MmuINT0083773 @ mm10
Intron Retention
Gene
ENSMUSG00000027111 | Itga6
Description
integrin alpha 6 [Source:MGI Symbol;Acc:MGI:96605]
Coordinates
chr2:71838578-71840677:+
Coord C1 exon
chr2:71838578-71838721
Coord A exon
chr2:71838722-71840561
Coord C2 exon
chr2:71840562-71840677
Length
1840 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGC
5' ss Score
6.16
3' ss Seq
CTGCATTTGGTTCCTTACAGGTC
3' ss Score
10.18
Exon sequences
Seq C1 exon
GAGAACATCAGAGACAAGCTGCGTCCCATCCCCATCACGGCTTCTGTGGAGATCCAGGAGCCCAGCTCTCGCCGGCGGGTGAACTCACTCCCCGAAGTTCTTCCCATCCTGAATTCAAATGAAGCCAAAACGGTCCAGACAGAT
Seq A exon
GTAAGCTGCTTGGCTTCTCTTTTGCCAGTGTTGGATTTTTTTTTTTACAGGCCACTTCCTGTGGCCACATATGGTGACCTTGTGTATGCTTTTAATCCCAGCACTCGGAGGCAGGGGCAGGAGATCTCTGAGTTCACGGTCAGTGTGATTTCCACAGCAAATTCCAGCTCAATCAGGGTTCCAGATCCTGTCTAAGAAAAAAATAATCAACAGAAATACCACTTATTTCTATATTCATAATTGGCCTCTGAGAAGGTGTTTCTCAAGGTAGCAGTGAAGATAACAACCTAAGATGAAATTTAGGGACCAGAGTTTTATTTTCTTCCTTGTTTTCTTCATTGTTTTTAGCCCCTGGTCCTTACTGAGATTATAGCTAGCCAAACCTTCATTCTCCTGTAGTTGACATACTTTATTTTACCACCGAGAACAACACAGTATGATAAATATATATTATTAAAACCAAAGAATAGCAAAACTTAGCAAAGCAAGGAAAAATTCACAATGAAATACTAAAGTGTCTAATGCAGCTCGGGTCATTGTGGGAAGCAAATGTGCATTCTGTGGCCTGCTGGGCATGGCGTAGGATATGGGATCTGTGTGTTAGGACAGAGCGGAAATGAGCCTAGGAAAGTATGACATCTTGATCTGGCATTATTATTGTTATAATTATTGTTGTTATTATTATCTTTTTGTTTTGCTTTTGAGACAGGTTTTCTCTGCATAGCCCTGGCTGTCCTAGAACTTGCCCTGTAGACCAGGTTGGCCTCCAACTCAGAGACCCACCTTCCTCTTCCTCCCCCTGAGTGCTAGATTAAAGGTGTGCGCCCCCACAGCCTGGCTATTATTATTATTATCATCTTGATTACTGTTTTGGTGCTGGAAATTATTCCCAGGGCCTCCCAGGCACTTACCACGTGCTTTGCTCTGACACTGCACATTAGCTGTCAAAATCCAATCAGTGGATAGAGATATGGCTGAGTCGGCAGAGTGCTTTCCTAGTGTGTACAAAACCTTGACTTCAGTCCCCAGCACCATGTAACAATGGCAAGTGCTCCACGCCTGTAGTGCTGACACTTGGGAGGTCGAGACAGGAGCATCTGACAGGCAAGGCCATCTTTGACTATATAGCAACTTTGAGACCTAACTCACACCCCATCTTCATAAAAACTCAAAACAACAACCACCACCACACACACACACACACACACACACACACAATCCAGCTGTTGCTGAATTACCCCTGGCTGTCCTGGAACTTACTTTGTAGACCAGGCTGGCCTCAAACTCAGAAATCTACCTGTCTCTGCCTCCCAAATGCTGGGATTAAAGGCATGTGCCACCACCACCTGGCTATTACTAATTCTTGTGTACATTCCTAGCTCCTGAGCCAAGTTAAACATAACAGGAAAGGAGACCTTGTTCCTAATTGTATTTTCCTCATCTGTACAATGGGCACAGAATGATAGTCCCTCAGACTGTCCTGAAGGTTAAGTGAGTTAAGCTATGTAAATCACTTTAGGTAGCATAAGGTCGTGATACTGCTATAGATCCCCTGAAAGTAAAGTCGTACTGCCCTATATGAGACCAAGCTAGAATGGAAAGTTAAGTGTCTTGTCTAAAGCCACACAGCTAAGCAGGTGTGAGAGGAGGGCTTGGAACTCAGATTCTCTAGCTTGGTGGGGGCTCATGCTCTGCTGCACCCCACCGCCTTGACCTGGTCAAAGTCACTTTGATAGAGCAGGAGCCAAGTGTTTGTCAAAGGAGGGTAGAAGATCATAGGGAAGTGGACTGACTGTGGAGACCTTTGGGAACTCATCTCTCTGCATTTGGTTCCTTACAG
Seq C2 exon
GTCCACTTCTTAAAGGAAGGATGTGGAGACGACAATGTCTGTAACAGCAACCTTAAGCTAGAGTATAAATTTGGTACCCGAGAAGGAAATCAAGACAAATTCTCTTACCTTCCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027111:ENSMUST00000028522:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.332 A=NA C2=0.057
Domain overlap (PFAM):
C1:
PF084417=Integrin_alpha2=FE(10.1=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(8.0=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:
ACATCAGAGACAAGCTGCGTC
R:
TGGAAGGTAAGAGAATTTGTCTTGA
Band lengths:
254-2094
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