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

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Pathways
Gene: Abca13 (ATP binding cassette subfamily A member 13) Rattus norvegicus
Analyze
Symbol: Abca13
Name: ATP binding cassette subfamily A member 13
RGD ID: 1305895
Description: Predicted to enable ABC-type transporter activity; ATP binding activity; and ATP hydrolysis 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21483,873,397 - 84,376,138 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1483,873,940 - 84,375,075 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01489,384,512 - 89,876,748 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1489,384,512 - 89,714,917 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01489,181,315 - 89,673,490 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41489,714,129 - 90,226,523 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11489,733,273 - 90,245,668 (+)NCBI
Celera1482,904,207 - 83,402,514 (+)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

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. Ara├║jo 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
mRatBN7.21483,873,397 - 84,376,138 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1483,873,940 - 84,375,075 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01489,384,512 - 89,876,748 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1489,384,512 - 89,714,917 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01489,181,315 - 89,673,490 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41489,714,129 - 90,226,523 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11489,733,273 - 90,245,668 (+)NCBI
Celera1482,904,207 - 83,402,514 (+)NCBICelera
Cytogenetic Map14q21NCBI
ABCA13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38748,171,458 - 48,647,497 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl748,171,458 - 48,647,497 (+)EnsemblGRCh38hg38GRCh38
GRCh37748,211,055 - 48,687,093 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36748,208,389 - 48,657,637 (+)NCBINCBI36Build 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 Ensembl
GRCm38119,191,942 - 9,684,871 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl119,191,942 - 9,684,259 (+)EnsemblGRCm38mm10GRCm38
MGSCv37119,091,945 - 9,584,262 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36119,091,945 - 9,584,854 (+)NCBIMGSCv36mm8
Celera119,626,362 - 10,117,712 (+)NCBICelera
Cytogenetic Map11A1NCBI
Abca13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554564,978,027 - 5,341,242 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554564,977,504 - 5,341,259 (-)NCBIChiLan1.0ChiLan1.0
ABCA13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan17101,371,630 - 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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha18105,137 - 345,216 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.018170,886 - 410,247 (+)NCBIROS_Cfam_1.0
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_1.0
LOC100514786
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9135,115,078 - 135,451,812 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247405,112,422 - 5,488,394 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Abca13
4224 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)148205747195876975Rat

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
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium
Low 3 1
Below cutoff 25 16 13 16 1 1 8 15 7 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035612   ⟹   ENSRNOP00000030281
RefSeq Status:
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
RefSeq Acc Id: ENSRNOT00000101007   ⟹   ENSRNOP00000088943
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1483,873,940 - 84,375,075 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107084   ⟹   ENSRNOP00000095482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1483,874,044 - 84,375,075 (+)Ensembl
RefSeq Acc Id: XM_039092858   ⟹   XP_038948786
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21483,873,397 - 84,376,138 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038948786 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76043 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000030281   ⟸   ENSRNOT00000035612
RefSeq Acc Id: XP_038948786   ⟸   XM_039092858
- UniProtKB: A0A8I6ABQ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000095482   ⟸   ENSRNOT00000107084
RefSeq Acc Id: ENSRNOP00000088943   ⟸   ENSRNOT00000101007
Protein Domains
ABC transporter

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 Protein ENSRNOP00000030281.7 UniProtKB/TrEMBL
  ENSRNOP00000088943 ENTREZGENE
  ENSRNOP00000088943.1 UniProtKB/TrEMBL
  ENSRNOP00000095482.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035612.7 UniProtKB/TrEMBL
  ENSRNOT00000101007 ENTREZGENE
  ENSRNOT00000101007.1 UniProtKB/TrEMBL
  ENSRNOT00000107084.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro AAA+_ATPase 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 ABC TRANSPORTER A FAMILY MEMBER 7-RELATED UniProtKB/TrEMBL
  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
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A8I6ABQ0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ALI8_RAT UniProtKB/TrEMBL
  D4A885_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