MmuINT0007528 @ mm9
Intron Retention
Gene
ENSMUSG00000015243 | Abca1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:MGI Symbol;Acc:MGI:99607]
Coordinates
chr4:53078773-53080027:-
Coord C1 exon
chr4:53079903-53080027
Coord A exon
chr4:53078872-53079902
Coord C2 exon
chr4:53078773-53078871
Length
1031 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TGTCTCTCTTGTATCTCTAGTAA
3' ss Score
8.48
Exon sequences
Seq C1 exon
ATTGTCCTGCCAGCTGTCTTTGTTTGCATTGCCCTGGTCTTCAGCCTGATTGTGCCACCCTTTGGCAAGTACCCCAGCCTGGAACTTCAGCCCTGGATGTATAATGAGCAGTATACATTTGTCAG
Seq A exon
GTATGTTTGTCCTTTGTGCCTCAGGGCAGAGAGGGTTGAAACAGACCAACAGTGTTTCGTATACTGAGAGCCAAGGAGTCAGAATCCACAATTCTACAGTGGGATGGGTCTTGTCATGATGGTTCAGGCTCCTATACAAGCCAATACTGTAGCAAAGAACAATAGTAAACGATACTGGGAAATACAGGTGAATCTCTGCTGGGCATTTCCCCTTGTATTGTTAGGCTCTTGTCAGGTATGCTTTAATTCACTAATCAGTAAATCTTTCAGGTTAGGATGTTAGCTAAGTGTGCATCTTCAGGCAAGAATGCCCCTATTCCATACTGATCCTGTTAAAAATCAGAAGATAGGGGACTTTTGAGACCTTGTTTAGTACAGGTTTTCTTCAGTTCTGATGCACGGGTAGGTCTGTAGATGGGAGAAAGTGGCAGTAATATAGAGGGACGTTTTAAAAACTCTGTGTGAATGTGTGTGTAGGATATGTATAGATCATATATAGATTGTTTATTAGCCTCTATTGCTCTAGCTCACTTTCATCTCCTATAGGTAAAAGTTCGTTCGATCCCTTTCTAGCCAATGACCTAGCATTGCCCATGGCTACAGATCATGACATTGGTTTGTGCTCTAGGCCCATTATTTCTTGGACTTTTTAATTGTGCATACCAATAATCAATAAAATCTTCCTGTCTGTTCTTGGAATATCCTAGCTGTCAGTGTCAAGTGGTAATTATCAAAGTAGTTTTGAAATACTGATCTTCAATGATTTTTGTATGTGTGTGTGTGTGTGTGTGTGTGTATATGCACACCTTCACATGTAATCTCTGCACATGCTTCATTGGGGACACTGTATGTCACCCTGATGGCAGATGTTTGAAGCTCCTTGCAGGTGGCTTTTGTATATAATTTATTTTAGTCTTAGAAGCCCATTCCTCAGAAAACACTTAGCAGAGCGTTTTCTGTAGGAACTTTTCCTGCCTCCAAGTCCTGGTTTGGATGAGCGACTGACCTGGATGTCTCTCTTGTATCTCTAG
Seq C2 exon
TAATGATGCTCCCGAGGACATGGGCACCCAGGAACTCCTGAATGCTCTGACCAAAGATCCAGGCTTTGGGACCCGCTGTATGGAAGGAAACCCAATCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015243-Abca1:NM_013454:29
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=0.206
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=FE(7.8=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(6.3=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:
TTGTCCTGCCAGCTGTCTTTG
R:
GGGATTGGGTTTCCTTCCATACA
Band lengths:
223-1254
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: