Abca12 (ATP binding cassette subfamily A member 12) - Rat Genome Database

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Gene: Abca12 (ATP binding cassette subfamily A member 12) Rattus norvegicus
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Symbol: Abca12
Name: ATP binding cassette subfamily A member 12
RGD ID: 1304586
Description: Predicted to enable ATPase-coupled transmembrane transporter activity; apolipoprotein A-I receptor binding activity; and lipid transporter activity. Predicted to be involved in several processes, including corneocyte desquamation; phospholipid efflux; and positive regulation of intracellular lipid transport. Predicted to act upstream of or within several processes, including establishment of skin barrier; positive regulation of cholesterol efflux; and positive regulation of protein localization to cell surface. Predicted to be located in bounding membrane of organelle; cytosol; and plasma membrane. Human ortholog(s) of this gene implicated in autosomal recessive congenital ichthyosis 1; autosomal recessive congenital ichthyosis 4A; and autosomal recessive congenital ichthyosis 4B. Orthologous to human ABCA12 (ATP binding cassette subfamily A member 12); INTERACTS WITH bisphenol A; gentamycin; paracetamol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: ATP-binding cassette sub-family A member 12; ATP-binding cassette, sub-family A (ABC1), member 12; ATP-binding cassette, subfamily A (ABC1), member 12; glucosylceramide transporter ABCA12; LOC301482
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8980,272,121 - 80,445,340 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl980,272,127 - 80,445,340 (-)EnsemblGRCr8
mRatBN7.2972,822,661 - 72,995,748 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl972,823,350 - 72,996,049 (-)EnsemblmRatBN7.2
Rnor_6.0978,521,477 - 78,693,421 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl978,522,464 - 78,693,028 (-)Ensemblrn6Rnor6.0
Rnor_5.0978,296,546 - 78,466,160 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4970,328,327 - 70,501,128 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera970,239,719 - 70,413,488 (-)NCBICelera
RGSC_v3.1970,475,308 - 70,648,110 (-)NCBI
Cytogenetic Map9q33NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Mutations in the transporter ABCA12 are associated with lamellar ichthyosis type 2. Lefevre C, etal., Hum Mol Genet. 2003 Sep 15;12(18):2369-78. Epub 2003 Jul 15.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12865426   PMID:16007253   PMID:18632686   PMID:18802465   PMID:18957418   PMID:23931754  


Genomics

Comparative Map Data
Abca12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8980,272,121 - 80,445,340 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl980,272,127 - 80,445,340 (-)EnsemblGRCr8
mRatBN7.2972,822,661 - 72,995,748 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl972,823,350 - 72,996,049 (-)EnsemblmRatBN7.2
Rnor_6.0978,521,477 - 78,693,421 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl978,522,464 - 78,693,028 (-)Ensemblrn6Rnor6.0
Rnor_5.0978,296,546 - 78,466,160 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4970,328,327 - 70,501,128 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera970,239,719 - 70,413,488 (-)NCBICelera
RGSC_v3.1970,475,308 - 70,648,110 (-)NCBI
Cytogenetic Map9q33NCBI
ABCA12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382214,931,542 - 215,138,626 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2214,931,542 - 215,138,626 (-)Ensemblhg38GRCh38
GRCh372215,796,266 - 216,003,349 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362215,504,511 - 215,711,396 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342215,621,772 - 215,828,657NCBI
Celera2209,565,986 - 209,772,883 (-)NCBICelera
Cytogenetic Map2q35NCBI
HuRef2207,652,444 - 207,860,132 (-)NCBIHuRef
CHM1_12215,801,932 - 216,008,974 (-)NCBICHM1_1
T2T-CHM13v2.02215,416,237 - 215,623,360 (-)NCBIT2T-CHM13v2.0
Abca12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39171,282,249 - 71,454,069 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl171,281,435 - 71,454,069 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38171,243,090 - 71,414,910 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl171,242,276 - 71,414,910 (-)Ensemblmm10GRCm38
MGSCv37171,289,664 - 71,461,484 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36171,176,298 - 71,348,118 (-)NCBIMGSCv36mm8
Celera171,798,849 - 71,970,916 (-)NCBICelera
Cytogenetic Map1C3NCBI
cM Map135.81NCBI
Abca12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955457879,510 - 1,062,713 (+)Ensembl
ChiLan1.0NW_004955457885,941 - 1,062,713 (+)NCBIChiLan1.0ChiLan1.0
ABCA12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213117,561,295 - 117,675,718 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B117,576,162 - 117,783,122 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B102,194,286 - 102,401,175 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B220,668,359 - 220,873,566 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B220,668,957 - 220,873,566 (-)EnsemblpanPan2panpan1.1
ABCA12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13722,136,732 - 22,306,917 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3722,138,245 - 22,405,736 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3722,965,092 - 23,134,494 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03722,160,884 - 22,330,640 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3722,161,609 - 22,374,148 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13722,049,739 - 22,219,457 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03722,001,062 - 22,170,768 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03722,017,286 - 22,187,312 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Abca12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303170,531,373 - 170,687,485 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365861,938,617 - 2,094,279 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365861,938,617 - 2,094,231 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCA12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15117,245,720 - 117,450,664 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.115117,244,704 - 117,451,009 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215129,788,302 - 129,879,763 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ABCA12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110100,759,196 - 100,972,307 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10100,759,225 - 100,888,912 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604098,407,554 - 98,614,915 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Abca12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247651,010,287 - 1,197,910 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247651,009,883 - 1,198,225 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Abca12
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14144,799,599 - 144,969,438 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Abca12
1190 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:65
Interacting mature miRNAs:67
Transcripts:ENSRNOT00000036359, ENSRNOT00000057672
Prediction methods:Microtar, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)94002992585029925Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)94445825685262605Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92956766483835942Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)94172029586720295Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1581517Bp284Blood pressure QTL 284arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)93922018684220186Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)94002992585029925Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat

Markers in Region
D9Mit11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2972,829,908 - 72,830,156 (+)MAPPERmRatBN7.2
Rnor_6.0978,528,736 - 78,528,983NCBIRnor6.0
Rnor_5.0978,303,111 - 78,303,358UniSTSRnor5.0
RGSC_v3.4970,334,583 - 70,334,831RGDRGSC3.4
RGSC_v3.4970,334,584 - 70,334,831UniSTSRGSC3.4
Celera970,246,956 - 70,247,191UniSTS
RGSC_v3.1970,481,501 - 70,481,924RGD
Cytogenetic Map9q33UniSTS
D9Rat95  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8980,349,577 - 80,349,795 (+)Marker Load Pipeline
mRatBN7.2972,900,112 - 72,900,329 (+)MAPPERmRatBN7.2
Rnor_6.0978,599,503 - 78,599,719NCBIRnor6.0
Rnor_5.0978,373,334 - 78,373,550UniSTSRnor5.0
RGSC_v3.4970,405,095 - 70,405,519RGDRGSC3.4
RGSC_v3.4970,405,175 - 70,405,391UniSTSRGSC3.4
Celera970,318,054 - 70,318,269UniSTS
RGSC_v3.1970,552,077 - 70,552,501RGD
RH 3.4 Map9670.0UniSTS
RH 3.4 Map9670.0RGD
RH 2.0 Map9725.5RGD
FHH x ACI Map947.12RGD
Cytogenetic Map9q33UniSTS
D9Got84  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2972,903,974 - 72,904,106 (+)MAPPERmRatBN7.2
Rnor_6.0978,603,365 - 78,603,496NCBIRnor6.0
Rnor_5.0978,377,196 - 78,377,327UniSTSRnor5.0
RGSC_v3.4970,409,036 - 70,409,168RGDRGSC3.4
RGSC_v3.4970,409,037 - 70,409,168UniSTSRGSC3.4
Celera970,321,915 - 70,322,044UniSTS
RGSC_v3.1970,556,019 - 70,556,150RGD
RH 3.4 Map9664.4UniSTS
RH 3.4 Map9664.4RGD
RH 2.0 Map9720.0RGD
Cytogenetic Map9q33UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
13 2 11 89 32 36 10 25 10 6 97 44 78 28 55 26 7 7

