MmuINT0007939 @ mm9
Intron Retention
Gene
ENSMUSG00000018800 | Abca5
Description
ATP-binding cassette, sub-family A (ABC1), member 5 [Source:MGI Symbol;Acc:MGI:2386607]
Coordinates
chr11:110140423-110140723:-
Coord C1 exon
chr11:110140606-110140723
Coord A exon
chr11:110140515-110140605
Coord C2 exon
chr11:110140423-110140514
Length
91 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGT
5' ss Score
8.46
3' ss Seq
AATTTTTCCCATATCTGTAGGAG
3' ss Score
8.03
Exon sequences
Seq C1 exon
AAGCCAGCCATTATGGTATGCAATTTGCATAAAGAGTATGATGACAAGAAAGATTTTCTTCATTCAAGAAAAACAACAAAAGTAGCAACAAAATACATCTCTTTCTGTGTGAAAAAAG
Seq A exon
GTTGGTATCTATTTTTCCTAAGAAAGTTTTCCAGAAGAGTAATTTCTGTTTTTAGTTTGACTTTAATATATAATTTTTCCCATATCTGTAG
Seq C2 exon
GAGAGATCTTGGGACTGTTGGGTCCAAATGGAGCTGGCAAAAGCACAGTCATTAACACTCTGGTTGGGGACGTTGAGCCAACTTCAGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000018800-Abca5:NM_147219:30
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.065
Domain overlap (PFAM):
C1:
PF0000522=ABC_tran=PU(6.8=25.0)
A:
NA
C2:
PF0000522=ABC_tran=FE(20.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCAGCCATTATGGTATGCA
R:
ATGACTGTGCTTTTGCCAGCT
Band lengths:
169-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: