Amph (amphiphysin) - Rat Genome Database

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Gene: Amph (amphiphysin) Rattus norvegicus
Analyze
Symbol: Amph
Name: amphiphysin
RGD ID: 620274
Description: Exhibits protein C-terminus binding activity. Involved in positive regulation of GTPase activity and positive regulation of endocytosis. Localizes to axon terminus and extrinsic component of synaptic vesicle membrane. Orthologous to human AMPH (amphiphysin); PARTICIPATES IN Fc gamma receptor mediated signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Amph1; amphiphysin 1; amphiphysin-like; LOC100909679; LOC687233; similar to amphiphysin 1; uncharacterized protein LOC100909679
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
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
mRatBN7.21745,739,385 - 45,982,905 (-)NCBI
Rnor_6.0 Ensembl1748,304,322 - 48,562,905 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01748,304,324 - 48,562,838 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01746,357,604 - 46,621,763 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41753,558,804 - 53,802,936NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11753,561,655 - 53,805,777NCBI
Cytogenetic Map17q11NCBI
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
1. Anggono V and Robinson PJ, J Neurochem. 2007 Aug;102(3):931-43. Epub 2007 Apr 16.
2. Chen-Hwang MC, etal., J Biol Chem 2002 May 17;277(20):17597-604.
3. Di Paolo G, etal., Neuron 2002 Feb 28;33(5):789-804.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Lai MM, etal., J Biol Chem. 2000 Nov 3;275(44):34017-20.
6. Lichte B, etal., EMBO J. 1992 Jul;11(7):2521-30.
7. MGD data from the GO Consortium
8. Nakanishi A, etal., Acta Med Okayama. 2008 Dec;62(6):385-91.
9. NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. Nemoto Y, etal., J Biol Chem 2001 Nov 2;276(44):41133-42.
11. Pipeline to import KEGG annotations from KEGG into RGD
12. RGD automated data pipeline
13. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. RGD automated import pipeline for gene-chemical interactions
15. Ritter B, etal., EMBO J. 2007 Sep 19;26(18):4066-77. Epub 2007 Aug 30.
16. Ritter B, etal., PLoS Biol. 2013 Oct;11(10):e1001670. doi: 10.1371/journal.pbio.1001670. Epub 2013 Oct 1.
17. Rosenthal JA, etal., J Biol Chem 1999 Nov 26;274(48):33959-65.
18. Tosoni D, etal., Cell. 2005 Dec 2;123(5):875-88.
19. Traub LM, etal., Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):8907-12.
20. Wigge P, etal., Mol Biol Cell 1997 Oct;8(10):2003-15.
21. Wilhelm BG, etal., Science. 2014 May 30;344(6187):1023-8. doi: 10.1126/science.1252884.
22. Wuertenberger S and Groemping Y, FEBS Lett. 2015 Apr 28;589(10):1156-63. doi: 10.1016/j.febslet.2015.03.014. Epub 2015 Mar 24.
23. Zanner R, etal., J Cell Sci. 2004 May 1;117(Pt 11):2369-76.
Additional References at PubMed
PMID:8552632   PMID:9195986   PMID:9259551   PMID:9341169   PMID:9694653   PMID:11382783   PMID:15090044   PMID:15207364   PMID:15262992   PMID:15821731   PMID:15953416   PMID:16903783  
PMID:17855509   PMID:18344231   PMID:19144635   PMID:19759398   PMID:21700703   PMID:22750946   PMID:22871113   PMID:23785143   PMID:28235806   PMID:29476059  


Genomics

Comparative Map Data
Amph
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21745,739,385 - 45,982,905 (-)NCBI
Rnor_6.0 Ensembl1748,304,322 - 48,562,905 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01748,304,324 - 48,562,838 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01746,357,604 - 46,621,763 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41753,558,804 - 53,802,936NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11753,561,655 - 53,805,777NCBI
Cytogenetic Map17q11NCBI
AMPH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl738,383,704 - 38,631,420 (-)EnsemblGRCh38hg38GRCh38
GRCh38738,383,694 - 38,631,497 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37738,423,305 - 38,670,973 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36738,389,830 - 38,637,545 (-)NCBINCBI36hg18NCBI36
Build 34738,196,545 - 38,444,260NCBI
Celera738,411,134 - 38,658,846 (-)NCBI
Cytogenetic Map7p14.1NCBI
HuRef738,307,292 - 38,555,371 (-)NCBIHuRef
CHM1_1738,425,940 - 38,673,786 (-)NCBICHM1_1
CRA_TCAGchr7v2738,460,969 - 38,708,834 (-)NCBI
Amph
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391319,132,325 - 19,338,202 (+)NCBIGRCm39mm39
GRCm39 Ensembl1319,132,375 - 19,335,091 (+)Ensembl
GRCm381318,948,142 - 19,154,032 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1318,948,205 - 19,150,921 (+)EnsemblGRCm38mm10GRCm38
MGSCv371319,040,240 - 19,242,784 (+)NCBIGRCm37mm9NCBIm37
MGSCv361318,955,836 - 19,158,380 (+)NCBImm8
Celera1319,259,525 - 19,457,406 (+)NCBICelera
Cytogenetic Map13A2NCBI
cM Map136.89NCBI
Amph
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554604,804,442 - 5,023,202 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554604,804,400 - 5,024,312 (+)NCBIChiLan1.0ChiLan1.0
AMPH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1739,250,081 - 39,495,844 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl739,250,081 - 39,495,844 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0739,015,699 - 39,262,120 (-)NCBIMhudiblu_PPA_v0panPan3
AMPH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11811,132,078 - 11,261,847 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1811,143,446 - 11,260,841 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1810,903,625 - 11,114,792 (+)NCBI
ROS_Cfam_1.01811,099,548 - 11,310,938 (+)NCBI
UMICH_Zoey_3.11811,076,355 - 11,287,485 (+)NCBI
UNSW_CanFamBas_1.01811,044,639 - 11,263,972 (+)NCBI
UU_Cfam_GSD_1.01811,160,063 - 11,371,410 (+)NCBI
Amph
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511894,747,942 - 94,972,174 (-)NCBI
SpeTri2.0NW_00493647813,959,669 - 14,183,835 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AMPH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9108,799,793 - 108,971,668 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19108,800,718 - 108,971,575 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29119,651,630 - 119,751,221 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Amph
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474022,399,302 - 22,615,736 (+)NCBI

Position Markers
RH131007  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2863,318,169 - 63,318,360 (+)MAPPER
mRatBN7.21745,886,101 - 45,886,303 (+)MAPPER
Rnor_6.01748,455,564 - 48,455,765NCBIRnor6.0
Rnor_6.0867,747,980 - 67,748,170NCBIRnor6.0
Rnor_5.01746,508,844 - 46,509,045UniSTSRnor5.0
Rnor_5.0867,476,727 - 67,476,917UniSTSRnor5.0
RGSC_v3.4867,001,823 - 67,002,013UniSTSRGSC3.4
RGSC_v3.41753,705,754 - 53,705,955UniSTSRGSC3.4
Celera1741,984,143 - 41,984,344UniSTS
Celera862,733,083 - 62,733,273UniSTS
Cytogenetic Map17q11UniSTS
Cytogenetic Map8q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17163676140Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17173413148Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17173413148Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17333697263676140Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17333697273413148Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17333697273413148Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17333697273413148Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17519104750191047Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17519104750191047Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17982730454827304Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171574375561036897Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171867614063676140Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171867614063676140Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172149095062195822Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172149095066490950Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172149095066490950Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172149095066490950Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172149095066490950Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172149095066490950Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172149095074823273Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172213681453475276Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172277506564946194Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172403061863676140Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172769095961794615Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172769095963994435Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172807358956207236Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172841314873413148Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)173097522875975228Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)173097522875975228Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173205588258468016Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173205588277922655Rat
2313854Bp343Blood pressure QTL 3433.9life span trait (VT:0005372)age at time of death (CMO:0001193)173330362753475276Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173330362778303627Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173628324577922655Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173779030673413148Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)174117605786176057Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)174117605786176057Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174173108086731080Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174254187285446768Rat
631497Bp98Blood pressure QTL 983.66arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)174295602163994435Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174435615789356157Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:81
Count of miRNA genes:78
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000017102
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

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 15
Low 2 8 6 57 26 25 11
Below cutoff 41 13 7 10 7 8 9 2 9 16 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017102   ⟹   ENSRNOP00000017102
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1748,304,322 - 48,562,838 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084702   ⟹   ENSRNOP00000070116
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1748,304,329 - 48,562,905 (-)Ensembl
RefSeq Acc Id: NM_022217   ⟹   NP_071553
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21745,740,464 - 45,982,807 (-)NCBI
Rnor_6.01748,304,324 - 48,562,838 (-)NCBI
Rnor_5.01746,357,604 - 46,621,763 (-)NCBI
RGSC_v3.41753,558,804 - 53,802,936 (-)RGD
Sequence:
RefSeq Acc Id: XM_039096040   ⟹   XP_038951968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21745,739,385 - 45,886,191 (-)NCBI
RefSeq Acc Id: XM_039096041   ⟹   XP_038951969
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21745,739,385 - 45,982,905 (-)NCBI
RefSeq Acc Id: XM_039096042   ⟹   XP_038951970
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21745,739,385 - 45,982,867 (-)NCBI
Protein Sequences
Protein RefSeqs NP_071553 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951968 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951969 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951970 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA73808 (Get FASTA)   NCBI Sequence Viewer  
  O08838 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_071553   ⟸   NM_022217
- UniProtKB: O08838 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070116   ⟸   ENSRNOT00000084702
RefSeq Acc Id: ENSRNOP00000017102   ⟸   ENSRNOT00000017102
RefSeq Acc Id: XP_038951969   ⟸   XM_039096041
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951970   ⟸   XM_039096042
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038951968   ⟸   XM_039096040
- Peptide Label: isoform X1
Protein Domains
BAR   SH3

Transcriptome

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

Promoters
RGD ID:13700504
Promoter ID:EPDNEW_R11028
Type:initiation region
Name:Amph_1
Description:amphiphysin
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_6.01748,562,914 - 48,562,974EPDNEW

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)
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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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/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
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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620274 AgrOrtholog
BIND 130419
  130420
  130421
  134465
  144371
Ensembl Genes ENSRNOG00000012490 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017102 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070116 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017102 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084702 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1270.60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AH/BAR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Amphiphysin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Amphiphysin_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Amphiphysin_I_SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BAR_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60668 UniProtKB/Swiss-Prot
NCBI Gene 60668 ENTREZGENE
PANTHER PTHR46514:SF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam BAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3_9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Amph PhenoGen
PRINTS AMPHIPHYSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AMPHIPHYSIN1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE BAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART BAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SH3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF103657 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50044 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JX32_RAT UniProtKB/TrEMBL
  AMPH_RAT UniProtKB/Swiss-Prot
  F1LPP0_RAT UniProtKB/TrEMBL
  O08838 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Amph  amphiphysin  LOC100909679  amphiphysin-like  Data Merged 737654 PROVISIONAL
2013-04-17 Amph  amphiphysin  LOC687233  similar to amphiphysin 1  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100909679  amphiphysin-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-02-22 Amph  amphiphysin  Amph1  amphiphysin 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC687233  similar to amphiphysin 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 Amph1  amphiphysin 1    amphiphysin  Symbol updated 1299863 APPROVED
2002-08-07 Amph1  amphiphysin      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a src homology 3 domain 631926
gene_physical_interaction forms a heterodimer with Amph2 that activates dynamin GTPase activity 631926