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

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Gene: Abca4 (ATP binding cassette subfamily A member 4) Ictidomys tridecemlineatus
Analyze
Symbol: Abca4
Name: ATP binding cassette subfamily A member 4
RGD ID: 12632822
Description: ENCODES a protein that exhibits 11-cis retinal binding (inferred); ABC-type transporter activity (inferred); all-trans retinal binding (inferred); INVOLVED IN phospholipid transfer to membrane (ortholog); photoreceptor cell maintenance (ortholog); visual perception (ortholog); PARTICIPATES IN altered retinoid cycle metabolic pathway; retinitis pigmentosa pathway; retinoid cycle metabolic pathway; ASSOCIATED WITH age related macular degeneration (ortholog); age related macular degeneration 14 (ortholog); age related macular degeneration 2 (ortholog); FOUND IN cytoplasmic vesicle (inferred); endoplasmic reticulum (inferred); intracellular membrane-bounded organelle (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC101965641; retinal-specific ATP-binding cassette transporter; retinal-specific phospholipid-transporting ATPase ABCA4
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405058103,621,291 - 103,978,517 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365375,202,093 - 5,323,527 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365374,969,456 - 5,326,682 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Abca4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405058103,621,291 - 103,978,517 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365375,202,093 - 5,323,527 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365374,969,456 - 5,326,682 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38193,992,834 - 94,121,148 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl193,992,834 - 94,121,148 (-)EnsemblGRCh38hg38GRCh38
GRCh37194,458,390 - 94,586,704 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,230,981 - 94,359,293 (-)NCBINCBI36Build 36hg18NCBI36
Build 34194,170,416 - 94,298,700NCBI
Celera192,712,080 - 92,840,399 (-)NCBICelera
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 (-)NCBIT2T-CHM13v2.0
Abca4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393121,837,547 - 121,973,719 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3121,838,092 - 121,973,772 (+)EnsemblGRCm39 Ensembl
GRCm383122,043,891 - 122,180,070 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3122,044,443 - 122,180,123 (+)EnsemblGRCm38mm10GRCm38
MGSCv373121,747,378 - 121,882,979 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363122,036,482 - 122,172,083 (+)NCBIMGSCv36mm8
Celera3128,448,730 - 128,585,363 (+)NCBICelera
Cytogenetic Map3G1NCBI
cM Map352.94NCBI
Abca4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82212,849,470 - 212,986,730 (+)NCBIGRCr8
mRatBN7.22210,164,813 - 210,302,069 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2210,164,813 - 210,302,069 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2217,837,756 - 217,975,083 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02215,745,511 - 215,882,846 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02210,587,485 - 210,724,819 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12218,675,724 - 218,812,957 (+)NCBI
Celera2202,594,748 - 202,731,906 (+)NCBICelera
Cytogenetic Map2q42NCBI
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
NHGRI_mPanPan1-v21132,900,976 - 133,029,375 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11132,055,894 - 132,184,432 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0196,659,703 - 96,784,876 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1195,386,263 - 95,514,589 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl195,386,266 - 95,514,589 (-)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0655,434,279 - 55,561,973 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl655,434,279 - 55,561,935 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1655,114,352 - 55,241,756 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0655,098,998 - 55,226,816 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0655,552,093 - 55,679,433 (+)NCBIUU_Cfam_GSD_1.0
ABCA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4123,202,753 - 123,333,041 (+)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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2039,140,922 - 39,267,638 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603378,780,073 - 78,910,160 (-)NCBIVero_WHO_p1.0Vero_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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247423,536,591 - 3,661,706 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSSTOT00000000305   ⟹   ENSSTOP00000000272
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049365375,202,093 - 5,323,527 (+)Ensembl
Ensembl Acc Id: ENSSTOT00000042788   ⟹   ENSSTOP00000024877
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049365375,202,093 - 5,323,153 (+)Ensembl
RefSeq Acc Id: XM_040289201   ⟹   XP_040145135
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405058103,621,291 - 103,978,517 (-)NCBI
Protein Sequences
Protein RefSeqs XP_040145135 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000000272.3
  ENSSTOP00000024877.1
RefSeq Acc Id: XP_040145135   ⟸   XM_040289201
- UniProtKB: A0A287CUA2 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSSTOP00000000272   ⟸   ENSSTOT00000000305
Ensembl Acc Id: ENSSTOP00000024877   ⟸   ENSSTOT00000042788
Protein Domains
ABC transporter


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000000294 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000000305.3 UniProtKB/TrEMBL
  ENSSTOT00000042788.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/TrEMBL
  ABC2_TM UniProtKB/TrEMBL
  ABC_transporter-like UniProtKB/TrEMBL
  ABCA UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
NCBI Gene LOC101965641 ENTREZGENE
PANTHER PTHR19229 UniProtKB/TrEMBL
  RETINAL-SPECIFIC PHOSPHOLIPID-TRANSPORTING ATPASE ABCA4 UniProtKB/TrEMBL
Pfam ABC2_membrane_3 UniProtKB/TrEMBL
  ABC_tran UniProtKB/TrEMBL
PROSITE ABC_TRANSPORTER_2 UniProtKB/TrEMBL
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A287CUA2 ENTREZGENE, UniProtKB/TrEMBL
  I3LWC8_ICTTR UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-26 Abca4  ATP binding cassette subfamily A member 4  LOC101965641  retinal-specific ATP-binding cassette transporter  Symbol and/or name change 5135510 APPROVED