MmuINT0084055 @ mm9
Intron Retention
Gene
ENSMUSG00000025809 | Itgb1
Description
integrin beta 1 (fibronectin receptor beta) [Source:MGI Symbol;Acc:MGI:96610]
Coordinates
chr8:131244175-131246522:+
Coord C1 exon
chr8:131244175-131244374
Coord A exon
chr8:131244375-131246283
Coord C2 exon
chr8:131246284-131246522
Length
1909 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GTGTTTGGATCTTTCTGCAGGTG
3' ss Score
10.96
Exon sequences
Seq C1 exon
GTTCAATTTGAAATTAGCATAACTGCTAATAAATGTCCAAATAAGGAGTCTGAAACCATTAAAATTAAACCTCTGGGCTTCACTGAAGAAGTAGAGGTCGTTCTTCAGTTCATCTGTAAGTGCAATTGTCAAAGCCATGGCATCCCAGCCAGTCCCAAGTGCCATGAGGGAAATGGGACATTTGAGTGTGGAGCCTGCAG
Seq A exon
GTAAGTGCAGCCTTGCTGCAGCACAACAGACAGTATAGGCCACTTTATCTGGGAAGCCTGTATAAAATAAAGACACAAATCCTTTGCTCCAGTCACTCATATACTCTTAAGGATCTCTCTGTTCTTAAGCTTTTAGCTAGGTAAGCAGTGTGTCCACTGTCTCTCAGGGCAGCATTTGGGCTTTGTTCTCTGAATGGCACTTCCAGTTCTTGACAGCAAAATACATTGAAAAGAAAAGGTAGATAGAAACATTTTTGTACAAACTGTCAATGGTGACTGTATTAGTCAGGGTTTTACTGCTGTGAATAGACACCATGACCAAGGCAAGTCTTATAAAAACAACATTTAATTGGGGCTGGCTTACAGGTTCAGTCAGAAGTTCTGTCCATTATCATCAAGGTGAGAGCATGGCAGTATCCCGGCAGGCATGGCGCAGGAGGAGCTGAGAGTTCTATGTCTTCATCCAAAGGCTTCTAGTGGAAGACTGACTTCCAGGCAACTGGGGTGAGGATCTTATATCCACACCCACAGCGACACACCCATTCCAACCAGGTCACACCTATTCCAACAAGGCCACACCTTCAGATGGTGCCACTCCCTGGTCCAAGGATATACAAACCATCACAGTGACTTTTTAAATTTTGTTTTATTTTGGATGACCCTAAATTTATGATCTTACTGTCTCAGTACTTGGGTTATAGGCAGAACTCAATACTCTCAGTGTTAAATGACAGTTTTATCTGTGACTTAGTTAACAAGAAAAATGTTTACCATGTCCAGGATTAAATTTTGTATTTCTGGGATAAAAATAAAATAGTACTTAAAGTTTACATTTATGTATGTATGTATGTATGTATGTATGTATATGTGTGTATGTGAGTGTGTGTGTATACCCTAGTGTCTTGGCACAGGCTTGTGGTGAGAACAGTTGTAAGAGTTGGTTCTCTGTCTACCTTGTGAATCCTAAGGTTGTCAGGTTTGGTGACAAGTACCTTTACCTTCACCAGACTTCTTGGCTACTTTTTATGTTAAAAACTAAACTGTGTTTGTAATACAGCCTTTTCTTTAAAGTAATAGAACCTTTTAATCTAAATGTCAGTCTCACATCACAGTGGTTTTGTTTATTGGCCCAAAGAAAAATGAATAGCTAATGTTTACTATTAATTGCCCATTTTAAGCAATGATTTAAATATTGTGTTTTTTCTGTTATATTTAACTTGAGACATTAAGATATCTTTTTGTTTAAACAGCATTTTATCAAAAAGGATTTTTTAAAAATTCTTTGTCTTCTTTTTGATTAGCATATGCAAAATCAGTTTATCCAGTGTCCAAGAACATGCTCCAAGATATGTAGGATATTTTAGAAGTCTAGATCTGTGCAGTAAACTTACCCTTAGTTAAAGCTAGTACTATTTTCAGTTTGTGTACTTTATGTATTTTTCAACTTTTGGGGTTGCATTCATTGCTATTTTTTATCCTAACAGACCCTTGCTTCAAATTTAGTGGCAGGTAGTCTGTAACAATAATATAATTGAAAATATTTGAGAATCTAGCCCTGCAAATTGATACATTCCTTTATTCCCCTGCATTTGGGAACTAGAGGCAGGCAGACTCTGTGGTCAAAGTTAGCCTGGTCTATTTTTCTATTTTTCTAGTTGTTTTGTTGTTTGTTGCTGGAGTATGCTTTCATTTTGCTCAGAGTGGTTCCTTGCTAAAGGTAAATTTTCCCCAAGGCTCCTGTATGTTCTATAAGAACTTGAGTTGCTACTTGCATGTGTGTATATATAAACACAGTGGACTTATCTTATGTTTGTACATGTGGAGTGAGCATCCCTACTTGATACTTTGCTAATGTGAGGAAATTGTTACACTTTTTGTTTTATGTGACTGTGTTTGGATCTTTCTGCAG
Seq C2 exon
GTGCAATGAGGGGCGTGTTGGGAGGCACTGTGAATGTAGCACAGATGAAGTGAACAGTGAAGACATGGACGCTTACTGCAGGAAAGAGAACAGTTCGGAAATCTGCAGTAACAATGGAGAATGTGTCTGTGGACAGTGTGTGTGTAGGAAGAGAGATAATACAAATGAAATTTACTCTGGAAAATTCTGCGAGTGTGATAACTTCAACTGTGATAGGTCTAATGGCTTAATTTGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025809-Itgb1:NM_010578:11
Average complexity
IR-S
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=PD(9.3=59.7)
A:
NA
C2:
PF079748=EGF_2=WD(100=64.4),PF079748=EGF_2=PU(32.3=16.9)
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:
ACCTCTGGGCTTCACTGAAGA
R:
ACAGTTGAAGTTATCACACTCGCA
Band lengths:
343-2252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: