MmuINT0083772 @ mm10
Intron Retention
Gene
ENSMUSG00000027111 | Itga6
Description
integrin alpha 6 [Source:MGI Symbol;Acc:MGI:96605]
Coordinates
chr2:71838268-71838721:+
Coord C1 exon
chr2:71838268-71838428
Coord A exon
chr2:71838429-71838577
Coord C2 exon
chr2:71838578-71838721
Length
149 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGTCCCTGCCCCCTTTGCAGGAG
3' ss Score
11.24
Exon sequences
Seq C1 exon
CAATTTTGGGTATTCTCGAAGCTGAAAAAGAAAGAAGAAAGTCAGGGTTGTCATCGAGAGTTCAGTTTCGAAACCAAGGTTCCGAGCCAAAGTATACTCAGGAGCTGACCCTGAATCGGCAGAAGCAGCGGGCGTGCATGGAGGAGACCCTCTGGCTGCAG
Seq A exon
GTGAGTGTGTGCCAGGGTCGTCTCCACAGGACTCCGGTGTTCTGTGAGACGCTTAGTTTCTGAACAGCACCGTTCATCTCTGCTCTGCCATCGTTTCGGAGGTCCGTTGGCATTTGGGCACACTGACTGTGTCCCTGCCCCCTTTGCAG
Seq C2 exon
GAGAACATCAGAGACAAGCTGCGTCCCATCCCCATCACGGCTTCTGTGGAGATCCAGGAGCCCAGCTCTCGCCGGCGGGTGAACTCACTCCCCGAAGTTCTTCCCATCCTGAATTCAAATGAAGCCAAAACGGTCCAGACAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027111:ENSMUST00000028522:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.332
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(11.1=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(10.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTTCGAAACCAAGGTTCCGA
R:
ATCTGTCTGGACCGTTTTGGC
Band lengths:
242-391
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