MmuINT0084209 @ mm10
Intron Retention
Gene
ENSMUSG00000026971 | Itgb6
Description
integrin beta 6 [Source:MGI Symbol;Acc:MGI:96615]
Coordinates
chr2:60627748-60628469:-
Coord C1 exon
chr2:60628335-60628469
Coord A exon
chr2:60628166-60628334
Coord C2 exon
chr2:60627748-60628165
Length
169 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
ACCAGCATTTTCTTTACCAGGCA
3' ss Score
7.63
Exon sequences
Seq C1 exon
GAACTGCGGTCTGAGGTGGAACTGGAAGTGTTAGGGGACACAGAAGGACTCAACCTGTCTTTCACAGCTCTCTGTAACAATGGTGTCCTCTTCCCACACCAAAAGAAATGCTCCCACATGAAAGTTGGAGACACA
Seq A exon
GTAAGTAGATCCCTGGTAGATCTTTAGAAACAACAATTTGATGGGTTGCAGGCTAGCTAGCTCAGCTTGCTGAAGCTGGGTTTCTTGGAGAAGCCAGTCTCACCAGCTTTATCTCAAATCCTGCAGGTTGCTGGATAGAGGAAGCAATAACCAGCATTTTCTTTACCAG
Seq C2 exon
GCATCCTTCAATGTGACTGTGAGCGTATCCAACTGTGAGAAAAGAAGCAGGAACCTCATCATAAAGCCAGTGGGGCTGGGGGACACCCTAGAAATACTCGTCAGTGCAGAATGTGACTGCGACTGCCAGAGAGAAATAGAAACTAACAGCTCTAAGTGTCACAATGGGAATGGCTCCTTCCAGTGTGGGGTGTGTACCTGCAACCCCGGCCACATGGGTCCTCACTGCGAGTGTGGTGAGGATATGGTGAGCACGGATTCCTGCAAGGAGTCCCCGGGTCACCCTTCATGCAGTGGAAGGGGTGACTGCTATTGTGGGCAGTGCATCTGCCACTTATCGCCGTACGGAAGCATCTACGGACCTTACTGCCAGTGTGACAACTTCTCCTGTCTGAGACACAAAGGCCTTCTCTGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026971:ENSMUST00000028348:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(10.4=100)
A:
NA
C2:
PF0036213=Integrin_beta=PD(9.2=27.9),PF079748=EGF_2=PU(32.3=7.1)
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:
CAATGGTGTCCTCTTCCCACA
R:
CCACACTGGAAGGAGCCATTC
Band lengths:
246-415
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