MmuINT0084065 @ mm10
Intron Retention
Gene
ENSMUSG00000025809 | Itgb1
Description
integrin beta 1 (fibronectin receptor beta) [Source:MGI Symbol;Acc:MGI:96610]
Coordinates
chr8:128716122-128717302:+
Coord C1 exon
chr8:128716122-128716277
Coord A exon
chr8:128716278-128717206
Coord C2 exon
chr8:128717207-128717302
Length
929 bp
Sequences
Splice sites
5' ss Seq
TATGTAAGT
5' ss Score
6.69
3' ss Seq
TGTATTACTTTATTCCTTAGGAT
3' ss Score
9.48
Exon sequences
Seq C1 exon
TCGCTGATTGGCTGGAGGAATGTAACACGACTGCTGGTGTTTTCCACGGATGCTGGGTTTCACTTTGCTGGAGATGGGAAACTTGGTGGTATTGTTTTACCCAATGATGGACAATGTCACCTGGAAAATAATGTATATACAATGAGCCATTACTAT
Seq A exon
GTAAGTACTTAGGCCTGCCTAGTGAGTGAGTTTTGGTGATTTTAGTGTAATCCTGAGCATGTGGGAGGGCAGGGTTTGCAGCTTTCTTGTTTTGGTTAGTGTGGGCCCTGATGATGGCTGGGAAAGCTGCATTGCTGCTTGTAAAGCTCTTGGCAATGTGCTATTCTGTCTGGGTGGTGGGAATGCTGAGATCCATCTGGTTCCTCACTTGAATACATCATTTGTCAGTCTTGCTGGTCATATTTCTAAATGTGCAATTTTTAACTAGGCTTACCCTCTATATCTTATGACTTAAAAATACACACTCTGGCTTTCATTGAAAGCAAATATAGGCAAATCACTCAGGTTCTAGAAGAAATCTAGTATTGGTGAATCTTAGTCTTAAGTGCTAGATAATGGGAACCTTTAGTTCTGGTTCCTTAATTTCACAGTCCTCACATTTAAAGTACATAGATTGTCTTGCTTTTGAAACCTCTTAAAATGGGACTGGAGAGATGTTCAGTAGTTAAGAGCACTTGGCAACTCTTCCAGAGGACCTGGGTTCAATTCCCAGCAGCCACATGGATGTTCACACCTTTCTGTAACTATCTAGTTCCAGGGTTTCAGATACTCTCACACAGATATACATGCAGACAAAATACCAATGAATATAAAAATAAATTATTAAAAAATGCCTTAAAAAATAGAAGTTCTTAAACATAGAAAAGAGAGACACGTGACCCAGCTTAGCACTTATTTGCATTTGATATTCTTTCTTGAAAGCAGTCTGTGTGAGTGCTCTGATTATGAATGCTTATTGACTCAAATACTGTACTCTTAGCAATTGAGAGTAAACCTGGACTATAGAGTGAGACCCAAACAAAATAAACAAAGCCTCATCATTGATTGCAATGTATTTATATACTAAATTGTATTACTTTATTCCTTAG
Seq C2 exon
GATTATCCTTCAATTGCTCACCTTGTTCAGAAACTAAGTGAAAATAATATTCAGACGATTTTTGCAGTTACTGAAGAGTTCCAACCTGTTTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025809:ENSMUST00000090006:7
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(11.8=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(7.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGCTGATTGGCTGGAGGAAT
R:
AACAGGTTGGAACTCTTCAGT
Band lengths:
246-1175
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