MmuINT1021457 @ mm10
Intron Retention
Gene
ENSMUSG00000020758 | Itgb4
Description
integrin beta 4 [Source:MGI Symbol;Acc:MGI:96613]
Coordinates
chr11:116005897-116006610:+
Coord C1 exon
chr11:116005897-116006055
Coord A exon
chr11:116006056-116006460
Coord C2 exon
chr11:116006461-116006610
Length
405 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTA
5' ss Score
5.89
3' ss Seq
CGTGGCCTTCAATAATCCAGATT
3' ss Score
4.84
Exon sequences
Seq C1 exon
GCCTCCCTCCTATCTGGGAAGATGGGAGGAGCAGGCTTCCGCTGTCCTGGACTCTTGGGTCCTTGAGCCGGGCTCACATGAAGGGTGTGCCCGCATCCAGGGGTTCACCAGACTCTATAATCCTGGCCGGGCAGTCAGCAGCACCCTCCTGGGGTACAG
Seq A exon
GTAGTACAGGGGGTGGTCACCATGGATCCATGGCTGTCACGCTCCATTTGTCACCCAGCTACCATCACAGCCTGTGCCTGTGCACTCCCTCACTGCTTCATCGCATACAGAACTCCAGTTCACCCACAGGAGCTAACCACTGCCCTGCCTGCCCACCCCCATCAGTGCTGAAGCCTAACACATCTGCCCTCCTGGGGTATAAAGCAAAAGAGCTGGGCAAGGCGCAGGGCCAGTTGTAGAGGGGATGGACTGAGGAGACTAGCAGACTCAAGGGGAAGTGTAGAGCAGCCTGGACAGGTTAATGTGAAGCCATAATATGACTGGAGAGGCAAGCACGGGGTAGACTGTAGCTCATCTCAGACCACAAACCCGGTCTTGGACTAACCGTGGCCTTCAATAATCCAG
Seq C2 exon
ATTCCCGTGGGGCTGTGGGTGTGCCTGACACACCCACTCGGCTGGTGTTCTCTGCCCTGGGGCCCACGTCTTTGAAGGTGAGCTGGCAGGAGCCACAGTGTGATCGGATGCTGCTGGGCTACAGTGTGGAATACCAGCTACTAAACGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020758:ENSMUST00000021107:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.259 A=NA C2=0.151
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004116=fn3=PU(48.8=80.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCCTATCTGGGAAGATGGG
R:
CGCCGTTTAGTAGCTGGTATTCC
Band lengths:
305-710
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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