MmuINT0007521 @ mm9
Intron Retention
Gene
ENSMUSG00000015243 | Abca1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:MGI Symbol;Acc:MGI:99607]
Coordinates
chr4:53087092-53088140:-
Coord C1 exon
chr4:53088003-53088140
Coord A exon
chr4:53087313-53088002
Coord C2 exon
chr4:53087092-53087312
Length
690 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
CTTGTGTTTGTGCCTGGCAGGCC
3' ss Score
8.92
Exon sequences
Seq C1 exon
GTGGGATGCAGAGAAAGCTGTCTGTGGCCTTGGCCTTCGTGGGTGGATCCAAGGTTGTCATTCTGGACGAGCCCACAGCCGGGGTGGACCCGTACTCTCGCAGGGGAATATGGGAACTCCTGCTAAAATACCGGCAAG
Seq A exon
GTACATGCTGTTACTTATTTCCAGTCATGACCCAGGGTAGAGAAGGGCTCGTGGGAATTGTGGCTGATTGTGTTAGTTGCTTCTCAAGAAAAGTTGGGAGCCTCCTTGAAGCTCCGTTTCTGTCCTGCTGTGCAAGATTCTTGTTTGTTTGTTTGTCTTGGGTTTTTTTTTTTTTTTCCGAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCTGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCGCCACCACACCTGGCTTTGCAAGATTCTTAAGACGTATACTTCATTATTTAAGGGCCTACTAGAAGAGCAGAAAGGGTATAAGCATACACATACATATTGTAGTTAGACCATGTCCTTGTTCATGTTGGCCATGACTAATGGGAATGTCTGTAAACTTCTTAGCACACTTGACGGAGCAGGATCCCAAATAAATACTGCTCTCCTTTTTGTGACAATTGTAAACTGCCATCCCCCCAAGCCTTGCCATCCTGGGGTCACATCTATGGAGGTTAAAGACCTCCCCATGTCTTTCTCATATGTGACATCTTTGCCGTTTGTGCCACTTTGATCAGTGAGAACTGACAAGTCCCACCGTCCCGTCTCCTTGTCTCCTTGTGTTTGTGCCTGGCAG
Seq C2 exon
GCCGCACCATTATTTTGTCTACACACCACATGGACGAAGCTGACATCCTTGGGGACAGAATTGCCATCATTTCCCATGGGAAGCTGTGTTGTGTGGGCTCCTCCCTGTTTTTGAAAAACCAGTTGGGAACGGGTTACTATCTGACCCTGGTTAAGAAAGATGTGGAATCGTCCCTCAGTTCCTGCAGAAACAGTAGCAGCACCGTGTCTTGTCTGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015243-Abca1:NM_013454:22
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:
PF0000522=ABC_tran=PD(17.8=55.3)
A:
NA
C2:
NO
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:
AGAAAGCTGTCTGTGGCCTTG
R:
TTCAGACAAGACACGGTGCTG
Band lengths:
344-1034
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: