MmuINT0084178 @ mm10
Intron Retention
Gene
ENSMUSG00000020758 | Itgb4
Description
integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613]
Coordinates
chr11:115980941-115982964:+
Coord C1 exon
chr11:115980941-115981112
Coord A exon
chr11:115981113-115982700
Coord C2 exon
chr11:115982701-115982964
Length
1588 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
TGCCCCTCCTTGCCTTGCAGAGG
3' ss Score
10.9
Exon sequences
Seq C1 exon
ACTGAAGGAGCCCTGGCCCAACAGTGATCCCCCGTTCTCCTTCAAGAACGTTATCAGCTTAACGGAGAATGTGGAAGAATTCTGGAACAAACTGCAAGGAGAACGCATCTCAGGCAACCTGGACGCTCCTGAAGGGGGCTTTGATGCCATCCTGCAGACAGCTGTGTGCACA
Seq A exon
GTGAGTGCCGAGGGTCCCCGCCAGCCTAGGCCAGGGCTGCGGCTTTCTGGGAAGGACATAAACTTCTGCTGGCCCATTCTACCACTGCTAGGCTCAGAATCCCTGTGGGGGTTCCCAGAGGCTTAGACCCCATTCCTTAAGATCATGAGATGTTTTAGCAACCCCTAACTCTAGTCCTAGTTCTGACACACTGGGAATCCAGGTCTGTGCCTGCATCGTCACAACTTGTGTTTGTATTGGCCAGTGAGGCAGACATGGCTCTAGTGGTCCTGGAATATTCAGGGTCCTGACACTAGCCTACCACACCATCTCCCAGGTCACAAGCTATCCAGTCTCCAACTGTGCTGGCAGCTAACTATTTGTTTGTTTATTTATTTGTTTGCTTATCATGTGTATGCATGCCACCATCTGGAGGTATATACACAGAGGTCAAGAGATAACTTTTGGGGGTCAGTTCTCTCCTTTCCCCATGTCTGGGAGTTATAACTCAGATTATCATGCTTGAAGACAAGTATCATTGCCTGTAGAGCCCTATAGCTGACCCAGGGCTAGCAGCTAAAATGACCACTTCATTGTATGCCTACATCAATTTTTTTTTCATTTTTGAAAATAATCTATCTGCACTGCAGATAAATTATTAGACAAAGACCGAAAATTGACTATAATTCCAAAACAACAAACAGCCATCTCTTTGATAGTCTGTCCTACATTTTGTTCCTTTTCCCATATTTTATGTAGTGGGATTGTTTCTCCTATAATTCTGTTTTTTGTTGTTGTTGTTGTTTTGTTTTGTTTTTTTGAGACAGGGTTTCTCTGTGTAGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCACCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGTGTGCGCCACCACGCCTGGCACAGCAACTCTTATAAAGGAAAGCATTGCATTGGGGCTGGCTTACAGTTTCAGCGGTTTAGTCCATTATCATGGCGGGAAGCATGGCGGCGTGCAGGGAGACATGGTGCTTCATCCACAGCCACAGGCAGCAGGAAGAGACGATGCCTAGAAATAAACTTCTGAACCCCCAAAGCCTCCAATAAGCCACGCCCCCAATCCCTCTCAAGTAGTCCCACTCCCCAATGACCAAGCATTCAAATATATGAGCCTGCGGGGGCCTGTCCTATGGAACCCACCATAACCACTCCATCTCCTTCCGCCTGCCCATTTCACTTAACATGGTGCTGGGAACATTCTCCTGTGTATCTAAACTATCCTTGCAGTGTGGCTGAGGGCTTGGGGTCAGGGGGAGCTGGTCCAGGACATCAGGTTTGACTCTCTCATGGTGCCCGTGCTGGGCACACCCTATGTCATGGTCCCGTGCTGAGCACAGTTTCTCTGCACACCATTGCTCTCTCCGGTTTTCTGTCATTCGAGTGCGGCATAGTAGACATGCTGCTAATCCCGTGGCTTCGGTCCAGCCCCCTGTTGGGAAACGCTTCCCTTTTCCTACCTCATAAAAGAATGTCAGTCCTCAGCAAGCAGCCTGCTCAGTGGATGTGCCCCTCCTTGCCTTGCAG
Seq C2 exon
AGGGACATTGGCTGGAGGGCTGACAGCACCCACCTGCTGGTGTTCTCCACCGAGTCTGCCTTCCACTACGAGGCTGATGGTGCCAACGTGCTGGCCGGCATCATGAACCGCAATGATGAGAAATGCCACCTGGACGCCTCGGGCGCCTACACCCAATACAAGACACAGGACTACCCATCAGTGCCCACGCTGGTTCGCCTGCTTGCCAAGCATAACATCATCCCCATCTTTGCTGTCACCAACTACTCTTACAGCTACTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020758:ENSMUST00000021107:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.138 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(13.6=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(20.7=100)
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:
CAACAGTGATCCCCCGTTCTC
R:
GTGGGCACTGATGGGTAGTCC
Band lengths:
342-1930
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