MmuINT1021435 @ mm10
Intron Retention
Gene
ENSMUSG00000027111 | Itga6
Description
integrin alpha 6 [Source:MGI Symbol;Acc:MGI:96605]
Coordinates
chr2:71841644-71843302:+
Coord C1 exon
chr2:71841644-71841746
Coord A exon
chr2:71841747-71843128
Coord C2 exon
chr2:71843129-71843302
Length
1382 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
TATACGTTGTTTTCCGACAGGTG
3' ss Score
10.7
Exon sequences
Seq C1 exon
AGTCGCTAAGCCTTCGCAGGTGTATTTTGGAGGTACAGTTGTTGGTGAGCAAGCTATGAAATCTGAAGATGAAGTAGGAAGTTTAATAGAGTATGAATTTAGG
Seq A exon
GTAAGGCCAGACACAATGTTTACATGTCATTTTAATCAATGATCAGTCGCAGACATCTTAAGGAACTACTCAGTTGAAAATGTTTGCCTGTTTTTTATTTTTTTAAACATGTATATATTATTATGTATATACTATTATATCTAATTACATTGTAGCTGTCTTCAGATGCACCAGAAGAGGTCATCAGATCTCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCAGGACCTTCGGAAGAGCAGTCAGTGCTCTTAACTGCTGAGCCATTTCTCCAGCCCCTGTTTGCCTGTTTTTAACAGTGGAAACCTTATTCTCCCAAGTACAGAATAACTTTTGGGAATTGTAATGTGCATGTAATATAGACAAGAAGTAATACTTAATTATTTTTCCCCCTCAGGGTCTGTAAAACAAAGAAAAAGGCCTAAGTAATTCGTTCTTTGTTAGAAAGTCATCTTCTGATGCCCTTGGCTGAAGGAATACTCTCGTTTACTTCCCTCTCACCAAGCCCAATTTTTTAGTGGTGAAAGTAGACTTGGTATTTGCCAGCAAAGGAGGCAGATGGGTGATAGGCTCAGAGTGGGCAACCACAGTGACTTTGGGTCCAGCTTAACAAACTGGACATGGACTGTGGTGTCTGCCTTATGCCTCGTATGGATTTGGGTCTGCATAGTGCAAATGAGTTCCTAAATGCCGGTGAGCATTGAGCTTAAAGCCTGAAATGGCAAGAGTGGCCGTGGCCCTAAGCCAGCACTCTAAAGAGGCAAGGTCTCCCCAGGAAGGCTGGCTGACCTGAGCGCTATGCAGTCAGGAAGATGGGGATCGGAACTGTGCTCAGTAGTGCAGGTAGGCCACTCTGCCCTCTCACTCTGGGCCTCTGTTGTAGAAAGCTACTCTGACCCCAGCACTGGCTCTGAGCTGTCATGCAGTTCTCCATAACCTTTCCTGTGTGGCTGATGGCAGAGGCAGCTTCATTTTCACAGTAGGGAGGTTTTCCAGAAGCAGGATATGGGTGCCTGGGCCATAGCAGAGGCTTTGCCATCTGCCAGGCAGGGTGCTCACTGAACAATCCACAAACAAGCCCGGGACTTTGCCTGTGCTGACGGGAACATGCCATAACTGCATAAGGTAGTTACTTGTGGATTGAGCAGGCAATCCTTCCTCTTTGACCATTTTCCCCTTCTATTTTTATGACAAAAATCTTCTAATTACTACTGACTATTTCGCAAGCTCTGTTCCTGATCCGTTTGTGGGATTTGTGCTTCCTTGTAGGTTTATGCTGGGAATTTAGCCTATGGGCAATAGGATGTGCTACTTAATTTTGCCATAAAAGGATGATATTATATCGATATACGTTGTTTTCCGACAG
Seq C2 exon
GTGATTAACTTAGGCAAGCCTCTTAAAAACCTCGGCACAGCAACCTTGAATATACAGTGGCCCAAGGAGATTAGCAATGGCAAATGGTTGCTTTATTTGATGAAAGTTGAATCCAAAGGTTTGGAGCAGATTGTTTGTGAGCCACACAATGAAATAAACTACCTGAAGCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027111:ENSMUST00000028522:19
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:
PF084417=Integrin_alpha2=FE(7.1=100)
A:
NA
C2:
PF084417=Integrin_alpha2=FE(12.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTAAGCCTTCGCAGGTGTAT
R:
CTTCAGCTTCAGGTAGTTTATTTCA
Band lengths:
273-1655
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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