MmuINT0007546 @ mm9
Intron Retention
Gene
ENSMUSG00000015243 | Abca1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:MGI Symbol;Acc:MGI:99607]
Coordinates
chr4:53051029-53051632:-
Coord C1 exon
chr4:53051491-53051632
Coord A exon
chr4:53051164-53051490
Coord C2 exon
chr4:53051029-53051163
Length
327 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTG
5' ss Score
7.76
3' ss Seq
ACGCTTTTTAATCTCTCTAGGTT
3' ss Score
10.05
Exon sequences
Seq C1 exon
CATCTTATCAAATATCCATGAAGTACACCAGAACATGGGCTACTGCCCTCAGTTTGACGCCATCACAGAGCTGCTGACGGGAAGAGAGCATGTGGAGTTCTTTGCCCTCCTGAGGGGAGTCCCAGAAAAGGAAGTTGGCAAG
Seq A exon
GTATTGTAGGAACCAGGAAAGCAGACTGTCTTTTGACACCTATATATTGAATACCTTCTTCATACATGACATCAACCTGAGACTGTCTCTTTACTCACACTGCAGTCTCTGCACTGACTTCAGGGGAAGGGAGGCATGCACAGGCTAGAGGGCGGGGGCAGGGAGTGCAGGTCCCACTACATAAGTCCCCTCTCCCTCCTGTGAGTCCTCAGAGGTAGCTGAGACTTGAGTCCGATTCAATGAAAGAACTTTCCTACATTGTGTGTAAGAAAGCATGGTGACAATACTCAGCCAGACAAAAATCAAAACGCTTTTTAATCTCTCTAG
Seq C2 exon
GTTGGTGAATGGGCAATTCGCAAACTGGGCCTGGTAAAGTATGGAGAAAAATATGCCAGTAACTACAGTGGCGGCAACAAACGAAAGCTCTCCACAGCCATGGCTTTGATTGGCGGACCTCCTGTGGTGTTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015243-Abca1:NM_013454:45
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=FE(32.4=100)
A:
NA
C2:
PF0000522=ABC_tran=PD(17.2=54.3)
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:
TCAAATATCCATGAAGTACACCAGA
R:
CAGAAACACCACAGGAGGTCC
Band lengths:
270-597
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: