MmuINT0007508 @ mm10
Intron Retention
Gene
ENSMUSG00000015243 | Abca1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:MGI Symbol;Acc:MGI:99607]
Coordinates
chr4:53089799-53090393:-
Coord C1 exon
chr4:53090254-53090393
Coord A exon
chr4:53089916-53090253
Coord C2 exon
chr4:53089799-53089915
Length
338 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
GATTCCCTACCTGACTGTAGGTG
3' ss Score
5.95
Exon sequences
Seq C1 exon
CTCCTTATTGCAATGATTTGATGAAGAACTTGGAGTCTAGTCCTCTTTCTCGAATTATTTGGAAGGCACTCAAGCCACTGCTTGTTGGAAAGATTCTCTATACACCTGACACACCAGCTACAAGGCAGGTCATGGCTGAG
Seq A exon
GTAAGCTGTCCAGGCTTAGGACTCCGTCCCCAAAATCTCCCCAGAATTAGGGGTAGGAAGTGAACGCAGCTTCAGGTAGTGTATGTTGAATATACTCTTGGCCATGATGGGGCTTTTAAATAGTCAAAAACAAAACAAAACAAATCCACATGTAATCTTGGGCTCCATATCCCCAGCCTTGAGTATTTGAACTATGTCTGTAGCAGGGGTTTCTTGAGGAAGGGAAGGACTGAGCAGAGGTTTCTGTAATGAGTGGTGTTTTTTAGGGAATCTTGGAATGTTCATTGCCTCTGCCTCTCTTCTATTTGTATGAATCCCGATTCCCTACCTGACTGTAG
Seq C2 exon
GTGAACAAGACCTTTCAGGAGTTGGCTGTGTTCCATGACCTGGAGGGCATGTGGGAAGAACTCAGCCCCCAAATTTGGACCTTCATGGAGAACAGCCAAGAGATGGACCTTGTCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015243:ENSMUST00000030010:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126982=ABC2_membrane_3=PU(0.9=8.5)
A:
NA
C2:
PF126982=ABC2_membrane_3=FE(8.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCTTATTGCAATGATTTGATGAAG
R:
GACAAGGTCCATCTCTTGGCTG
Band lengths:
254-592
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types