Abca4 (ATP binding cassette subfamily A member 4)

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Gene: Abca4 (ATP binding cassette subfamily A member 4) Ictidomys tridecemlineatus

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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

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405058	103,621,291 - 103,978,517 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936537	5,202,093 - 5,323,527 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936537	4,969,456 - 5,326,682 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

age related macular degeneration (ISO)

Bietti crystalline corneoretinal dystrophy (ISO)

blindness (ISO)

cleft lip (ISO)

Colorectal Neoplasms (ISO)

Concentric Annular Macular Dystrophy (ISO)

cone dystrophy (ISO)

cone-rod dystrophy (ISO)

cone-rod dystrophy 3 (ISO)

congenital stationary night blindness (ISO)

exudative vitreoretinopathy (ISO)

Eye Abnormalities (ISO)

fundus dystrophy (ISO)

genetic disease (ISO)

globe disease (ISO)

Leber congenital amaurosis (ISO)

Leber congenital amaurosis 14 (ISO)

macular degeneration (ISO)

Mandibulofacial Dysostosis with Mental Deficiency (ISO)

neuropathy (ISO)

peripheral nervous system disease (ISO)

retinal degeneration (ISO)

Retinal Dystrophy, Early Onset Severe (ISO)

retinitis pigmentosa (ISO)

retinitis pigmentosa 1 (ISO)

retinitis pigmentosa 19 (ISO)

scotoma (ISO)

Stargardt disease (ISO)

Stargardt Disease 1 (ISO)

Stargardt Disease 3 (ISO)

Vision Disorders (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

lipid translocation (IEA)

lipid transport (IEA)

phospholipid transfer to membrane (IEA,ISO)

phospholipid translocation (IEA)

phospholipid transport (IEA)

photoreceptor cell maintenance (IEA,ISO)

retinal metabolic process (IEA)

transmembrane transport (IEA)

visual perception (IEA,ISO)

Cellular Component

cytoplasmic vesicle (IEA)

endoplasmic reticulum (IEA)

intracellular membrane-bounded organelle (IEA)

membrane (IEA)

photoreceptor outer segment (IEA)

Molecular Function

11-cis retinal binding (IEA)

ABC-type transporter activity (IEA)

all-trans retinal binding (IEA)

ATP binding (IEA)

ATP hydrolysis activity (IEA)

ATPase-coupled intramembrane lipid transporter activity (IEA)

ATPase-coupled transmembrane transporter activity (IEA)

flippase activity (IEA)

N-retinylidene-phosphatidylethanolamine flippase activity (IEA)

phosphatidylethanolamine flippase activity (IEA)

phospholipid transporter activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

altered retinoid cycle metabolic pathway (ISO)

retinitis pigmentosa pathway (ISO)

retinoid cycle metabolic pathway (ISO)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Abca4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405058	103,621,291 - 103,978,517 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936537	5,202,093 - 5,323,527 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936537	4,969,456 - 5,326,682 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ABCA4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	93,992,834 - 94,121,148 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	93,992,834 - 94,121,148 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	94,458,390 - 94,586,704 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	94,230,981 - 94,359,293 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	1	94,170,416 - 94,298,700	NCBI
Celera	1	92,712,080 - 92,840,399 (-)	NCBI		Celera
Cytogenetic Map	1	p22.1	NCBI
HuRef	1	92,579,378 - 92,707,578 (-)	NCBI		HuRef
CHM1_1	1	94,573,360 - 94,701,680 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	1	93,841,050 - 93,969,344 (-)	NCBI		T2T-CHM13v2.0

Abca4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	3	121,837,547 - 121,973,719 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	3	121,838,092 - 121,973,772 (+)	Ensembl		GRCm39 Ensembl
GRCm38	3	122,043,891 - 122,180,070 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	3	122,044,443 - 122,180,123 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	3	121,747,378 - 121,882,979 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	3	122,036,482 - 122,172,083 (+)	NCBI		MGSCv36	mm8
Celera	3	128,448,730 - 128,585,363 (+)	NCBI		Celera
Cytogenetic Map	3	G1	NCBI
cM Map	3	52.94	NCBI

Abca4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	2	212,849,470 - 212,986,730 (+)	NCBI		GRCr8
mRatBN7.2	2	210,164,813 - 210,302,069 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	2	210,164,813 - 210,302,069 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	2	217,837,756 - 217,975,083 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	2	215,745,511 - 215,882,846 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	2	210,587,485 - 210,724,819 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	2	225,645,539 - 225,783,288 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	2	225,645,568 - 225,783,287 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	2	243,682,218 - 243,818,930 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	218,712,663 - 218,849,896 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	2	218,675,724 - 218,812,957 (+)	NCBI
Celera	2	202,594,748 - 202,731,906 (+)	NCBI		Celera
Cytogenetic Map	2	q42	NCBI

Abca4
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955423	612,098 - 736,035 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955423	612,098 - 738,702 (+)	NCBI	ChiLan1.0	ChiLan1.0

ABCA4
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	1	132,900,976 - 133,029,375 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	132,055,894 - 132,184,432 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	96,659,703 - 96,784,876 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	95,386,263 - 95,514,589 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	95,386,266 - 95,514,589 (-)	Ensembl	panpan1.1		panPan2

ABCA4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	55,058,361 - 55,186,255 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	6	55,058,361 - 55,186,253 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	6	57,766,484 - 57,894,185 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	6	55,434,279 - 55,561,973 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	6	55,434,279 - 55,561,935 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	6	55,114,352 - 55,241,756 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	6	55,098,998 - 55,226,816 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	6	55,552,093 - 55,679,433 (+)	NCBI		UU_Cfam_GSD_1.0

ABCA4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	4	123,202,753 - 123,333,041 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	4	123,202,720 - 123,333,044 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	4	134,845,979 - 134,978,727 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

ABCA4
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	20	39,140,288 - 39,271,169 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	39,140,922 - 39,267,638 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666033	78,780,073 - 78,910,160 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Abca4
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624742	3,536,591 - 3,661,468 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624742	3,536,591 - 3,661,706 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_021728042	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040289201	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000117	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000000305 ⟹ ENSSTOP00000000272

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936537	5,202,093 - 5,323,527 (+)	Ensembl

Ensembl Acc Id:

ENSSTOT00000042788 ⟹ ENSSTOP00000024877

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936537	5,202,093 - 5,323,153 (+)	Ensembl

RefSeq Acc Id:

XM_040289201 ⟹ XP_040145135

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024405058	103,621,291 - 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

External Database Links

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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations