Ambn (ameloblastin) - Rat Genome Database

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Gene: Ambn (ameloblastin) Rattus norvegicus
Analyze
Symbol: Ambn
Name: ameloblastin
RGD ID: 2101
Description: Predicted to enable growth factor activity. Predicted to be involved in cell adhesion and regulation of cell population proliferation. Predicted to be located in extracellular region. Human ortholog(s) of this gene implicated in amelogenesis imperfecta type 1F. Orthologous to human AMBN (ameloblastin); INTERACTS WITH ammonium chloride; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: amelin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
mRatBN7.21419,601,761 - 19,614,382 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1419,601,702 - 19,614,393 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1419,591,037 - 19,603,705 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01420,909,907 - 20,922,580 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01419,612,560 - 19,625,205 (-)NCBIRnor_WKY
Rnor_6.01421,239,887 - 21,252,534 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,240,398 - 21,252,538 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,151,232 - 21,164,256 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,183,338 - 21,196,650 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,183,341 - 21,196,650 (-)NCBI
Celera1418,940,192 - 18,974,478 (-)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. A novel gene expressed in rat ameloblasts codes for proteins with cell binding domains. Cerny R, etal., J Bone Miner Res 1996 Jul;11(7):883-91.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Full-length sequence, localization, and chromosomal mapping of ameloblastin. A novel tooth-specific gene. Krebsbach PH, etal., J Biol Chem 1996 Feb 23;271(8):4431-5.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12803485   PMID:16674693   PMID:17184233   PMID:18281204   PMID:19648121   PMID:20854943   PMID:21149578   PMID:27193486  


Genomics

Comparative Map Data
Ambn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21419,601,761 - 19,614,382 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1419,601,702 - 19,614,393 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1419,591,037 - 19,603,705 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01420,909,907 - 20,922,580 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01419,612,560 - 19,625,205 (-)NCBIRnor_WKY
Rnor_6.01421,239,887 - 21,252,534 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1421,240,398 - 21,252,538 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01421,151,232 - 21,164,256 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41421,183,338 - 21,196,650 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11421,183,341 - 21,196,650 (-)NCBI
Celera1418,940,192 - 18,974,478 (-)NCBICelera
Cytogenetic Map14p22NCBI
AMBN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38470,592,256 - 70,607,288 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl470,592,256 - 70,607,288 (+)EnsemblGRCh38hg38GRCh38
GRCh37471,457,973 - 71,473,005 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36471,492,590 - 71,507,594 (+)NCBINCBI36Build 36hg18NCBI36
Build 34471,638,760 - 71,653,762NCBI
Celera468,816,162 - 68,831,378 (+)NCBICelera
Cytogenetic Map4q13.3NCBI
HuRef467,260,447 - 67,275,390 (+)NCBIHuRef
CHM1_1471,493,982 - 71,509,012 (+)NCBICHM1_1
T2T-CHM13v2.0473,933,220 - 73,948,252 (+)NCBIT2T-CHM13v2.0
Ambn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39588,603,850 - 88,616,390 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl588,603,850 - 88,616,390 (+)EnsemblGRCm39 Ensembl
GRCm38588,455,991 - 88,468,531 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl588,455,991 - 88,468,531 (+)EnsemblGRCm38mm10GRCm38
MGSCv37588,885,036 - 88,897,556 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36589,530,572 - 89,543,092 (+)NCBIMGSCv36mm8
Celera586,604,818 - 86,617,344 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map543.63NCBI
Ambn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554472,363,240 - 2,374,827 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554472,363,240 - 2,374,827 (-)NCBIChiLan1.0ChiLan1.0
AMBN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1459,961,939 - 59,976,750 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl459,961,939 - 59,976,750 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0453,616,553 - 53,631,566 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
AMBN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11359,899,968 - 59,912,699 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1359,899,960 - 59,912,655 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1359,634,149 - 59,647,121 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01360,705,599 - 60,718,555 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1360,705,595 - 60,718,250 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11360,320,956 - 60,333,943 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01359,812,504 - 59,825,448 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01360,959,429 - 60,972,465 (+)NCBIUU_Cfam_GSD_1.0
Ambn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528515,702,487 - 15,715,557 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365984,154,801 - 4,166,565 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AMBN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl867,381,137 - 67,394,394 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1867,381,137 - 67,394,394 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2871,288,922 - 71,302,169 (+)NCBISscrofa10.2Sscrofa10.2susScr3
AMBN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1719,107,182 - 19,121,992 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl719,107,299 - 19,122,285 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660843,763,200 - 3,778,295 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ambn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248901,942,559 - 1,954,490 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248901,943,471 - 1,954,948 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ambn
63 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:82
Count of miRNA genes:63
Interacting mature miRNAs:74
Transcripts:ENSRNOT00000005003
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141757341219726296Rat
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


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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 5 14 3 2
Below cutoff 3 14 4 5 4 2 2 32 5 8 7 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005003   ⟹   ENSRNOP00000005003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1419,601,765 - 19,614,386 (-)Ensembl
Rnor_6.0 Ensembl1421,240,398 - 21,252,538 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105630   ⟹   ENSRNOP00000087626
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1419,601,702 - 19,614,393 (-)Ensembl
RefSeq Acc Id: NM_012900   ⟹   NP_037032
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21419,601,761 - 19,614,382 (-)NCBI
Rnor_6.01421,239,887 - 21,252,534 (-)NCBI
Rnor_5.01421,151,232 - 21,164,256 (-)NCBI
RGSC_v3.41421,183,338 - 21,196,650 (-)RGD
Celera1418,940,192 - 18,974,478 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037032   ⟸   NM_012900
- Peptide Label: precursor
- UniProtKB: Q63043 (UniProtKB/Swiss-Prot),   Q62840 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000005003   ⟸   ENSRNOT00000005003
RefSeq Acc Id: ENSRNOP00000087626   ⟸   ENSRNOT00000105630

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q62840-F1-model_v2 AlphaFold Q62840 1-422 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2101 AgrOrtholog
BioCyc Gene G2FUF-16157 BioCyc
Ensembl Genes ENSRNOG00000003718 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005003.7 UniProtKB/TrEMBL
  ENSRNOP00000087626 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000005003.7 UniProtKB/TrEMBL
  ENSRNOT00000105630 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Amelin UniProtKB/Swiss-Prot
KEGG Report rno:25376 UniProtKB/Swiss-Prot
NCBI Gene 25376 ENTREZGENE
PANTHER PTHR14115 UniProtKB/Swiss-Prot
Pfam Amelin UniProtKB/Swiss-Prot
PhenoGen Ambn PhenoGen
SMART Amelin UniProtKB/Swiss-Prot
UniProt A0A8L2Q1Q4_RAT UniProtKB/TrEMBL
  AMBN_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q63043 ENTREZGENE
UniProt Secondary Q540J9 UniProtKB/Swiss-Prot
  Q63043 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ambn  Ameloblastin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains integrin recognition sequence DGEA 632199
gene_expression expressed in ameloblasts during enamel matrix formation 632199
gene_process may serve as a structural component of the enamel matrix 632199
gene_protein encodes two variant forms containing 407 and 324 amino acids 632199