MmuINT0083787 @ mm10
Intron Retention
Gene
ENSMUSG00000027111 | Itga6
Description
integrin alpha 6 [Source:MGI Symbol;Acc:MGI:96605]
Coordinates
chr2:71818481-71820254:+
Coord C1 exon
chr2:71818481-71818560
Coord A exon
chr2:71818561-71819998
Coord C2 exon
chr2:71819999-71820254
Length
1438 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
CCATTTCCACTTGTTGACAGACG
3' ss Score
5.02
Exon sequences
Seq C1 exon
CTGATCCTATGTCAGAAAGCAAGGAAGACCAGTGGATGGGAGTCACTGTTCAGAGCCAAGGTCCAGGGGGCAAAGTGGTG
Seq A exon
GTAAGTGTGGAAAACCGCACCATCCTCAGTGCTGACTGGCTATGGGCTCACAGCAGTGGCCACCAAGCTCCTGCCTCTGTTTACCTTTGAGCAAGAAGCACCCTGCTCTAACACCAGACCTGATGCCAGGAATGAGCCAAAACTTCAAGTCTCCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACCTTAAAATATCCAGATTCAAAGACCTTAATAACACATTTTTTTAACATCTCTAATACTAGCTGCTCTTTAGACAAAAACAAAGTGAAAAAGCAAAGCCAAAGGATACCATTTCTGCCCTAGGAACATTTTGGAGTTTTATAGACAAAAGTATTGTAAACCATGGGGATGACTAAGGACAAACACTTCACCTTTACTCTGTTTACCCTTAACCTTCTCAGGCAGAAGGCAGGCAGCTTGATGGGTAGGCTGGTGGGAAGAGCATGACCTTGTCTCTTTCACAGTCTAGTTGCTGTAATAAAGTTTACACAGAAACTCGAGAGCAATGAGAAGCTTATACTTAAGGGGCACAGTATAGGATATCAACTGGGTTCCCTGTAACTAACCCAGACTGGGTTCCATGGAAGTAACCACAAAGACCCTTTAGAAAATGGAGAGTATTCTGTCTTTCTGGGCTGGGTAATTCTTTCTGCCTTTTAATGATGGGGAATAGTTCTCAAGACTTTGAGAGCACAGAATATCAACTGGGATTCACTGCCAGGGGATAGTGCCAGGAGAAAGAGAACACCTCTGCCTTAGCTGTGTTTGCTTTATCTCCTGAGAAAATATGTCCTTGCCCCTGTCCAGGACGCAGTTATTTACAGCCATTAAAAGCCAATTAAATAAAGAAGACGCAGGGAGGTGGTGTTGCCTTTTTTTCTGTGCAGGTGAATTTACAGGTGAATTGCCTGTGGATGTGAACTGGTATGTTAATACTTGGAATGAGGCTTTATTCTCTTAAGAGTAAGGCAGAAGCCCTGGGTCCTCTCTGTCTTGGTCATGACCTCTCGGAGTGGGGGGTGATTGGTATGCTCTGGGATCCCCTCCCTGGATAAGGACATATTTAATCATCTTACTTAGAACCAACCTCTTTATTATTGCTAAGCGTTCCAGTTCTGTCAAGTTTTTTGTTGTTGTTGTTGTTGTTTTGTTTTTAAAGATTCATTTATTTATGTCGTGTTATGTATGTGAGTACACTATAGTTGTCTGCAGACACACCAGAAGAGGGCATTGGGTCCCATTACAGGTGGTTGTGAGCCACCATGTGGTAGCTGGGGATTGAACTCAAGACCTCTGGAAGAACAGTTTAGATGCTCTAAACCACTGCACCATCACTTCAGCCCCCAGTTCTGTCAAGTTTTAAATAACAGGGTTTACCATTTCCACTTGTTGACAG
Seq C2 exon
ACGTGTGCACATCGATATGAGAAACGGCAGCACGTCAACACGAAGCAGGAGTCGCGGGATATCTTTGGAAGATGTTATGTCCTAAGTCAGAATCTCAGAATTGAAGATGATATGGACGGAGGAGACTGGAGTTTCTGCGATGGCCGGTTGAGAGGCCATGAAAAGTTTGGCTCCTGTCAGCAAGGAGTAGCGGCTACTTTCACTAAGGACTTTCATTACATTGTTTTTGGAGCCCCAGGGACTTACAACTGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027111:ENSMUST00000028522:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.556 A=NA C2=0.012
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CTGATCCTATGTCAGAAAGCAAGGA
R:
TTCCAGTTGTAAGTCCCTGGGG
Band lengths:
334-1772
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