Sequence


Ensembl Acc Id: ENSRNOT00000036359   ⟹   ENSRNOP00000034671
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl978,585,500 - 78,693,028 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000057672   ⟹   ENSRNOP00000054481
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl980,272,127 - 80,445,340 (-)Ensembl
mRatBN7.2 Ensembl972,823,350 - 72,996,049 (-)Ensembl
Rnor_6.0 Ensembl978,522,464 - 78,607,307 (-)Ensembl
RefSeq Acc Id: NM_001427691   ⟹   NP_001414620
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8980,272,127 - 80,445,340 (-)NCBI
RefSeq Acc Id: XM_039084630   ⟹   XP_038940558
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8980,272,121 - 80,320,656 (-)NCBI
mRatBN7.2972,822,661 - 72,872,910 (-)NCBI
RefSeq Acc Id: XM_039084631   ⟹   XP_038940559
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8980,272,121 - 80,320,693 (-)NCBI
mRatBN7.2972,822,661 - 72,872,910 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414620 (Get FASTA)   NCBI Sequence Viewer  
  XP_038940558 (Get FASTA)   NCBI Sequence Viewer  
  XP_038940559 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000054481
  ENSRNOP00000054481.5
Ensembl Acc Id: ENSRNOP00000054481   ⟸   ENSRNOT00000057672
Ensembl Acc Id: ENSRNOP00000034671   ⟸   ENSRNOT00000036359
RefSeq Acc Id: XP_038940559   ⟸   XM_039084631
- Peptide Label: isoform X2
- UniProtKB: A6KFG0 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038940558   ⟸   XM_039084630
- Peptide Label: isoform X1
- UniProtKB: A6KFG0 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001414620   ⟸   NM_001427691
- UniProtKB: D4A7J3 (UniProtKB/TrEMBL)
Protein Domains
ABC transporter

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A7J3-F1-model_v2 AlphaFold D4A7J3 1-2269 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304586 AgrOrtholog
BioCyc Gene G2FUF-27252 BioCyc
Ensembl Genes ENSRNOG00000015248 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057672 ENTREZGENE
  ENSRNOT00000057672.7 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro ABC2_TM UniProtKB/TrEMBL
  ABC_A UniProtKB/TrEMBL
  ABC_transporter-like UniProtKB/TrEMBL
  ABC_transporter_CS UniProtKB/TrEMBL
  ATPase_AAA+_core UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  R2_ABCA1-4-like UniProtKB/TrEMBL
NCBI Gene 301482 ENTREZGENE
PANTHER ABC TRANSPORTER DOMAIN-CONTAINING PROTEIN-RELATED UniProtKB/TrEMBL
  PTHR19229 UniProtKB/TrEMBL
Pfam ABC2_membrane_3 UniProtKB/TrEMBL
  ABC_tran UniProtKB/TrEMBL
  R1_ABCA1 UniProtKB/TrEMBL
PhenoGen Abca12 PhenoGen
PROSITE ABC_TRANSPORTER_1 UniProtKB/TrEMBL
  ABC_TRANSPORTER_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000015248 RatGTEx
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A6KFG0 ENTREZGENE, UniProtKB/TrEMBL
  D4A7J3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-16 Abca12  ATP binding cassette subfamily A member 12  Abca12  ATP-binding cassette, subfamily A (ABC1), member 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-11-16 Abca12  ATP-binding cassette, subfamily A (ABC1), member 12  Abca12  ATP-binding cassette, sub-family A (ABC1), member 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Abca12  ATP-binding cassette, sub-family A (ABC1), member 12   Abca12_predicted  ATP-binding cassette, sub-family A (ABC1), member 12 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Abca12_predicted  ATP-binding cassette, sub-family A (ABC1), member 12 (predicted)      Symbol and Name status set to approved 70820 APPROVED