MmuINT0008121 @ mm9
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:109997352-109999643:-
Coord C1 exon
chr11:109999448-109999643
Coord A exon
chr11:109997519-109999447
Coord C2 exon
chr11:109997352-109997518
Length
1929 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
ATTTATTTTCCTCCACTTAGGTT
3' ss Score
9.72
Exon sequences
Seq C1 exon
ATGTTGGAATTTGTGGGCGCTTACAAAGCGATGGGGCAAGAGACATGGAAAGCCTCGTTGAGCTGGAGCAAGTGTTGTCTTTAGATTCGTCAGGAAGCTCAGTGAGTGGCATGGCGCTGTGGAGGCAGCAGCTCTGCGCAGTCGCGAAGGTTCGCTTCTTCAAGCTCAAGAATGAACGGAAAAGTCTGATGACTGT
Seq A exon
GTGAGTACGGAGTCTCTGAATGGTTGAGAGCGCGATGTAAAAATCAGACAGAGTACATTCCGGCCCTTGCAGAGATAGTCCTCTAAGCATTTGTTTAATAAACCTGCCCCTGGGCATATGTGATCAAAATACATAAAGATAGGGATTATCTTAATTGCACACAGAATTTGTCCTTACCAAAGACCTCGTTCTCTTCTTTTCCCAAAACACCAAAATCTCTTAGCACTTTCCATAGTATAAGGTAAGGGGAAGGGGTAGGGGAGAGAGAAATGATATATAGATATACAGATAGATAGGTAGACAGATGATAGATAGATAGATAGATAGATAGATAGATAGATATTGATTTTATGGAATTGGTTTGCACCACCATGTGGCCTGGAAGCTGAGATTTATAGGACATATCAGCAGCCTGAAAACTCAGGTTGGTGTTAGTGTTCCTGTCAACAGGCTGGGCACAGAGGCTCCGTGTCTTTATTATTTAATTTCTCAGTGGTGCTTGTACAGCAGGCTTTTCCACCCATACCCCACTTCCCAGAATCATGACTTTGAGACTTGTATATGAACGAATGCCTACGCCATAAGCTTGGGTTTGTTCCCCATTAGCTCATAACTTAATCCATTTGTAATATTCTGTGAGGGCCACATGGCTGGTTTCTTCTTCTCAGTTCCACACGTCTGTCTCCTCAGATAAATCTAGGCAAATCTTTTCCAGCCTGACTTTATCCCAGAGTTCTTCTCTCCCTAATGGAACACCCACTTCCTGTTTCCTGCCCCAACACTTTGGCCAATCAGCTTTTTATTGACGGGTGATACTTCCATACAGTTCACAAGAGATTATCTCTGCAAATGCCCGTTGTTGCAAACCCCTGCATCTCCAGCTTACCCCTCACGGATAAGTGCTGCCTCCTAGCATAAACGCAACTCTACACTCAGAAGACATATTTATTTACTCAAATATTTGCAAGCACTTCTACACAAAATTCTGGTGTTTGGTGTTTGCGCATATATTAAAGTAAAGCAGACATATTTTGCATTGTCTTTCTGTGACTGTAATGAGATAGCCAAGATGATGAACTTATGAAGAGAAAATCTGTCTGCATCACAGTCAAGTAGGTTTGTATCCAAGACCAGGGTATCCCAAGTGTCTAGTTTCATCGTTCCCTTTAAGGACACTCCCCAGTAACCTGTGTTCCATGCTCTCTCTTCTGGCTCTTACATACTTCCTGCTCCCTCTTCTGCAGCATTCCCTGAGTGACTTGTTAGGGGCTGGGCACACAGCCTCTGCTTATTTTCTGCATTGTAGGCAGCCATGAGTCTGTGTTCAGCGTAGTTCATTGTAAGGAGGGGCTTCTCTGACTAAGGCTGGCAGCTGCCTTTGTCTCCGTGGATAAACTTCGATTTAGAGGGCAGTTTTCTGCTATGCCAGTTTAGCTAACTATCAGGAGTAAGCTCCCCACATGGCTTTCTATCTGCCCAGCCCTGAGTCGTCAGACAATTATCCCCATCCCTCCATTTGTCTTTCTGTACTTTCAGAGGACCGGGTCTTATCTGAGATTTTAGTATGCCAGTAATCCCATGGCTCAGGAAGTAGAGGCGGGATGATCAGAAGTTCTAGGTCATCCTAGGTTATGTAGTCAATTCAAGGTCCCCCTGGACTACAGGATACTCTGCTTAAAACAGAAATCAAAGGGAGTCAGAACCAGGAACTTGGAAGAACCGAAGGAAATGTTGAAAGCAGTAGGTGGTTAGTGGAAGACCAAAGCGACACCATTTCATTTCAGAAAGAGAACGAGAAAGCAATATGACTTGAACATTTCCTATATCCGTATTTTATCACTATTCATTATCTGTTGAACCCTAGAGCCCCACAGAGTTGCCCTAGGTTATTGATTATTACTCTTTTAATATTTATTTTCCTCCACTTAG
Seq C2 exon
GTTATTGCTTTTTGGCATTAGCTTTGTCCCCCAACTTTTGGAACATCTCGTCTACAAGGTATACCACAAAAGTTATTCATGGGGGCTATCTCCAAGTATGTATTTCCTTTCACCAGGACAGCCACCACAGGATCCTCTGACCCACTTACTGGTCATCAATAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797-Abca9:NM_147220:19
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:
NO
A:
NA
C2:
PF126982=ABC2_membrane_3=PU(0.7=3.5)
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:
ATGTTGGAATTTGTGGGCGCT
R:
AGTGGGTCAGAGGATCCTGTG
Band lengths:
342-2271
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: