Abca13 (ATP binding cassette subfamily A member 13) - Rat Genome Database

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Gene: Abca13 (ATP binding cassette subfamily A member 13) Rattus norvegicus
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Symbol: Abca13
Name: ATP binding cassette subfamily A member 13
RGD ID: 1305895
Description: Predicted to enable ATPase-coupled transmembrane transporter activity and lipid transporter activity. Predicted to be involved in ceramide transport; positive regulation of cholesterol transport; and positive regulation of synaptic vesicle endocytosis. Predicted to be located in intracellular vesicle. Human ortholog(s) of this gene implicated in gastric adenocarcinoma. Orthologous to human ABCA13 (ATP binding cassette subfamily A member 13); INTERACTS WITH acetamide; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: ATP-binding cassette sub-family A member 13; ATP-binding cassette, sub-family A (ABC1), member 13; ATP-binding cassette, subfamily A (ABC1), member 13; LOC289797
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
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
GRCr81488,087,146 - 88,589,868 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1488,087,801 - 88,589,392 (+)EnsemblGRCr8
mRatBN7.21483,873,397 - 84,376,138 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1483,873,940 - 84,375,075 (+)EnsemblmRatBN7.2
Rnor_6.01489,384,512 - 89,876,748 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1489,384,512 - 89,714,917 (+)Ensemblrn6Rnor6.0
Rnor_5.01489,181,315 - 89,673,490 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41489,714,129 - 90,226,523 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1482,904,207 - 83,402,514 (+)NCBICelera
RGSC_v3.11489,733,273 - 90,245,668 (+)NCBI
Cytogenetic Map14q21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Recurrent amplification of RTEL1 and ABCA13 and its synergistic effect associated with clinicopathological data of gastric adenocarcinoma. Araújo TM, etal., Mol Cytogenet. 2016 Jun 29;9:52. doi: 10.1186/s13039-016-0260-x. eCollection 2016.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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

Genomics

Comparative Map Data
Abca13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81488,087,146 - 88,589,868 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1488,087,801 - 88,589,392 (+)EnsemblGRCr8
mRatBN7.21483,873,397 - 84,376,138 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1483,873,940 - 84,375,075 (+)EnsemblmRatBN7.2
Rnor_6.01489,384,512 - 89,876,748 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1489,384,512 - 89,714,917 (+)Ensemblrn6Rnor6.0
Rnor_5.01489,181,315 - 89,673,490 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41489,714,129 - 90,226,523 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1482,904,207 - 83,402,514 (+)NCBICelera
RGSC_v3.11489,733,273 - 90,245,668 (+)NCBI
Cytogenetic Map14q21NCBI
ABCA13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38748,171,458 - 48,647,497 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl748,171,458 - 48,647,497 (+)Ensemblhg38GRCh38
GRCh37748,211,055 - 48,687,093 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36748,208,389 - 48,657,637 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34748,015,103 - 48,464,352NCBI
Celera748,310,673 - 48,789,160 (+)NCBICelera
Cytogenetic Map7p12.3NCBI
HuRef748,123,477 - 48,573,410 (+)NCBIHuRef
CHM1_1748,214,726 - 48,691,744 (+)NCBICHM1_1
T2T-CHM13v2.0748,333,668 - 48,808,476 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2748,250,847 - 48,729,205 (+)NCBI
Abca13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39119,141,942 - 9,634,871 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl119,141,942 - 9,634,259 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38119,191,942 - 9,684,871 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl119,191,942 - 9,684,259 (+)Ensemblmm10GRCm38
MGSCv37119,091,945 - 9,584,262 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36119,091,945 - 9,584,854 (+)NCBIMGSCv36mm8
Celera119,626,362 - 10,117,712 (+)NCBICelera
Cytogenetic Map11A1NCBI
cM Map116.13NCBI
Abca13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554564,978,027 - 5,341,242 (-)Ensembl
ChiLan1.0NW_0049554564,977,504 - 5,341,259 (-)NCBIChiLan1.0ChiLan1.0
ABCA13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2653,046,782 - 53,560,530 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17101,371,604 - 101,847,546 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0748,812,624 - 49,288,605 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1748,920,381 - 49,395,168 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl748,920,381 - 49,393,235 (+)EnsemblpanPan2panpan1.1
ABCA13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.118136,338 - 353,974 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl18135,690 - 352,871 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha18105,137 - 345,216 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.018170,886 - 410,247 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl18190,807 - 409,144 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.118145,704 - 385,777 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.018148,601 - 382,649 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.018283,754 - 516,659 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC100514786
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9135,115,078 - 135,451,812 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.19135,104,047 - 135,452,477 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29148,623,167 - 148,905,164 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ABCA13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12110,124,078 - 10,618,136 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2110,124,126 - 10,616,750 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606211,615,711 - 12,116,107 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Abca13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247405,114,019 - 5,488,385 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247405,112,422 - 5,488,394 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Abca13
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11178,232,591 - 78,796,827 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Abca13
3787 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:1048
Count of miRNA genes:346
Interacting mature miRNAs:479
Transcripts:ENSRNOT00000035612
Prediction methods:Microtar, Miranda, 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
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1459848686104848686Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147764007196755654Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)1484164970100078267Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1477914838104348525Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1474255551109089856Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147764007196755654Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1477640071100078267Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1460854936105854936Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1474255551109089856Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)1486271332100078267Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147764007196755654Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1459848686104848686Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147764007196755654Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144261625899224555Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)146592028399224555Rat

Markers in Region
AI843389  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21483,993,364 - 83,993,460 (+)MAPPERmRatBN7.2
mRatBN7.2214,793,436 - 14,793,532 (+)MAPPERmRatBN7.2
Rnor_6.01489,503,731 - 89,503,826NCBIRnor6.0
Rnor_5.01489,300,131 - 89,300,226UniSTSRnor5.0
RGSC_v3.41489,833,777 - 89,833,872UniSTSRGSC3.4
Celera1483,023,003 - 83,023,098UniSTS
Cytogenetic Map14q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
2 2 10 62 38 40 23 41 23 106 63 11 51 17 60 17 11 11

Sequence


Ensembl Acc Id: ENSRNOT00000035612   ⟹   ENSRNOP00000030281
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1483,873,940 - 84,375,075 (+)Ensembl
Rnor_6.0 Ensembl1489,384,512 - 89,714,917 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101007   ⟹   ENSRNOP00000088943
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1483,873,940 - 84,375,075 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000107084   ⟹   ENSRNOP00000095482
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1488,087,801 - 88,589,392 (+)Ensembl
mRatBN7.2 Ensembl1483,874,044 - 84,375,075 (+)Ensembl
RefSeq Acc Id: XM_063273790   ⟹   XP_063129860
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81488,087,146 - 88,589,868 (+)NCBI
Protein Sequences
Protein RefSeqs XP_063129860 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76043 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000095482
  ENSRNOP00000095482.2
Ensembl Acc Id: ENSRNOP00000030281   ⟸   ENSRNOT00000035612
Ensembl Acc Id: ENSRNOP00000095482   ⟸   ENSRNOT00000107084
Ensembl Acc Id: ENSRNOP00000088943   ⟸   ENSRNOT00000101007
RefSeq Acc Id: XP_063129860   ⟸   XM_063273790
- UniProtKB: A0A8I6ABQ0 (UniProtKB/TrEMBL)

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:1305895 AgrOrtholog
BioCyc Gene G2FUF-15019 BioCyc
Ensembl Genes ENSRNOG00000025645 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000107084 ENTREZGENE
  ENSRNOT00000107084.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/TrEMBL
  ABC2_TM UniProtKB/TrEMBL
  ABC_A UniProtKB/TrEMBL
  ABC_transporter-like UniProtKB/TrEMBL
  ABC_transporter_CS UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
NCBI Gene 289797 ENTREZGENE
PANTHER ATP-BINDING CASSETTE SUB-FAMILY A MEMBER 13 UniProtKB/TrEMBL
  PTHR19229 UniProtKB/TrEMBL
Pfam ABC2_membrane_3 UniProtKB/TrEMBL
  ABC_tran UniProtKB/TrEMBL
PhenoGen Abca13 PhenoGen
PROSITE ABC_TRANSPORTER_1 UniProtKB/TrEMBL
  ABC_TRANSPORTER_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025645 RatGTEx
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A8I6ABQ0 ENTREZGENE
  A0A8I6ALI8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Abca13  ATP binding cassette subfamily A member 13  Abca13  ATP-binding cassette, subfamily A (ABC1), member 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-11-16 Abca13  ATP-binding cassette, subfamily A (ABC1), member 13  Abca13  ATP-binding cassette, sub-family A (ABC1), member 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Abca13  ATP-binding cassette, sub-family A (ABC1), member 13   Abca13_predicted  ATP-binding cassette, sub-family A (ABC1), member 13 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Abca13_predicted  ATP-binding cassette, sub-family A (ABC1), member 13 (predicted)      Symbol and Name status set to approved 70820 APPROVED