MmuINT0083790 @ mm10
Intron Retention
Gene
ENSMUSG00000027111 | Itga6
Description
integrin alpha 6 [Source:MGI Symbol;Acc:MGI:96605]
Coordinates
chr2:71825509-71826583:+
Coord C1 exon
chr2:71825509-71825719
Coord A exon
chr2:71825720-71826389
Coord C2 exon
chr2:71826390-71826583
Length
670 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
CCCCTTCGTTGTGTTTCTAGGTG
3' ss Score
11.61
Exon sequences
Seq C1 exon
GCTTTTCACTGGACTCAGGGAAGGGTATTGTTTCTAAAGATGACATCACTTTTGTGTCTGGTGCTCCAAGAGCCAATCACAGTGGGGCTGTAGTTTTGCTAAAAAGAGACATGAAGTCCGCGCATCTGCTCCCTGAGTATATATTTGACGGAGAAGGCCTGGCTTCCTCGTTTGGCTATGATGTGGCAGTGGTGGACCTCAATGCAGATGG
Seq A exon
GTAAGCATATCTTTGTTGTTATGTTCAGCTAACGTTGCTGATGGCTGCCTTCCGTAGGTCTAGAGAAGGGACTACGGGTTCGTTGATTAAAAAAACGTGCTTTACTATCCTGTCTTCATCATTGATTGACAGCTGGGCATTCATCATCATCCCCCTGCCCCAGCCCCGTGGTGTGGAATGACCTTTTAAATGCTATGCTTTCACTTGAGTTTGGAGACCATAATTTCTTAAAAATTTAAATTTGAAAAAAAAAAAAAGACTTAGAAAATGATATCGGCTACATGACAATCTCTGGTTTCTTGGGGGTAAAGGGCACAGCTGTTAAGCATCCAGAACGTCTCACAGAAAGCAGGAAGTGGTGACCATGTTGATACCTAGAGGATTCATTGCTCTTAGGGCCAGCTGGAAATGGAAATGGAGTGGCAGGTCCCTGTTGGAAGTCCTCTTGTTCTGTGGCTCCGACTTGAGGAGCTGCCTTTAAATTGCTACCTTCGCTATTTCCTTGGCTTATCGCAGATCTTCTGTTCAGTATTTTAATTGATGACATGTGAGTCTTTGATTTGAGGCTCTCTGTTGTTGTGTTTCTTGGAGCCTGGATTGTTAGTAATTTCCCTAAGCCTTTTGGCATCTTAGCAGTGGTCCCTAGCTCTCCCCTTCGTTGTGTTTCTAG
Seq C2 exon
GTGGCAAGACATTGTTATCGGAGCTCCACAGTATTTTGATAGGGATGGTGAAGTCGGGGGTGCAGTTTACGTCTACATTAACCAGCAAGGCAAATGGAGTAATGTGAAGCCGATTCGTCTAAATGGGACCAAAGACTCGATGTTTGGAATCTCTGTGAAAAATATAGGTGATATTAACCAAGATGGCTATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027111:ENSMUST00000028522:6
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:
PF135171=VCBS=PU(6.8=7.0)
A:
NA
C2:
PF135171=VCBS=FE(87.8=100)
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:
ACTGGACTCAGGGAAGGGTAT
R:
AACATCGAGTCTTTGGTCCCA
Band lengths:
348-1018
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