MmuINT0084057 @ mm10
Intron Retention
Gene
ENSMUSG00000025809 | Itgb1
Description
integrin beta 1 (fibronectin receptor beta) [Source:MGI Symbol;Acc:MGI:96610]
Coordinates
chr8:128722810-128724428:+
Coord C1 exon
chr8:128722810-128723032
Coord A exon
chr8:128723033-128724195
Coord C2 exon
chr8:128724196-128724428
Length
1163 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
TGTAACAATTTCTGTCTTAGAGA
3' ss Score
7.45
Exon sequences
Seq C1 exon
GCAATGGCGTGTGCAGGTGTCGTGTTTGTGAATGCTATCCCAATTACACTGGCAGTGCATGTGACTGTTCTTTGGACACTGGTCCATGTCTAGCGTCAAATGGTCAGATCTGCAATGGCCGGGGTATTTGTGAATGTGGTGCTTGTAAGTGCACAGATCCCAAGTTTCAAGGGCCAACTTGTGAGACATGTCAGACCTGCCTTGGCGTCTGTGCAGAGCATAA
Seq A exon
GTAAGTACTGCCAAAGTGTTTCACATAGTCACATTCACTTTACTGACCCTACACCACTAGAGCCAGAGGAGAGTGCTGATAGAGTATACTTCAAAGAGAATATTTGCTGCCTTTTATGTACCATTTTTTATGTCCTAAAAATTCTTAATTGTGTAACAATGAAGTGTGCCATGAGAGTTGTACTATTTTTTTTGTTGTTGTTTGTTTTTAATCTGAAATCACTGTATAAGTTTGCTGTTAGTTGGCAATACTATCCTCTGTTTTTAAGGTTTAGTGGTAGAGATAAAACAATGAACTCTACCATAGAGGAATATTCTCTAGTCTAGTTGCTATCTTTTGCTTCAGGAGAATGGAAGGTGAATTATTATACCAATACTGCTTAAGTTATTGTGGTTTTTATGTTACAAATTTAATGTGACATAGGTCCAGTTTTATTAACTACATCTTAATTTTGTGTTGTGAAGATTTATATGCATACATGTGAATGTATGTATGTGTGTGTGGGCTATCACCAAGGGCTTAGAGTAGATTTTAATATATGTCCCCCACGTCTGCAATGTGCTACTTGTTGGTCTTAGACATACCTGTTAGAGGTTTGTCATGGACATGCTGGTGTCTTTACAAAAAGGATTCACAGTGTAGGCCTAATTGGCATCTGTGTAGCAACCATAGCTGTGCTCTGGATGCCAGGGTCTGTACTGGATGCTGAGCAGGTCCCCATAGCTGACTAGGAAGTAAGGTTTGTGAATCCGATGTTGGGTGAACTCTTCTTGATAAGGCTTGGTGTTACTAGGCCCCATAGTCACTGGCCTTTACTGAAGCTCCTTATTCCTCCAGTGGAGGGCACATGCTTCAGGCAGCTTCTGTAGCCAGAGGCTTCCTGGGTGCTTTGCTACTGCCAGTGGACTTAGTCCAAGGTGGGTCTGGAGAATTTATTACCTACCCCTTTATTCTTTGACAGGTTTGCCAGCCAGAGTGTTGCTGGCCTTAGTGGCCGTGGCTTGGCTGAGGCTGCTGGAAACCAGGATCTCATGTGGAGCATAATGCCTATTTCCTCTGAATGTATATTGCCCTTAGATTGGTATGGCCATTAGTTTAGCACATGAAGTATTCTAAGCAAAGTTAATCTTAATACACGCTAAGTGTAACAATTTCTGTCTTAG
Seq C2 exon
AGAATGTGTTCAGTGCAGAGCCTTCAATAAAGGAGAAAAGAAAGACACGTGTGCACAGGAGTGCTCCCACTTCAATCTCACCAAAGTAGAAAGCAGGGAGAAGTTGCCCCAGCCGGTGCAGGTCGATCCTGTGACCCATTGCAAGGAGAAGGACATTGATGACTGCTGGTTCTATTTCACCTATTCAGTGAATGGCAACAATGAAGCTATCGTGCATGTTGTGGAGACTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025809:ENSMUST00000090006:13
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:
PF079748=EGF_2=PD(64.5=26.7),PF079748=EGF_2=WD(100=42.7),PF079657=Integrin_B_tail=PU(4.5=5.3)
A:
NA
C2:
PF079657=Integrin_B_tail=PU(91.7=97.5)
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:
TGCAGGTGTCGTGTTTGTGAA
R:
TTGCAATGGGTCACAGGATCG
Band lengths:
356-1519
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