MmuINT0007541 @ mm9
Intron Retention
Gene
ENSMUSG00000015243 | Abca1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:MGI Symbol;Acc:MGI:99607]
Coordinates
chr4:53055536-53057110:-
Coord C1 exon
chr4:53056987-53057110
Coord A exon
chr4:53055666-53056986
Coord C2 exon
chr4:53055536-53055665
Length
1321 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
GTCTGCATTGTGTCTCACAGGGG
3' ss Score
8.87
Exon sequences
Seq C1 exon
AAGCTCAATGACATCAATGACATCCTGAAGTCTGTGTTTCTTATCTTCCCACATTTTTGCCTGGGGCGAGGGCTCATCGACATGGTGAAGAACCAGGCCATGGCCGATGCCCTGGAGAGGTTTG
Seq A exon
GTGAGTAAGGCAGTGGGAAGCTTCGATGGCGGTGTGACAGTTTTGTAGGCATCGGCACTCTGATTGCTGCTTTAGAAGGGGGACTGGGTGCAGGCCATCTGTCCTCCCAACTGTCATGGGCCAATGCCAACACAGCTGCTCTGTCTGTCATGAGTCCCACCATATAGGTGTGTATTCGTGCCTCTGATAGCACTGAGATAAATGGCGGGTGTGGGGGGGGGGGTTGTAAACAAGAAAATCCTAGCATTTGTTTGAGATAAATTCCTAAGCTCACTACTGGTGAGCTTGTCAAATCACTGGAAAAATCAAGCCACAGCTTTGGCAAGTAGGTGAGGCTGGAGATTAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATACCCTTTGATTCTACTAAGAAAACCTGGGCCTGCAGGTGTGCTCATATATTGTGTTTTATGCCTTCTCTAAAGAGATAATTTATTGAATCTTTTTTTCTACTTTTATAATGGTTAAAATATCTCTGTCCATTATGTGACTATTATTCATTTGCTGATTAATTGAGTTAATTAATGCTACTTAACAAACATAGAAGAGGAACATTTTCAGTTTAGTGATACAGAGGAGACATGAAGAATTAAGGGATATTATCCTAAAACCATCTAACTTAAGTCACTAGGTTACATTAGATACTGTAGAAATAGACATCTTTTGAATGCATTTTCTAATACCCATACTTTCTGACCCCCCCCCCAAATTATCCAGGATTATTGGTCAACCCAAACTTGAATTGTTTGGGTTTGGGTGGGGGCATGTCTCATTAAAAAGGAAATCTTATCAATCCTAATGAACTTACAGATCTAAAAGCTAATTGACTCCGAAATTCTGACCTGATACCAGGTTGTATTATAGTTTTCCAAATGAAATCTCAAAGTAGACACCTATGTTACTCCTTTTTCTTCTTGTCATGAGTCATGTTTCTAGAAAAATTGTGTGAAACTGACCCCCCAAATGAGGAAATCCTTTCTTCCTTTCCTCACTTTCCTTCCCCTCCCTCCCTCCCTCCCTCCCTCTCTTCCTCCCATCCTTCCTTTTTTTTAATATGAAGGAAGTCCTTTAATATTTCAAGTGTGAAAAAAAAAAACGAAATTTTACGTTAAGCTAGCCTTTAAGGTTTAGCATAATATTAACTAATTTAAATGAAAAAGCATACAAACAACAAAGTCACGCACAGAATCTCATCTCAGAAACAGGAAGTAGGGCCATGATTTCTGATGCCCGCCCCTCTGACCAGATTATGTCTGCATTGTGTCTCACAG
Seq C2 exon
GGGAGAACCGCTTCGTCTCTCCGCTCTCTTGGGACTTGGTAGGACGGAACCTTTTTGCCATGGCCGTGGAAGGGGTGGTGTTCTTCCTCATTACTGTTCTGATCCAGTACAGATTTTTCATCAGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015243-Abca1:NM_013454:40
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(7.8=100)
A:
NA
C2:
PF126982=ABC2_membrane_3=PD(6.3=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGCTCAATGACATCAATGACATCC
R:
CTGGGCCTGATGAAAAATCTGT
Band lengths:
254-1575
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: