MmuINT0008132 @ mm9
Intron Retention
Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:109975538-109976878:-
Coord C1 exon
chr11:109976758-109976878
Coord A exon
chr11:109975656-109976757
Coord C2 exon
chr11:109975538-109975655
Length
1102 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGAG
5' ss Score
4.86
3' ss Seq
GTTTTCATCTGTCTTCACAGAAA
3' ss Score
9.92
Exon sequences
Seq C1 exon
AATTTCTCCGAGAAGTTGTCCTGCTGTTCCGAACCCAGAAGAGCCCGGAGAAGAGGATGAAGATGTTCAGATGGAAAGAGTGAGAACAACGGGCGCCATGGCTACCCTACAGACTGATGAG
Seq A exon
GTAGAGCTCATGGAAGTAACCGATTCTGCCAGAGACCTGAGAAACGTTCCCATCTTGATTCTCTTAAAGGCCTGCTGGGTGTGTGTGTTCTTTTGCTTTTACAGTGCATTCCTTGATGTCAGTAGGTATGCAGTGTCCACAAGCTACGATAGCAAAGGCTACACACACACACACAATCAGTTAATCAATCAATCAATCAATCAATCAATGTGTTAATTTATTTTTAGAGCCATAGTTTTGATAAGTGCAGTTAAACATTAAAACACTTAAGATTTTAACGAGTCTCCTTTAAAGATTTGTTTTGTATTTTGTGCATACATGTGTGTGACTGTGCCTGAGTGTCTGTATTGTATCATTTTATATAGATGCCCATAAGTGCTAGAAACAAGATGGGGATGTCAAATTCTCCTAGAACAGAACTGACAGGCAGTTCTGAGCCACTTCATGTGGGTGCTAGAAACCAAACCCAGATACTCTCTGTAAGAACAGAAAGTGCTCTTAACCACTGAGCCATCTCTTCAGCCCTGGCTTTTATGAGTTTTATAATTCAAGTTAAACTAACTGCAAACAATTCAGAAGAGAATTTCTTTGTGCTGTGTATCTGTGTATGTGCTTGTGTATGTGTGTGTGTATGTATGTGTGTGCATATGTGTGTGTCTGTGTGTATATATGTGCCTGTGTGCATGTGTGTATGTGTGTATGTCTGTGTGTATATATGTGCCTGTGTGCATGTGTATATGTCTGTGTGTATATATGTGTGTGCAAGTGTGTGCATGTGTGTGTATATGTGCCTGCGTGTGTGTATGTGCCTGCATGTGTGTATGTGCCTGTGTGCATTGTGTGCATGTGTTGACAAATTATTAGTTTATGTGAATGGCCTCATTCCAGCTCTCTGCAGACTGGCAAGCACATATCACACACAGCACTGTAAATCAAATGTCCATAGGGGACTTGGGATGGTTCCCTTGAAAACAGCAGTTTGTAGCAGGAGTGGGTGGGCTTATGGCTCTGTACAAGGAAAGGCCTGGGGGAAGAGGTGTGAGCAGTCTCTGGGGGGAAGGGGTAAGAAAAATGCTACACTGGTTTTCATCTGTCTTCACAG
Seq C2 exon
AAACCAGTCATCATTGCAAGCTGTCTGCGGAAGGAATATATAGGCAGAACGAAAAGGTGCTTTTCCAAAATGAAGAAAAAGATCGCCACGAGGAACATCTCCTTCTGTGTTAAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797-Abca9:NM_147220:29
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.415 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000522=ABC_tran=PU(7.1=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:
ATTTCTCCGAGAAGTTGTCCTGC
R:
GGAGATGTTCCTCGTGGCGAT
Band lengths:
222-1324
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: