MmuINT0084063 @ mm10
Intron Retention
Gene
ENSMUSG00000025809 | Itgb1
Description
integrin beta 1 (fibronectin receptor beta) [Source:MGI Symbol;Acc:MGI:96610]
Coordinates
chr8:128713208-128714165:+
Coord C1 exon
chr8:128713208-128713378
Coord A exon
chr8:128713379-128713926
Coord C2 exon
chr8:128713927-128714165
Length
548 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGA
5' ss Score
5
3' ss Seq
AAGTACATTCTTTTCTTTAGGCT
3' ss Score
6.35
Exon sequences
Seq C1 exon
GAGAACCACAGAAGTTTACATTAAAATTCAAGAGGGCTGAAGATTACCCTATTGATCTCTACTACCTTATGGATCTCTCCTACTCTATGAAAGATGATCTGGAGAATGTGAAAAGTCTTGGAACGGATTTGATGAATGAAATGAGGAGGATTACTTCAGACTTCCGCATTG
Seq A exon
GTAGGAATGTTGGGAACATTTTGTGTGTGTGTGTGTTGAGGGGTGGTTCTGCATGTGTGCAGAGCAGGCTATTGAGTGTCTTATGTTATCACTTTGTGTCTCATTTCTGTGAGACACAGTTTATCACTTACCTAGGTTTGTGGCCTATAATTTCCTGTCTTTTCCTGCAGCAGTGCTGGGGTGCAAGGTGTGTATGTGCACGCCTGGCCTTTTACCTGGCTGCTAGGATCTGAACTTATCCTCACGCTAATGCAGCAGGAGCTCTTCCCACAGTGCAGTCCCTGCAGCCTCCATACTGGGCTTTAGAAAAAGATGTGCATTTAGAGTTGGTGAGAGATGGCTCAGGGGATAAGGGTCCTGCCTTTAAGTGTGATGACTGAGCTCAGTCTCCAAAATCAGTTCCTGCTTGTCCTTTGACCTCCAGACATGCATTGTGGTATATGTGTGCACATCCTTCACCCAAATAAATAAGTAAATATCAATTTAAAAGTGATGTAAGTTTGTTGGTCTCTTCCCACTCATCTATCCAAGTACATTCTTTTCTTTAG
Seq C2 exon
GCTTTGGCTCATTTGTGGAGAAAACTGTGATGCCGTATATTAGCACAACCCCAGCAAAGCTAAGAAATCCTTGTACAAGTGAACAAAACTGCACCAGCCCATTTAGCTACAAAAATGTGCTTAGTCTTACTGACAGAGGAGAGTTTTTCAATGAACTTGTTGGTCAGCAACGCATATCTGGAAACTTGGATTCTCCAGAAGGTGGCTTTGATGCAATCATGCAGGTTGCGGTTTGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025809:ENSMUST00000090006:5
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=0.037
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(9.5=50.0),PF0036213=Integrin_beta=PD(20.8=62.5)
A:
NA
C2:
PF0036213=Integrin_beta=FE(18.3=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:
TCAAGAGGGCTGAAGATTACCCT
R:
GCATCAAAGCCACCTTCTGGA
Band lengths:
358-906
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