MmuINT0083792 @ mm9
Intron Retention
Gene
ENSMUSG00000027111 | Itga6
Description
integrin alpha 6 [Source:MGI Symbol;Acc:MGI:96605]
Coordinates
chr2:71664780-71666071:+
Coord C1 exon
chr2:71664780-71664868
Coord A exon
chr2:71664869-71665952
Coord C2 exon
chr2:71665953-71666071
Length
1084 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACC
5' ss Score
8.66
3' ss Seq
CAGTGCCCCGTGTATTCCAGGTT
3' ss Score
7.09
Exon sequences
Seq C1 exon
ATATTGCTGTTGGAGCTCCCTATGATGATCTGGGGAAGGTTTTTATCTATCATGGATCCCCGACTGGCATAATTACCAAGCCAACACAG
Seq A exon
GTAACCAGATAACGTCTCTAAAACAGTGAACAGTGTCAGCTTTCTACCTGTATGTAGGATTACGTTAATCTTCACACGTATTTGTTTCAAATATTCAATAGTATGAATTTTAAAAAAGTTTTTATTTTACTTCTAATTATGTGTGTGAGAGAGAGGAGGGAAGGGACAGGGAAGGAGGGAGGGAGGGAGGAGAGACAGAGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAGGAAGAGAGGAAGAGAGAAAGAGAACGCCCCTCAGGAGGTTATCGGATCTGCTGAAACTAGAGTTACAGGTGGTTGTGACCCTCCTGACACAGGTGCAGGGAATAGAACGGGAGTCCCCTGGGTGAGCCATCTCTCAAGCCCTGTGTGAACTGGGAGATGGCTTTGGCTCACTTACACAGATGCAGTGACCTGCTTGCTTTAACTGTAAAATGTCTTAACTAAGTTAGGAAATCAGCATAAACCCAGGGTGAGGACCGTTCTGTCCAGGAAGCGGCTGGGGGTGGCCTGTGCTCTGTTGCCCTTAGCAGTGGGTTTAATAGAATTGAAACTGAGCAGACGAATAGAGGATTGTAATTACACAGAGAATTCAGACAGCAAAAGTTCTAACTTGTTTTGACAATACGACGGGGGGGGGGGGGGGGGTGCGGTTAGATTTGATTTTAAACTACTCTGTTTAACTTAATAAACAAAATAGGCTTTTGTCCTTTGGAATATACTCTGTGACTCAGGTGGATTTTATGAAATAAATCATACGATATGAAATAAATCATACTGTACACCCATAATGTAATATAGCTTGTTTGAAAGTGAACGGAAGCTTTTGTTTGGAATGAAATTTATCTTTTTCTTTCTCTGTTTTCTTTGTTCCTGCTCGTGGTGACAGGGACCCCAGTCACCGCTCTGTCCGTGCCAGGGAAGTGCTGTACCCCTGAACTCCCTCCCTAGCTCGTTTGTGTTTTTCTCAGAGGTAGCCAGCCAGCTCAGTTAGTGGCCCAGTGTTCACTCCAGTGCCCCGTGTATTCCAG
Seq C2 exon
GTTCTCGAGGGGACATCGCCTTACTTCGGCTATTCAATCGCTGGGAATATGGACCTGGATCGGAATTCCTACCCCGACCTTGCTGTGGGCTCCCTCTCAGACTCGGTCACTATTTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027111-Itga6:NM_008397:8
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:
PF135171=VCBS=PD(4.1=10.0)
A:
NA
C2:
PF0183918=FG-GAP=WD(100=77.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGTTGGAGCTCCCTATGATG
R:
AATAGTGACCGAGTCTGAGAGGG
Band lengths:
198-1282
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: