MmuINT0008120 @ mm9
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:109999448-110000952:-
Coord C1 exon
chr11:110000833-110000952
Coord A exon
chr11:109999644-110000832
Coord C2 exon
chr11:109999448-109999643
Length
1189 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TGGCTGACCTTACGTTTCAGATG
3' ss Score
8.58
Exon sequences
Seq C1 exon
ACCTTTACCGGGATCTTGATAGATGTTCTAACCAAGGCATTGAGGATTATGGCGTTTCCATGACAACCCTGAATGAGGTGTTCCTGAAGTTAGAAGGGAAGTCGATGGCTGATGAATCAG
Seq A exon
GTAAGGGTGGTGCTTTGAGGGGGATGATATGCATGCTGCTGTTAGCACCAGCCTTGGGAAAACTTAGAGAAGAAACACAGTCTTAATAAGCATGGCGATATATCACACTAGGTCCTAATGGAATAGACAATAAATCTGAGGTGTCATATTCTCTGAATCTAAGGGGCTGTGGCAGAGAGAAAACTAGAAGTAATATTGAAAATTCATTTTCTTGGATGTATTATTCCGGTGCTTTTGGGATTCAGCCACTGTTGTCCTGAGTACTGTTGTCAGTCTGTCCGCCCTTGGGAAGCTCTGACTTAATGACTGTTTCTTTGCTTGCTTGTATTAATCTTACTGTGTTGACTCTATCTGCCTTTTAACTTTTGTTGCCTTTGACTTTTTAAAGTATCAGTCAAGTGGTTATTATTCAATCTATTTTCTCCTCTTCTCATTTCTGAAGTTACATATTTGGTACATATGTTAGCAGTTATACTTTTAAAAAATCAATTAATTAACACATTCATTTTTGAGACAGTCTCCCTCAGTAGCTCTGGCTGCTTGGAGCTTGCTGTGTAGATCAGAAAGCAAAGAGATCTCCTTGGCCCCGCCTACCAAGAGCTAGGATTAAAGGCAGGCACTACCACACTCAGCCATACACTTAATTTTTACTATTATACTAGGCAAGAGCCAAACTGCAGCCTTTTATCCATTCCTTAACGTGTATACATTTTACATCTTTCTATAAATCAATTTTTCCTAGGTTTCTATTAAAAAGAAGCGAAGGTTTATCTGGGTTTTCAAATGTGGCTATATCAAAAATGTTATGTCTCCCATTCTTACATTCTTAGAGGGCAGGAGGGGCTTCTCTATGTGTTAGCTTTGATTCTTTGTTCAGAAATACCAAAGTGGCTTATCTCTTGCAATGAGGACATTTGTACATGGGTTCCTTTTCATGGGTATCTGAGAATATGTCATAAAAAGCTGTGTATGCCTTTTTTAAAAATTACAATATTTCTCTATTATTGTCTCAGGTTGTTTTGTTTCTCTTCCACTTCCTCGGTAGTTGCTTTAAGATAGCCATGACTTAGTCTGCATATTTGGTCACAACACTAATGCTGGAACGTTCTCTCGAGCAAATGGTTGTGGGGGAAAAAAAAAAACTAAGCACAAAAAGCTGGTATCATAGGTGGCTGACCTTACGTTTCAG
Seq C2 exon
ATGTTGGAATTTGTGGGCGCTTACAAAGCGATGGGGCAAGAGACATGGAAAGCCTCGTTGAGCTGGAGCAAGTGTTGTCTTTAGATTCGTCAGGAAGCTCAGTGAGTGGCATGGCGCTGTGGAGGCAGCAGCTCTGCGCAGTCGCGAAGGTTCGCTTCTTCAAGCTCAAGAATGAACGGAAAAGTCTGATGACTGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797-Abca9:NM_147220:18
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:
NO
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:
ACCTTTACCGGGATCTTGATAGA
R:
GTCATCAGACTTTTCCGTTCATTCT
Band lengths:
313-1502
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: