MmuINT0008112 @ mm10
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:110147215-110148909:-
Coord C1 exon
chr11:110148741-110148909
Coord A exon
chr11:110147274-110148740
Coord C2 exon
chr11:110147215-110147273
Length
1467 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACG
5' ss Score
10.52
3' ss Seq
TTTTTTTTTCTTTTCTACAGGAT
3' ss Score
12.9
Exon sequences
Seq C1 exon
GTAAGTACGGACATCAACGGTCTCCATTGTTTTTCCTGAAGTCGTCTTACTGGTTTAAACGCAGAGGAGCTAGTCACGTGGTCCTTGAGAATGAAATAGATTCGGATCCCTCGCTGAATGACTCACTGGAACCAGTGTCTCCAGAATTCCAGGGGAAAGAAGCCATCAG
Seq A exon
GTAACGAATACGTCAAATGGAAGTACTTACAATAGAGAGGAGGCCCAGATCAGACACCTACAGGCCAGACGCTGATGTTCAAAGATTTCCTTCTGAGCGCGCCTGCGCCCACCTCCTCCCAGCCCCCTGTTCTTATGAAGTGAGACTTTCATTCTAGATGCCACAGTCTTTTATCTCCTCTCCCAGATTTGCACTTACTAGTATTGTTTGGTACAGTAGTGACTGTCAACAGCTGTGTCAAAGTGTGAACAAAGGACTTTAGTTCCACATTCCTCACTATCTTCCTTGAGTTTCCTCTTCGTATTTTGCTCTGATGTGCTCTTGATGATAGGTTGGGGCGCCACTCCCCTATTTGCATCCTTGTTTTGTAGAATCCACTTTGTCTCTTTTTGTTTCCCTTCTTGGAGGATTAGATGAAAACACAAGCATAAGTGATGTAGAAAGGGGGGTTAGAGACACCCCAGAAAGGTGGGAAGAAATGATCAGACCACGAAGCACTAAAGCCTTGCATCATGAGACCACAAGGCACTGAAGCTCTGCATGGCGAGACCGCAAGGCACTATGCCCAGCATTGCCTTCCATGAAGCCATACCTGTGCTATTGTCAACGCTTTGACTTCCAAAGAGCTACACATCCCAAAGATCCTTATCTTTGCTCAAATTTTGAATATAGCTCACCTGATGTTTTGTTTTGATATTATAGGGAATTAATTCAGGTAGACTGTGCAACCTCTACAGCATAATAGAACTTCAACTCATTAAAAGTCTGTGTGCTTTTTTTTTTTCTTTAAGACAGAGCATTATTTTATAAGTCAGTCTGGCCTGGAACACAAGATGTATCCCAGGCTGGCCTTAGACTTCGACACTTCCTGCCTGTGTTCTGAGTGCTGTGATCATGGGCATGCGTCACCATGCGTCACGTCTGTGGGCTTTTAAAACAGGTCTCATCATTTCATTCTCTTTTCCTCTTCTTTGGAAACTTCAAGCATCCTGGATTATGCAACTCTTCCTTTTCTTAGGAACCAACCTTACGCTGTAATTAGTGTTGCCATCCTTGCTTTATTACCAAAGACATGGACTCTGTGACTTGCATACTTGCACAGGAGCTCCGTGTAAATGACACAGATGGGACCTCACTCCGAGTGTCTTGACTCCAAAGCACAAGTCCGTTTGATCTGATGTGGGATCTTCCACCAAGGATTTCATCTCCAACTTTCCTCTTCAGTCATCTGTCACCGTCTGTACACATGGCTGCTTGTATCCACACACTGGCTACTCCCTCTGTTTATGTTCTGTTGGGGTACAGTGGGCAGAGATGCTGCCTCTCATGGGATGCCCGGGATGCTTCTGACAGTGCCTGTGCAAAACAAAAAGAAAACCAAAAAAACAAAAACAAAACCCTCTAAGTTTCATCAGGCCTCCCCCAATTGCTGCAATTTCCTCCAAACTTTTTTTTTCTTTTCTACAG
Seq C2 exon
GATCAAAAATCTTAAAAAAGAATATTCTGGAAAGCATGGGAAAGTAGAAGCCTTGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797:ENSMUST00000044850:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.070 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000522=ABC_tran=PU(1.4=9.5)
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:
TACGGACATCAACGGTCTCCA
R:
TCTCAAGGCTTCTACTTTCCCA
Band lengths:
222-1689
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