 11,221,443 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X3,898,819 - 3,930,686 (+)NCBIMhudiblu_PPA_v0panPan3
AMELX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X7,822,513 - 7,828,692 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX7,822,859 - 7,830,351 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX7,779,650 - 7,787,144 (+)NCBI
ROS_Cfam_1.0X7,776,327 - 7,783,824 (+)NCBI
UMICH_Zoey_3.1X7,759,322 - 7,766,816 (+)NCBI
UNSW_CanFamBas_1.0X7,795,375 - 7,802,872 (+)NCBI
UU_Cfam_GSD_1.0X7,790,231 - 7,797,728 (+)NCBI
Amelx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X1,168,483 - 1,174,166 (+)NCBI
SpeTri2.0NW_0049364701,169,906 - 1,174,166 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AMELX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX8,055,780 - 8,073,744 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X8,055,246 - 8,063,457 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X8,669,948 - 8,677,620 (+)NCBISscrofa10.2Sscrofa10.2susScr3
AMELX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X9,927,740 - 9,934,104 (+)NCBI
ChlSab1.1 EnsemblX9,741,594 - 9,745,776 (+)Ensembl
ChlSab1.1 EnsemblX9,741,594 - 9,745,776 (+)NCBI
Vero_WHO_p1.0NW_02366605611,535,786 - 11,539,980 (+)NCBI
Amelx
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248823,072,970 - 3,083,832 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1815335263153352Rat
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2159262344320739Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2159262344468300Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:89
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000005328, ENSRNOT00000052176
Prediction methods:Microtar, Miranda, Pita, 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.


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
Low 1 10 8 10 8 8 9 6 8 6 10 8
Below cutoff 1 8 16 2 8 2 1 21 2 3 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001271073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_019154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU168858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U01245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U07054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U51195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U60562 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U60563 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U60564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U67130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000005328   ⟹   ENSRNOP00000005328
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX26,440,598 - 26,445,191 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000052176   ⟹   ENSRNOP00000048382
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX26,439,197 - 26,450,495 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078843   ⟹   ENSRNOP00000069787
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX26,439,197 - 26,446,499 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087268   ⟹   ENSRNOP00000068556
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX26,439,197 - 26,450,495 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087293   ⟹   ENSRNOP00000075671
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX26,440,584 - 26,446,499 (+)Ensembl
RefSeq Acc Id: NM_001271073   ⟹   NP_001258002
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X25,076,362 - 25,087,660 (+)NCBI
Rnor_6.0X26,439,197 - 26,450,495 (+)NCBI
Rnor_5.0X26,843,989 - 26,855,287 (+)NCBI
CeleraX25,496,279 - 25,507,557 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001271074   ⟹   NP_001258003
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X25,076,362 - 25,087,660 (+)NCBI
Rnor_6.0X26,439,197 - 26,450,495 (+)NCBI
Rnor_5.0X26,843,989 - 26,855,287 (+)NCBI
CeleraX25,496,279 - 25,507,557 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001271075   ⟹   NP_001258004
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X25,076,362 - 25,087,660 (+)NCBI
Rnor_6.0X26,439,197 - 26,450,495 (+)NCBI
Rnor_5.0X26,843,989 - 26,855,287 (+)NCBI
CeleraX25,496,279 - 25,507,557 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001271076   ⟹   NP_001258005
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X25,076,362 - 25,087,660 (+)NCBI
Rnor_6.0X26,439,197 - 26,450,495 (+)NCBI
Rnor_5.0X26,843,989 - 26,855,287 (+)NCBI
CeleraX25,496,279 - 25,507,557 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001271077   ⟹   NP_001258006
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X25,076,362 - 25,083,672 (+)NCBI
Rnor_6.0X26,439,197 - 26,446,507 (+)NCBI
Rnor_5.0X26,843,989 - 26,855,287 (+)NCBI
CeleraX25,496,279 - 25,503,569 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001271078   ⟹   NP_001258007
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X25,076,362 - 25,083,672 (+)NCBI
Rnor_6.0X26,439,197 - 26,446,507 (+)NCBI
Rnor_5.0X26,843,989 - 26,855,287 (+)NCBI
CeleraX25,496,279 - 25,503,569 (+)NCBI
Sequence:
RefSeq Acc Id: NM_019154   ⟹   NP_062027
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X25,076,362 - 25,083,672 (+)NCBI
Rnor_6.0X26,440,584 - 26,446,507 (+)NCBI
Rnor_5.0X26,843,989 - 26,855,287 (+)NCBI
RGSC_v3.4X45,763,451 - 45,769,374 (+)RGD
CeleraX25,497,666 - 25,503,569 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062027   ⟸   NM_019154
- Peptide Label: isoform 5 precursor
- UniProtKB: P63278 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001258003   ⟸   NM_001271074
- Peptide Label: isoform 1 precursor
- UniProtKB: P63278 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001258002   ⟸   NM_001271073
- Peptide Label: isoform 2 precursor
- UniProtKB: P63278 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001258004   ⟸   NM_001271075
- Peptide Label: isoform 3 precursor
- UniProtKB: P63278 (UniProtKB/Swiss-Prot),   Q63642 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001258005   ⟸   NM_001271076
- Peptide Label: isoform 4 precursor
- UniProtKB: P63278 (UniProtKB/Swiss-Prot),   A0A0G2JT37 (UniProtKB/TrEMBL),   Q63641 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001258006   ⟸   NM_001271077
- Peptide Label: isoform 6 precursor
- UniProtKB: P63278 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001258007   ⟸   NM_001271078
- Peptide Label: isoform 7 precursor
- UniProtKB: P63278 (UniProtKB/Swiss-Prot),   Q63642 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075671   ⟸   ENSRNOT00000087293
RefSeq Acc Id: ENSRNOP00000068556   ⟸   ENSRNOT00000087268
RefSeq Acc Id: ENSRNOP00000005328   ⟸   ENSRNOT00000005328
RefSeq Acc Id: ENSRNOP00000069787   ⟸   ENSRNOT00000078843
RefSeq Acc Id: ENSRNOP00000048382   ⟸   ENSRNOT00000052176

Transcriptome

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


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)
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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
LN/MavRrrc (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
M520/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
MHS/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
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)
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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2107 AgrOrtholog
Ensembl Genes ENSRNOG00000003965 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005328 UniProtKB/Swiss-Prot
  ENSRNOP00000048382 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000068556 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069787 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075671 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000005328 UniProtKB/Swiss-Prot
  ENSRNOT00000052176 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000078843 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000087268 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000087293 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Amelogenin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29160 UniProtKB/Swiss-Prot
NCBI Gene 29160 ENTREZGENE
PANTHER PTHR46794 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Amelx PhenoGen
PRINTS AMELOGENIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Amelogenin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JT37 ENTREZGENE, UniProtKB/TrEMBL
  AMELX_RAT UniProtKB/Swiss-Prot
  B2BY38_RAT UniProtKB/TrEMBL
  P63278 ENTREZGENE
  Q63641 ENTREZGENE, UniProtKB/TrEMBL
  Q63642 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary P45559 UniProtKB/Swiss-Prot
  Q62945 UniProtKB/Swiss-Prot
  Q63640 UniProtKB/Swiss-Prot
  Q78E56 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-01-06 Amelx  amelogenin, X-linked  Amelx  amelogenin X chromosome  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-03-01 Amelx  amelogenin X chromosome  Amel  amelogenin  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 APPROVED
2002-06-10 Amel  amelogenin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function structural component of the enamel matrix 632201
gene_process may play a role in mineralization 632201