ABCA2 (ATP binding cassette subfamily A member 2) - Rat Genome Database

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Gene: ABCA2 (ATP binding cassette subfamily A member 2) Canis lupus familiaris
Analyze
Symbol: ABCA2
Name: ATP binding cassette subfamily A member 2
RGD ID: 12316055
Description: ENCODES a protein that exhibits ceramide floppase activity (ortholog); endopeptidase regulator activity (ortholog); INVOLVED IN central nervous system myelin formation (ortholog); ceramide translocation (ortholog); cholesterol homeostasis (ortholog); ASSOCIATED WITH Adams-Oliver Syndrome 5 (ortholog); autism spectrum disorder (ortholog); autosomal dominant intellectual developmental disorder 8 (ortholog); FOUND IN cytoplasmic vesicle (ortholog); endosome (ortholog); endosome membrane (ortholog)
Type: protein-coding (Ensembl: pseudogene)
RefSeq Status: MODEL
Previously known as: ATP-binding cassette sub-family A member 2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,610,906 - 48,630,932 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl948,613,996 - 48,629,857 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha947,824,500 - 47,844,585 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,611,199 - 48,631,304 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
central nervous system myelin formation  (ISO)
ceramide translocation  (ISO)
cholesterol homeostasis  (ISO)
ganglioside metabolic process  (ISO)
glycosphingolipid metabolic process  (ISO)
intracellular sphingolipid homeostasis  (ISO)
lipid transport  (IEA)
locomotory behavior  (ISO)
negative regulation of cholesterol efflux  (ISO)
negative regulation of intracellular cholesterol transport  (ISO)
negative regulation of phospholipid biosynthetic process  (ISO)
negative regulation of receptor-mediated endocytosis involved in cholesterol transport  (ISO)
negative regulation of sphingolipid biosynthetic process  (ISO)
negative regulation of steroid metabolic process  (ISO)
positive regulation of amyloid precursor protein biosynthetic process  (ISO)
positive regulation of amyloid precursor protein catabolic process  (ISO)
positive regulation of amyloid-beta formation  (ISO)
positive regulation of low-density lipoprotein particle receptor catabolic process  (ISO)
regulation of cholesterol biosynthetic process  (ISO)
regulation of intracellular cholesterol transport  (ISO)
regulation of post-translational protein modification  (ISO)
regulation of protein glycosylation  (ISO)
regulation of protein localization to cell periphery  (ISO)
regulation of protein localization to cell surface  (ISO)
regulation of steroid metabolic process  (ISO)
response to cholesterol  (ISO)
response to steroid hormone  (ISO)
sphingomyelin metabolic process  (ISO)
sphingosine biosynthetic process  (ISO)
transmembrane transport  (IEA)

Cellular Component

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
ABCA2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,610,906 - 48,630,932 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl948,613,996 - 48,629,857 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha947,824,500 - 47,844,585 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,611,199 - 48,631,304 (+)NCBIUU_Cfam_GSD_1.0
ABCA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389137,007,234 - 137,028,922 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9137,007,234 - 137,028,915 (-)EnsemblGRCh38hg38GRCh38
GRCh379139,901,686 - 139,923,374 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,021,507 - 139,043,195 (-)NCBINCBI36Build 36hg18NCBI36
Build 349137,177,522 - 137,199,211NCBI
Celera9110,414,121 - 110,431,191 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,360,841 - 109,382,226 (-)NCBIHuRef
CHM1_19140,050,436 - 140,072,137 (-)NCBICHM1_1
T2T-CHM13v2.09149,241,651 - 149,263,357 (-)NCBIT2T-CHM13v2.0
Abca2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,318,611 - 25,338,556 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,318,715 - 25,338,552 (+)EnsemblGRCm39 Ensembl
GRCm38225,428,599 - 25,448,544 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,428,703 - 25,448,540 (+)EnsemblGRCm38mm10GRCm38
MGSCv37225,284,194 - 25,304,059 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,250,779 - 25,270,208 (+)NCBIMGSCv36mm8
Celera225,156,185 - 25,176,102 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.25NCBI
Abca2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,642,660 - 28,662,689 (+)NCBIGRCr8
mRatBN7.238,244,515 - 8,264,545 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,244,639 - 8,264,537 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,349,736 - 11,369,666 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,935,958 - 19,955,888 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,125,806 - 18,145,736 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,648,787 - 2,668,770 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,648,885 - 2,668,809 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,630,237 - 2,650,183 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,595,423 - 3,615,328 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,595,422 - 3,615,327 (+)NCBI
Celera33,069,743 - 3,089,646 (+)NCBICelera
Cytogenetic Map3p13NCBI
Abca2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,033,771 - 5,051,200 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,035,879 - 5,051,140 (-)NCBIChiLan1.0ChiLan1.0
ABCA2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2112,369,797 - 2,391,636 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan192,372,769 - 2,393,970 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09108,067,633 - 108,089,742 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19137,039,264 - 137,057,527 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,036,696 - 137,057,776 (-)Ensemblpanpan1.1panPan2
Abca2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,433,062 - 202,454,661 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936669926,622 - 942,167 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936669922,978 - 941,996 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCA2
(Sus scrofa - pig)		 No map positions available.
ABCA2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,161,340 - 1,183,807 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl121,162,865 - 1,183,113 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660584,118,329 - 4,134,713 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Abca2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624760880,148 - 898,751 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624760880,216 - 898,753 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in ABCA2
150 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 3 14 6 6 12 10 3
Low 2 5 8 6 6 6 8 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_014116866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038486823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038486824 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038486825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038548692 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038548693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038548694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038612627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038612628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038612629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038614392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038614399 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038614408 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038677914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038677915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038677916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCAFT00000031220
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl948,613,996 - 48,629,857 (+)Ensembl
RefSeq Acc Id: XM_038486823   ⟹   XP_038342751
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBI
RefSeq Acc Id: XM_038486824   ⟹   XP_038342752
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBI
RefSeq Acc Id: XM_038486825   ⟹   XP_038342753
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBI
RefSeq Acc Id: XM_038548692   ⟹   XP_038404620
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0948,611,199 - 48,631,304 (+)NCBI
RefSeq Acc Id: XM_038548693   ⟹   XP_038404621
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0948,611,199 - 48,631,304 (+)NCBI
RefSeq Acc Id: XM_038548694   ⟹   XP_038404622
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0948,611,199 - 48,631,304 (+)NCBI
RefSeq Acc Id: XM_038612627   ⟹   XP_038468555
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBI
RefSeq Acc Id: XM_038612628   ⟹   XP_038468556
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBI
RefSeq Acc Id: XM_038612629   ⟹   XP_038468557
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBI
RefSeq Acc Id: XM_038614392   ⟹   XP_038470320
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha947,824,500 - 47,844,585 (+)NCBI
RefSeq Acc Id: XM_038614399   ⟹   XP_038470327
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha947,824,500 - 47,844,585 (+)NCBI
RefSeq Acc Id: XM_038614408   ⟹   XP_038470336
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha947,824,500 - 47,844,585 (+)NCBI
RefSeq Acc Id: XM_038677914   ⟹   XP_038533842
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBI
RefSeq Acc Id: XM_038677915   ⟹   XP_038533843
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBI
RefSeq Acc Id: XM_038677916   ⟹   XP_038533844
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_038342751   ⟸   XM_038486823
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038342753   ⟸   XM_038486825
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038342752   ⟸   XM_038486824
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038468555   ⟸   XM_038612627
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038468557   ⟸   XM_038612629
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038468556   ⟸   XM_038612628
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038533842   ⟸   XM_038677914
- Peptide Label: isoform X1
- UniProtKB: A0A8P0TTP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038533844   ⟸   XM_038677916
- Peptide Label: isoform X3
- UniProtKB: A0A8P0TTP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038533843   ⟸   XM_038677915
- Peptide Label: isoform X2
- UniProtKB: A0A8P0PFE8 (UniProtKB/TrEMBL),   A0A8P0TTP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038470320   ⟸   XM_038614392
- Peptide Label: isoform X1
- UniProtKB: A0A8P0TTP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038470336   ⟸   XM_038614408
- Peptide Label: isoform X3
- UniProtKB: A0A8P0TTP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038470327   ⟸   XM_038614399
- Peptide Label: isoform X2
- UniProtKB: A0A8P0PFE8 (UniProtKB/TrEMBL),   A0A8P0TTP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038404620   ⟸   XM_038548692
- Peptide Label: isoform X1
- UniProtKB: A0A8P0TTP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038404622   ⟸   XM_038548694
- Peptide Label: isoform X3
- UniProtKB: A0A8P0TTP5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038404621   ⟸   XM_038548693
- Peptide Label: isoform X2
- UniProtKB: A0A8P0PFE8 (UniProtKB/TrEMBL),   A0A8P0TTP5 (UniProtKB/TrEMBL)
Protein Domains
ABC transporter

Promoters
RGD ID:13684749
Promoter ID:EPDNEW_C2817
Type:multiple initiation site
Name:ABCA2_1
Description:ATP binding cassette subfamily A member 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1948,610,884 - 48,610,944EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000023212 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030004739 UniProtKB/TrEMBL
  ENSCAFG00040013461 UniProtKB/TrEMBL
  ENSCAFG00845025386 ENTREZGENE
Ensembl Transcript ENSCAFT00000031220.5 UniProtKB/TrEMBL
  ENSCAFT00000099855.1 UniProtKB/TrEMBL
  ENSCAFT00000109637.1 UniProtKB/TrEMBL
  ENSCAFT00030008734.1 UniProtKB/TrEMBL
  ENSCAFT00040024869.1 UniProtKB/TrEMBL
  ENSCAFT00845044828 ENTREZGENE
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/TrEMBL
  ABC2_TM UniProtKB/TrEMBL
  ABC_transporter-like_ATP-bd UniProtKB/TrEMBL
  ABC_transporter-like_CS UniProtKB/TrEMBL
  ABCA UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
NCBI Gene ABCA2 ENTREZGENE
PANTHER ATP-BINDING CASSETTE SUB-FAMILY A MEMBER 2 UniProtKB/TrEMBL
  ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA UniProtKB/TrEMBL
Pfam ABC2_membrane_3 UniProtKB/TrEMBL
  ABC_tran UniProtKB/TrEMBL
PROSITE ABC_TRANSPORTER_1 UniProtKB/TrEMBL
  ABC_TRANSPORTER_2 UniProtKB/TrEMBL
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP P-loop containing nucleoside triphosphate hydrolases UniProtKB/TrEMBL
UniProt A0A8C0SHW5_CANLF UniProtKB/TrEMBL
  A0A8P0PFE8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0TL98_CANLF UniProtKB/TrEMBL
  A0A8P0TTP5 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:37425 ENTREZGENE