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
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Symbol: ABCA2
Name: ATP binding cassette subfamily A member 2
RGD ID: 12316055
Description: ENCODES a protein that exhibits ATP binding (ortholog); ceramide floppase activity (ortholog); endopeptidase regulator activity (ortholog); INVOLVED IN cellular sphingolipid homeostasis (ortholog); central nervous system myelin formation (ortholog); ceramide translocation (ortholog); ASSOCIATED WITH autosomal dominant non-syndromic intellectual disability 8 (ortholog); Candidiasis, Familial, 2 (ortholog); developmental and epileptic encephalopathy 14 (ortholog); FOUND IN cytoplasmic vesicle (ortholog); endosome (ortholog); endosome membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Also known as: ATP-binding cassette sub-family A member 2; LOW QUALITY PROTEIN: 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 (+)NCBI
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBI
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBI
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBI
UU_Cfam_GSD_1.0948,611,199 - 48,631,304 (+)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular sphingolipid homeostasis  (ISO)
central nervous system myelin formation  (ISO)
ceramide translocation  (ISO)
cholesterol homeostasis  (ISO)
ganglioside metabolic process  (ISO)
glycosphingolipid metabolic process  (ISO)
locomotory behavior  (ISO)
negative regulation of cholesterol efflux  (ISO)
negative regulation of cholesterol esterification  (ISO)
negative regulation of intracellular cholesterol transport  (ISO)
negative regulation of low-density lipoprotein receptor activity  (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)
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 cholesterol esterification  (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 transcription by RNA polymerase II  (ISO)
response to cholesterol  (ISO)
response to steroid hormone  (ISO)
sphingomyelin metabolic process  (ISO)
sphingosine biosynthetic process  (ISO)

Cellular Component

Molecular Function

References

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 (+)NCBI
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBI
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBI
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBI
UU_Cfam_GSD_1.0948,611,199 - 48,631,304 (+)NCBI
ABCA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9137,007,234 - 137,028,922 (-)EnsemblGRCh38hg38GRCh38
GRCh389137,007,234 - 137,028,922 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379139,901,686 - 139,923,374 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,021,507 - 139,043,195 (-)NCBINCBI36hg18NCBI36
Build 349137,177,522 - 137,199,211NCBI
Celera9110,414,121 - 110,431,191 (-)NCBI
Cytogenetic Map9q34.3NCBI
HuRef9109,360,841 - 109,382,226 (-)NCBIHuRef
CHM1_19140,050,436 - 140,072,137 (-)NCBICHM1_1
Abca2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,318,611 - 25,338,556 (+)NCBIGRCm39mm39
GRCm39 Ensembl225,318,715 - 25,338,552 (+)Ensembl
GRCm38225,428,599 - 25,448,544 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,428,703 - 25,448,540 (+)EnsemblGRCm38mm10GRCm38
MGSCv37225,284,194 - 25,304,059 (+)NCBIGRCm37mm9NCBIm37
MGSCv36225,250,779 - 25,270,208 (+)NCBImm8
Celera225,156,185 - 25,176,102 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.25NCBI
Abca2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.238,244,515 - 8,264,545 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl38,244,639 - 8,264,537 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
PanPan1.19137,039,264 - 137,057,527 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,036,696 - 137,057,776 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09108,067,633 - 108,089,742 (-)NCBIMhudiblu_PPA_v0panPan3
Abca2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,433,062 - 202,454,661 (-)NCBI
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 (+)NCBI
ChlSab1.1 Ensembl121,162,865 - 1,183,113 (+)Ensembl
Vero_WHO_p1.0NW_0236660584,118,329 - 4,134,713 (-)NCBI
Abca2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624760880,216 - 898,753 (+)NCBI


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
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl948,613,996 - 48,629,857 (+)Ensembl
RefSeq Acc Id: XM_014116866   ⟹   XP_013972341
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1948,610,906 - 48,630,932 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038486823   ⟹   XP_038342751
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBI
RefSeq Acc Id: XM_038486824   ⟹   XP_038342752
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBI
RefSeq Acc Id: XM_038486825   ⟹   XP_038342753
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1948,265,133 - 48,285,232 (+)NCBI
RefSeq Acc Id: XM_038548692   ⟹   XP_038404620
RefSeq Status:
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
RefSeq Status:
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
RefSeq Status:
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
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBI
RefSeq Acc Id: XM_038612628   ⟹   XP_038468556
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBI
RefSeq Acc Id: XM_038612629   ⟹   XP_038468557
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0948,563,850 - 48,583,927 (+)NCBI
RefSeq Acc Id: XM_038614392   ⟹   XP_038470320
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha947,824,500 - 47,844,585 (+)NCBI
RefSeq Acc Id: XM_038614399   ⟹   XP_038470327
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha947,824,500 - 47,844,585 (+)NCBI
RefSeq Acc Id: XM_038614408   ⟹   XP_038470336
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha947,824,500 - 47,844,585 (+)NCBI
RefSeq Acc Id: XM_038677914   ⟹   XP_038533842
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBI
RefSeq Acc Id: XM_038677915   ⟹   XP_038533843
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBI
RefSeq Acc Id: XM_038677916   ⟹   XP_038533844
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0949,488,905 - 49,509,018 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_013972341   ⟸   XM_014116866
- Sequence:
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
RefSeq Acc Id: XP_038533844   ⟸   XM_038677916
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038533843   ⟸   XM_038677915
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038470320   ⟸   XM_038614392
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038470336   ⟸   XM_038614408
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038470327   ⟸   XM_038614399
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038404620   ⟸   XM_038548692
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038404622   ⟸   XM_038548694
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038404621   ⟸   XM_038548693
- Peptide Label: isoform X2

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, ENTREZGENE
NCBI Gene ABCA2 ENTREZGENE
VGNC ID VGNC:37425 ENTREZGENE