MmuINT0007937 @ mm10
Intron Retention
Gene
ENSMUSG00000018800 | Abca5
Description
ATP-binding cassette, sub-family A (ABC1), member 5 [Source:MGI Symbol;Acc:MGI:2386607]
Coordinates
chr11:110279292-110279752:-
Coord C1 exon
chr11:110279626-110279752
Coord A exon
chr11:110279410-110279625
Coord C2 exon
chr11:110279292-110279409
Length
216 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACT
5' ss Score
8.77
3' ss Seq
AAAGTTGTTTCCCTTATTAGAAG
3' ss Score
4.86
Exon sequences
Seq C1 exon
GGCCCTTTCACAAAAGGCCAAAAATAAGAAGTTTCCAGAACCACCCATCAATGAGGATGAAGATGAAGATGTCAAAGCTGAAAGACTGAAGGTTAAAGAGCTGATGGGTTGCCAGTGTTGTGAGGAG
Seq A exon
GTAACTTGCTCCTTTCTGTTAAGTCATATTTTGTCTCAAATGGTAGATTACCAAGGCACTGGAATGAAGAAGAAACACTTTTTATCGCATATGAATATAAAATTTATTTTACACTGCCCTCTTAGAGGTGAATTTAGTTATTAGGATACATATCTGAGATAGGAAATGATAGACATCTAACTTGGGACTCTATTTAAAAGTTGTTTCCCTTATTAG
Seq C2 exon
AAGCCAGCCATTATGGTATGCAATTTGCATAAAGAGTATGATGACAAGAAAGATTTTCTTCATTCAAGAAAAACAACAAAAGTAGCAACAAAATACATCTCTTTCTGTGTGAAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000018800:ENSMUST00000043961:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.256 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000522=ABC_tran=PU(6.8=25.0)
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:
CTTTCACAAAAGGCCAAAAATAAGA
R:
TTCACACAGAAAGAGATGTATTTTGT
Band lengths:
236-452
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