Abca4 (ATP binding cassette subfamily A member 4) - Rat Genome Database

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Gene: Abca4 (ATP binding cassette subfamily A member 4) Rattus norvegicus
Analyze
Symbol: Abca4
Name: ATP binding cassette subfamily A member 4
RGD ID: 1309445
Description: Predicted to enable several functions, including ATP hydrolysis activity; glycerophospholipid flippase activity; and retinal binding activity. Predicted to be involved in phospholipid translocation and retinal metabolic process. Predicted to act upstream of or within lipid transport; photoreceptor cell maintenance; and visual perception. Predicted to be located in cytoplasmic vesicle; endoplasmic reticulum; and photoreceptor outer segment. Predicted to be active in intracellular membrane-bounded organelle. Human ortholog(s) of this gene implicated in fundus dystrophy and retinal degeneration (multiple). Orthologous to human ABCA4 (ATP binding cassette subfamily A member 4); PARTICIPATES IN altered retinoid cycle metabolic pathway; retinitis pigmentosa pathway; retinoid cycle metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; cobalt dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ABCR; ATP-binding cassette, sub-family A (ABC1), member 4; ATP-binding cassette, subfamily A (ABC1), member 4; LOC310836; retinal-specific ATP-binding cassette transporter; retinal-specific phospholipid-transporting ATPase ABCA4
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
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22210,164,813 - 210,302,069 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2210,164,813 - 210,302,069 (+)Ensembl
Rnor_6.02225,645,539 - 225,783,288 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2225,645,568 - 225,783,287 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02243,682,218 - 243,818,930 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42218,712,663 - 218,849,896 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12218,675,724 - 218,812,957 (+)NCBI
Celera2202,594,748 - 202,731,906 (+)NCBICelera
Cytogenetic Map2q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mutation of the Stargardt disease gene (ABCR) in age-related macular degeneration. Allikmets R, etal., Science. 1997 Sep 19;277(5333):1805-7.
2. Retinal phenotypes in patients homozygous for the G1961E mutation in the ABCA4 gene. Burke TR, etal., Invest Ophthalmol Vis Sci. 2012 Jul 3;53(8):4458-67. doi: 10.1167/iovs.11-9166.
3. Clinical characterization of the Stargardt disease and molecular exploration of the c.2041C>T mutation (ABCA4 gene) in Tunisian patients. Chouchene I, etal., Ann Biol Clin (Paris). 2013 Dec 1;71(6):645-651.
4. Autosomal recessive retinitis pigmentosa and cone-rod dystrophy caused by splice site mutations in the Stargardt's disease gene ABCR. Cremers FP, etal., Hum Mol Genet. 1998 Mar;7(3):355-62.
5. Genes and mutations causing retinitis pigmentosa. Daiger SP, etal., Clin Genet. 2013 Aug;84(2):132-41. doi: 10.1111/cge.12203. Epub 2013 Jun 19.
6. 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.
7. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
8. Key enzymes of the retinoid (visual) cycle in vertebrate retina. Kiser PD, etal., Biochim Biophys Acta. 2012 Jan;1821(1):137-51. Epub 2011 Apr 5.
9. Correction of the disease phenotype in the mouse model of Stargardt disease by lentiviral gene therapy. Kong J, etal., Gene Ther. 2008 Oct;15(19):1311-20. doi: 10.1038/gt.2008.78. Epub 2008 May 8.
10. Limited roles of Rdh8, Rdh12, and Abca4 in all-trans-retinal clearance in mouse retina. Maeda A, etal., Invest Ophthalmol Vis Sci. 2009 Nov;50(11):5435-43. doi: 10.1167/iovs.09-3944. Epub 2009 Jun 24.
11. ABCA4 mutations and discordant ABCA4 alleles in patients and siblings with bull's-eye maculopathy. Michaelides M, etal., Br J Ophthalmol. 2007 Dec;91(12):1650-5.
12. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. Comprehensive gene review and curation RGD comprehensive gene curation
16. Stargardt macular dystrophy: common ABCA4 mutations in South Africa--establishment of a rapid genetic test and relating risk to patients. Roberts LJ, etal., Mol Vis. 2012;18:280-9. Epub 2012 Feb 1.
17. Homozygous null mutations in the ABCA4 gene in two families with autosomal recessive retinal dystrophy. Singh HP, etal., Am J Ophthalmol. 2006 May;141(5):906-13. Epub 2006 Mar 20.
18. Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait. Wright AF, etal., Nat Rev Genet. 2010 Apr;11(4):273-84. doi: 10.1038/nrg2717.
Additional References at PubMed
PMID:10412977   PMID:11431429   PMID:15715676   PMID:23943788   PMID:24097981   PMID:25002582   PMID:33970551  


Genomics

Comparative Map Data
Abca4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22210,164,813 - 210,302,069 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2210,164,813 - 210,302,069 (+)Ensembl
Rnor_6.02225,645,539 - 225,783,288 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2225,645,568 - 225,783,287 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02243,682,218 - 243,818,930 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42218,712,663 - 218,849,896 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12218,675,724 - 218,812,957 (+)NCBI
Celera2202,594,748 - 202,731,906 (+)NCBICelera
Cytogenetic Map2q41NCBI
ABCA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38193,992,834 - 94,121,148 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl193,992,834 - 94,121,148 (-)EnsemblGRCh38hg38GRCh38
GRCh37194,458,390 - 94,586,704 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,230,981 - 94,359,293 (-)NCBINCBI36hg18NCBI36
Build 34194,170,416 - 94,298,700NCBI
Celera192,712,080 - 92,840,399 (-)NCBI
Cytogenetic Map1p22.1NCBI
HuRef192,579,378 - 92,707,578 (-)NCBIHuRef
CHM1_1194,573,360 - 94,701,680 (-)NCBICHM1_1
T2T-CHM13v2.0193,841,050 - 93,969,344 (-)NCBI
Abca4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393121,837,547 - 121,973,719 (+)NCBIGRCm39mm39
GRCm39 Ensembl3121,838,092 - 121,973,772 (+)Ensembl
GRCm383122,043,891 - 122,180,070 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3122,044,443 - 122,180,123 (+)EnsemblGRCm38mm10GRCm38
MGSCv373121,747,378 - 121,882,979 (+)NCBIGRCm37mm9NCBIm37
MGSCv363122,036,482 - 122,172,083 (+)NCBImm8
Celera3128,448,730 - 128,585,363 (+)NCBICelera
Cytogenetic Map3G1NCBI
cM Map352.94NCBI
Abca4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955423612,098 - 736,035 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955423612,098 - 738,702 (+)NCBIChiLan1.0ChiLan1.0
ABCA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1195,386,263 - 95,514,589 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl195,386,266 - 95,514,589 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0196,659,703 - 96,784,876 (-)NCBIMhudiblu_PPA_v0panPan3
ABCA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1655,058,361 - 55,186,255 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl655,058,361 - 55,186,253 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha657,766,484 - 57,894,185 (+)NCBI
ROS_Cfam_1.0655,434,279 - 55,561,973 (+)NCBI
ROS_Cfam_1.0 Ensembl655,434,279 - 55,561,935 (+)Ensembl
UMICH_Zoey_3.1655,114,352 - 55,241,756 (+)NCBI
UNSW_CanFamBas_1.0655,098,998 - 55,226,816 (+)NCBI
UU_Cfam_GSD_1.0655,552,093 - 55,679,433 (+)NCBI
Abca4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405058103,621,291 - 103,978,517 (-)NCBI
SpeTri2.0NW_0049365374,969,456 - 5,326,682 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4123,202,753 - 123,331,144 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14123,202,720 - 123,333,044 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24134,845,979 - 134,978,727 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ABCA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12039,140,288 - 39,271,169 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2039,140,922 - 39,267,638 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603378,780,073 - 78,910,160 (-)NCBIVero_WHO_p1.0
Abca4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247423,536,591 - 3,661,468 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247423,536,591 - 3,661,706 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH134002  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22210,301,835 - 210,302,047 (+)MAPPERmRatBN7.2
Rnor_6.02225,783,054 - 225,783,265NCBIRnor6.0
Rnor_5.02243,818,696 - 243,818,907UniSTSRnor5.0
RGSC_v3.42218,849,663 - 218,849,874UniSTSRGSC3.4
Celera2202,731,673 - 202,731,884UniSTS
RH 3.4 Map21522.1UniSTS
Cytogenetic Map2q41UniSTS
RH143198  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22210,228,530 - 210,229,480 (+)MAPPERmRatBN7.2
Rnor_6.02225,710,027 - 225,710,976NCBIRnor6.0
Rnor_5.02243,745,621 - 243,746,570UniSTSRnor5.0
RGSC_v3.42218,775,977 - 218,776,926UniSTSRGSC3.4
Celera2202,658,452 - 202,659,401UniSTS
RH 3.4 Map21520.6UniSTS
Cytogenetic Map2q41UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2184165752229165752Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2185876309219753474Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2185876309219753474Rat
61458Bp10Blood pressure QTL 103.42arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
1298083Bp158Blood pressure QTL 1582.62arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
1331745Bp203Blood pressure QTL 2034.377arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2189599258218414891Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2189599258226936289Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2189599258234599258Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189599258234599258Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2190613715226808892Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2199341726234244620Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2202446871237938339Rat
2299161Iddm33Insulin dependent diabetes mellitus QTL 332.98blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2206312063220876787Rat
631203Gluco14Glucose level QTL 140.0001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)2206665645219003804Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:18
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000017878
Prediction methods:Miranda, 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 24 23 23 8 23 39 35 33 10
Below cutoff 3 19 34 18 11 18 8 11 35 8 1 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017878   ⟹   ENSRNOP00000017878
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2210,164,813 - 210,302,069 (+)Ensembl
Rnor_6.0 Ensembl2225,645,568 - 225,783,287 (+)Ensembl
RefSeq Acc Id: NM_001107721   ⟹   NP_001101191
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22210,164,813 - 210,302,069 (+)NCBI
Rnor_6.02225,645,568 - 225,783,287 (+)NCBI
Rnor_5.02243,682,218 - 243,818,930 (+)NCBI
RGSC_v3.42218,712,663 - 218,849,896 (+)RGD
Celera2202,594,748 - 202,731,906 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101191 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL82093 (Get FASTA)   NCBI Sequence Viewer  
  EDL82094 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101191   ⟸   NM_001107721
- UniProtKB: D4AB29 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017878   ⟸   ENSRNOT00000017878

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AB29-F1-model_v2 AlphaFold D4AB29 1-2290 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 225691252 225691253 C G snv SHRSP/Gcrc (RGD), WKY/NHsd (RGD), WKY/N (2020), WKY/NCrl (2019), SHRSP/A3NCrl (2019), WKY/NCrl (RGD), WKY/N (MCW), WKY/Gcrc (RGD)
2 225763071 225763072 A C snv WKY/NCrl (RGD), M520/NRrrcMcwi (2019), LEXF4/Stm (2020), LEXF2B/Stm (2019), LEXF11/Stm (2020), F344/Stm (2019), F344/N (2020), WKY/NHsd (RGD), WKY/Gcrc (RGD), SHRSP/Gcrc (RGD), MHS/Gib (RGD), WKY/N (MCW), F344/NRrrc (MCW), WKY/N (2020), WN/N (2020), WKY/NCrl (2019), SHRSP/A3NCrl (2019), M520/N (2020), F344/NCrl (2019), F344/DuCrl (2019), F344/NCrl (RGD), WN/N (MCW), M520/N (MCW)
2 225767942 225767943 G A snv WAG/RijCrl (2020), SBN/Ygl (MCW), CDR, CDS, SBH/Ygl (MCW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), MWF/Hsd (2019), FHH/EurMcwi (2019), DA/OlaHsd (2019), ACI/N (2020), ACI/EurMcwi (2019), WAG/Rij (RGD), SR/JrHsd (RGD), SBN/Ygl (RGD), SBH/Ygl (RGD), MNS/Gib (RGD), FHH/EurMcwi (RGD), ACI/EurMcwi (RGD), ACI/N (MCW), SR/JrHsd (MCW), SR/JrHsd (2020)


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 243722889 243722890 C A snv BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU)
2 243726846 243726847 C G snv WKY/NHsd (KNAW), DOB/Oda (KyushuU), WKY/NCrl (KNAW), SHRSP/Gcrc (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW)
2 243743040 243743041 G A snv IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)
2 243798713 243798714 A C snv DOB/Oda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), F344/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), WKY/NHsd (KNAW), WKY/NCrl (KNAW), WKY/N (KNAW), WKY/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), SHRSP/Gcrc (KNAW), M520/N (KNAW), F344/NHsd (KNAW), F344/NCrl (KNAW), F344/NRrrc (SOLiD) (KNAW), MHS/Gib (KNAW), WN/N (KNAW)
2 243803584 243803585 G A snv SBN/Ygl (MCW), DA/BklArbNsi (KNAW), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW), SR/JrHsd (MCW), SR/JrHsd (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), ZFDM (KyushuU), ZF (KyushuU), HWY/Slc (KyushuU), NIG-III/Hok (KyushuU), Crl:SD (UDEL), SDLEF7/Barth (UDEL), SBN/Ygl (KNAW), SBH/Ygl (KNAW), MNS/Gib (KNAW), FHH/EurMcwi (KNAW), SBH/Ygl (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 218757202 218757203 C G snv SHRSP/Gcrc (MDC), WKY/N (KNAW), SHRSP/Gcrc (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL)
2 218829680 218829681 A C snv WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), HCR/1Mco (UMich), HCR/2Mco (UMich), F344/NHsd (ICAHN), SHRSP/Gcrc (ICL), MHS/Gib (ICL), F344/NCrl (ICL), WN/N (KNAW), WKY/N (KNAW), F344/NRrrc (KNAW), M520/N (KNAW)
2 218834551 218834552 G A snv ACI/EurMcwi (ICL), COP/CrCrl (MCW & UW), MNS/Gib (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SR/JrHsd (ICL), WAG/Rij (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), LCR/2Mco (UMich), ACI/N (KNAW), FHH/EurMcwi (MDC), SR/JrHsd (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), FHH/EurMcwi (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309445 AgrOrtholog
BioCyc Gene G2FUF-51382 BioCyc
Ensembl Genes ENSRNOG00000012892 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000017878 ENTREZGENE
NCBI Gene 310836 ENTREZGENE
PhenoGen Abca4 PhenoGen
UniProt D4AB29 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Abca4  ATP binding cassette subfamily A member 4  Abca4  ATP-binding cassette, subfamily A (ABC1), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-11-16 Abca4  ATP-binding cassette, subfamily A (ABC1), member 4  Abca4  ATP-binding cassette, sub-family A (ABC1), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Abca4  ATP-binding cassette, sub-family A (ABC1), member 4   Abca4_predicted  ATP-binding cassette, sub-family A (ABC1), member 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Abca4_predicted  ATP-binding cassette, sub-family A (ABC1), member 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED