MmuINT0084066 @ mm9
Intron Retention
Gene
ENSMUSG00000025809 | Itgb1
Description
integrin beta 1 (fibronectin receptor beta) [Source:MGI Symbol;Acc:MGI:96610]
Coordinates
chr8:131241107-131241574:+
Coord C1 exon
chr8:131241107-131241202
Coord A exon
chr8:131241203-131241484
Coord C2 exon
chr8:131241485-131241574
Length
282 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATA
5' ss Score
8.49
3' ss Seq
TTTTACATATTTAATTTCAGGAA
3' ss Score
9.42
Exon sequences
Seq C1 exon
GATTATCCTTCAATTGCTCACCTTGTTCAGAAACTAAGTGAAAATAATATTCAGACGATTTTTGCAGTTACTGAAGAGTTCCAACCTGTTTACAAG
Seq A exon
GTAATACAAAGAATGAAAGTTCTATATTTTTCCTATTGTTTAGTCATTAGTAGCTGAATTATATTTTTGGAATGTAAGAAAATGCCACAAGGCATTATGTTCAGTAGCTAGACTGAATTTGACAACCGTCATTTATGTTCATTTTAGTTGTGTATTATTAGGATTGTTATTTTAAGTTTGCCTTTGAAAGATACTTAGGAAATGAGGTGTCAAAATACTACTTTTCAGTGGATTTTAATTGGTTGAAAAAGTAATATTTATGTTTTACATATTTAATTTCAG
Seq C2 exon
GAATTGAAGAATTTGATTCCTAAGTCAGCAGTGGGCACACTGTCTGGAAACTCTAGTAATGTGATCCAGCTAATCATCGATGCCTACAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025809-Itgb1:NM_010578:8
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=FE(7.2=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(6.7=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:
TCCTTCAATTGCTCACCTTGTTCA
R:
TTGTAGGCATCGATGATTAGCTGG
Band lengths:
180-462
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: