Abca3 ATP binding cassette subfamily A member 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Abca3provided by RGD
Official Full Name: ATP binding cassette subfamily A member 3provided by RGD
Primary source: RGD:1307174
See related: Ensembl:ENSRNOG00000050057 AllianceGenome:RGD:1307174
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable ABC-type xenobiotic transporter activity; phosphatidylcholine flippase activity; and phosphatidylcholine transfer activity. Involved in response to glucocorticoid. Located in alveolar lamellar body membrane. Human ortholog(s) of this gene implicated in pulmonary alveolar proteinosis. Orthologous to human ABCA3 (ATP binding cassette subfamily A member 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 418.0), Kidney (RPKM 227.1) and 9 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10q12

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (13886948..13944286)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (13382439..13439748)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (13723365..13780558)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

These findings demonstrate that glucocorticoid-induced up-regulation of ABCA3 expression in vivo is mediated by transcriptional activation through the GRE in the promoter.
Title: Expression of ABCA3, a causative gene for fatal surfactant deficiency, is up-regulated by glucocorticoids in lung alveolar type II cells.
Identification of LBM180, a lamellar body limiting membrane protein of alveolar type II cells, as the ABC transporter protein ABCA3.
Title: Identification of LBM180, a lamellar body limiting membrane protein of alveolar type II cells, as the ABC transporter protein ABCA3.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH132645 (e-PCR)
- UniSTS:215928

D10Got29 (e-PCR)
- UniSTS:115393

D10Got27 (e-PCR)
- UniSTS:111822

Abca3 (e-PCR), detects polymorphism
- UniSTS:502766

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ABC-type transporter activity	IEA Inferred from Electronic Annotation more info
enables ABC-type xenobiotic transporter activity	ISO Inferred from Sequence Orthology more info
enables ABC-type xenobiotic transporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATPase-coupled transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables lipid transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylcholine flippase activity	ISO Inferred from Sequence Orthology more info
enables phosphatidylcholine flippase activity	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylcholine transfer activity	ISO Inferred from Sequence Orthology more info
enables phosphatidylcholine transfer activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in intermembrane lipid transfer	IEA Inferred from Electronic Annotation more info
involved_in lipid translocation	IEA Inferred from Electronic Annotation more info
involved_in lipid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in lung development	ISO Inferred from Sequence Orthology more info
involved_in lung development	ISS Inferred from Sequence or Structural Similarity more info
involved_in organelle assembly	ISO Inferred from Sequence Orthology more info
involved_in phosphatidylcholine metabolic process	ISO Inferred from Sequence Orthology more info
involved_in phosphatidylcholine metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in phosphatidylglycerol metabolic process	ISO Inferred from Sequence Orthology more info
involved_in phospholipid homeostasis	ISO Inferred from Sequence Orthology more info
involved_in phospholipid transport	ISO Inferred from Sequence Orthology more info
involved_in phospholipid transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cholesterol efflux	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cholesterol efflux	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phospholipid efflux	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of phospholipid efflux	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phospholipid transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of phospholipid transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein homooligomerization	ISO Inferred from Sequence Orthology more info
involved_in regulation of lipid biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of lipid transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of phosphatidylcholine metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of phosphatidylcholine metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to glucocorticoid	IEP Inferred from Expression Pattern more info	PubMed
involved_in surfactant homeostasis	ISO Inferred from Sequence Orthology more info
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in xenobiotic export from cell	ISO Inferred from Sequence Orthology more info
involved_in xenobiotic export from cell	ISS Inferred from Sequence or Structural Similarity more info
involved_in xenobiotic transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in xenobiotic transmembrane transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in xenobiotic transport	ISO Inferred from Sequence Orthology more info
involved_in xenobiotic transport	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in alveolar lamellar body	ISO Inferred from Sequence Orthology more info
located_in alveolar lamellar body membrane	IDA Inferred from Direct Assay more info	PubMed
located_in alveolar lamellar body membrane	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle membrane	ISO Inferred from Sequence Orthology more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in lamellar body	ISO Inferred from Sequence Orthology more info
located_in lamellar body membrane	ISO Inferred from Sequence Orthology more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in multivesicular body membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: phospholipid-transporting ATPase ABCA3

Names: ATP-binding cassette sub-family A member 3; ATP-binding cassette, sub-family A (ABC1), member 3; ATP-binding cassette, subfamily A (ABC1), member 3; xenobiotic-transporting ATPase ABCA3

NP_001382963.1

EC 7.6.2.1

EC 7.6.2.2

XP_006246101.1

EC 7.6.2.1

EC 7.6.2.2

XP_038943008.1

EC 7.6.2.1

EC 7.6.2.2

XP_038943009.1

EC 7.6.2.1

EC 7.6.2.2

XP_063124987.1

EC 7.6.2.1

EC 7.6.2.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001396034.1 → NP_001382963.1 phospholipid-transporting ATPase ABCA3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

A0A0G2K1Q8

UniProtKB/TrEMBL

A6HCR5

Related

ENSRNOP00000071944.1, ENSRNOT00000079700.2

Conserved Domains (1) summary

TIGR01257
Location:206 → 1699

rim_protein; retinal-specific rim ABC transporter

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

13886948..13944286

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039087081.2 → XP_038943009.1 phospholipid-transporting ATPase ABCA3 isoform X2

Conserved Domains (1) summary

TIGR01257
Location:206 → 1047

rim_protein; retinal-specific rim ABC transporter
XM_063268917.1 → XP_063124987.1 phospholipid-transporting ATPase ABCA3 isoform X1

UniProtKB/Swiss-Prot

A0A0G2K1Q8
XM_006246039.5 → XP_006246101.1 phospholipid-transporting ATPase ABCA3 isoform X1

See identical proteins and their annotated locations for XP_006246101.1

UniProtKB/Swiss-Prot

A0A0G2K1Q8

UniProtKB/TrEMBL

A6HCR5

Conserved Domains (1) summary

TIGR01257
Location:206 → 1699

rim_protein; retinal-specific rim ABC transporter
XM_039087080.2 → XP_038943008.1 phospholipid-transporting ATPase ABCA3 isoform X1

UniProtKB/Swiss-Prot

A0A0G2K1Q8

UniProtKB/TrEMBL

A6HCR5

Conserved Domains (1) summary

TIGR01257
Location:206 → 1699

rim_protein; retinal-specific rim ABC transporter

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001013113.1: Suppressed sequence

Description

NM_001013113.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.