MmuINT0007535 @ mm9
Intron Retention
Gene
ENSMUSG00000015243 | Abca1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:MGI Symbol;Acc:MGI:99607]
Coordinates
chr4:53063161-53063881:-
Coord C1 exon
chr4:53063807-53063881
Coord A exon
chr4:53063331-53063806
Coord C2 exon
chr4:53063161-53063330
Length
476 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAC
5' ss Score
7.56
3' ss Seq
TTTGGTCTGTTTTACTTCAGGTG
3' ss Score
10.02
Exon sequences
Seq C1 exon
GACAGCTCCGCAGATCGCTTCCTCAGCAGCCTGGGAAGGTTCATGGCAGGGCTGGATACGAAAAACAATGTCAAG
Seq A exon
GTACACCCCTGCCTGTGTTCTGCCAGCTTCTTGCTAAACAATAATCCCGTGTTCCTTGAAATCTTACGGGCAAGTAACTAGGGACATTCGTGGTAGAAAAGGGCAAACTGTTAGTCTTACCAGTGACATGATTCAGCATAGTTAGTGACTAAGAGAATGTGTTTTGCCACCAGACGTAACTTGTAAACTGCTGTGGTCTTTGCCTTAAGCTACCTGACCTGTTTAAGTATCCGTTTCCTGTGCAGCAGGAAGGCGGCAACCATGGCTGCCTCTCACTCGATGTGGGTAACTAGTTAAAAGTGTAAAGGTCTTCACCTAGTCCCTCGGCCAGTGGTTGGTGGATCCTGAATCTATAATGCTTTTGTTTGGTGTGTCACTAAGTTTCTGAAGTTTCCATGCACGTTTTGTGCATATACGCTTACTTCTTGAAGAACAGTTTGGCAGTATTACCTTGAGTTTGGTCTGTTTTACTTCAG
Seq C2 exon
GTGTGGTTCAATAACAAGGGCTGGCATGCTATCAGTTCGTTCCTGAATGTCATCAACAATGCCATTCTCCGGGCCAACCTGCAGAAGGGAGAGAACCCGAGCCAGTATGGAATCACTGCTTTCAACCACCCCTTGAACCTCACTAAACAGCAGCTCTCAGAGGTGGCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015243-Abca1:NM_013454:35
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=0.000
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=FE(4.6=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(10.6=100)
Main Inclusion Isoform:
NA

Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCGCAGATCGCTTCCTCAG
R:
AGAGCCACCTCTGAGAGCTG
Band lengths:
240-716
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: