MmuINT0007542 @ mm9
Intron Retention
Gene
ENSMUSG00000015243 | Abca1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:MGI Symbol;Acc:MGI:99607]
Coordinates
chr4:53055186-53055665:-
Coord C1 exon
chr4:53055536-53055665
Coord A exon
chr4:53055307-53055535
Coord C2 exon
chr4:53055186-53055306
Length
229 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TAAACACTCTTTCTCCCAAGACC
3' ss Score
5.87
Exon sequences
Seq C1 exon
GGGAGAACCGCTTCGTCTCTCCGCTCTCTTGGGACTTGGTAGGACGGAACCTTTTTGCCATGGCCGTGGAAGGGGTGGTGTTCTTCCTCATTACTGTTCTGATCCAGTACAGATTTTTCATCAGGCCCAG
Seq A exon
GTGAGCTTTATCTGAGAACTGTTCCAGGGACGTGATGGGTGCAGAGAGGACTCACGAGTCCTGGGTGGGCTGAACTCGCCCAGTTAAAGGGATTTTCCCAGCCGTGAGCATGCTCTGTCCACCCACGAAGTGATGGCGCGGGGCCTTGATAAAGTGCTTTAGAAGCTTGAATTTTCCCTTGGAAAAGAGCTGAAAAGATTGACTTTTCTTAAACACTCTTTCTCCCAAG
Seq C2 exon
ACCTGTAAAGGCGAAGCTTCCTCCTTTGAATGACGAGGATGAGGATGTGAGGCGGGAGAGACAGAGGATTCTGGACGGTGGCGGACAGAATGACATCCTAGAGATCAAGGAACTGACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015243-Abca1:NM_013454:41
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=0.268
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PD(6.3=75.0)
A:
NA
C2:
PF0000522=ABC_tran=PU(10.3=36.6)
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:
GGAGAACCGCTTCGTCTCTCC
R:
TGGTCAGTTCCTTGATCTCTAGGA
Band lengths:
248-477
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: