MmuINT0083789 @ mm10
Intron Retention
Gene
ENSMUSG00000027111 | Itga6
Description
integrin alpha 6 [Source:MGI Symbol;Acc:MGI:96605]
Coordinates
chr2:71822438-71825719:+
Coord C1 exon
chr2:71822438-71822569
Coord A exon
chr2:71822570-71825508
Coord C2 exon
chr2:71825509-71825719
Length
2939 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
GCTCTGTATTGTTTTTCTAGGCT
3' ss Score
8.62
Exon sequences
Seq C1 exon
GGATCGTCCGTGTAGAACAAAAGAATAACACTTTTTTTGACATGAACATCTTTGAAGATGGGCCCTATGAAGTTGGTGGAGAGACTGATCATGATGAAAGTCTCGTGCCCGTTCCTGCTAACAGTTACCTAG
Seq A exon
GTAGGAGCCAGCAGAGGCACCACACCTGTCTCCTCAGACACTGGGTGACTCTCCACCTGAGGACCCAGAGCTGGGACTAGGTCTGGTGGGAGCCGGGGCCTTGCTGTGTTTGCTGTGTTTGCTTCAGCTTCACCTCTGTGCTCGTGGGAAGGCAGGCTGCCTGCTGACTGACTCCTCTGGCCTGAGCTTCCACAAAGTGGGGTGGAATCTGCCATCACCTCCAAATCATGCTTCCTCCCATTTGGAAGGGAGCTACGTTTCCTGAGCTGATGGTAGCCTGTGTAGACTGCAGCAGGACCATCGTGAAGCCATGAGGAAATGTCTGGGTGTTCAGAGTAGGCTGAGGGGTCCTTCCTCTGCCTTCAGGGCCATTTTTAGACAAACACTTAAGAGCTCCACTCACAAAGTTACTTTTAAGTGGCAGGTCAGGGCTTCCAGATCCTTCCTTGGTGATTGCTGTTCTCAAAGGCCTGGCCCTGCGACTGGATTGAGCTCCATGTCAGAGGGCCCTGTGGGTGGCACAGGGCGTCCCAGAGGAGGCCAACTAGGACCTGCTAACGCAGCTTGGAGAACACCCAGATTGTGTCTAAGTGCCAATTCCTTAACTCCTGAGGCTTGTTTGCATTACTAATGGTGTCCTAAATTATTCCTGCACATTATGGTAATTACACAAAGGCTTTTAAAAGCTTTAATTCTTGGTGTGAGTTGACATAAAGAATAATTACTGTACATTTCTTGGAAAAATGTAAAAAATCTTCTAGAGCTACATAGTAACCTATTTTTAAAAAGTGATGGGCAGGGGAATACACATATTCTAGAGATATTACTGGAACAATGGAAGGTTTAATAAAAAGGGAGAAAAAGCTGCTCTGAATAAGTAAATACATCTAAACAGTATGCTACAGTAAACATACATGTAAGTAAATCTAATTGTATAAATACACATGAGCAGTAGTATTTATGAAAAAAGAAAATCCCATACCAATTCATGCACCATTCCCACCCTCTCTACAAACTTGATAAGACAGTATTGAAAGAACGTTTATAGCAGCTGCTTATTAAACACTTGTTCTATGAGTAGGGTACTATGGTCAGTACTTTACACATTTACAGTATTATTAAAGATTGTTGTTGCCCCTCCCTGTGTTTACTGAGGGAGCTTAATTTCCCAAGCAATAGAGAAACACTCATGAAAAACAGTGCGCCCATGTAGCGACTGCGTGCACGAGGTCTGTTAGTGGCTTTGCGGGACAAGACAGGCTCTCTGGGCTAGGATCTTCCAGGAAAATGGCAACAAACCACTCTTTTCCATGGGCATATATTAACTAGCAAGCTCTCTTTCGGGATATGTGCTACTAAGGGATCATTTTATGATGGGTTGCATCTAATATTAATTATTCCGGTGAACAAGCCAGAAGTTTGGTCATTCAGATGCCCTTGGGGTTTATAAACAGGCTACTGGTAGAACATAGGGAGATGTGAGCCACTTTGTTTGTTTGTTCTCAGACCCCTTTGCCTCCTTCAGAATGGGTTTCCTCAAAAGTATATGTCTGAGAAAGAAGTCCGGTGTACGTTGTTACGTTTTGCTGGTCTGTGCCGCGAGGTTCTCATTTCCAAAGATGAGTGGGTGTAGGGTGTAATGATCTGCCTGAGCCTGTGGAAGGGGCACTGCTTGTCAGACACGACGCCACGGTCCGGCCTCTTACCACACTGCTTAACCGTTTTTCTTCAATCTCTCCATGCACACGGACAGGCCTGCTGTTTCTGACCAGCCTTTCCTATACAGATCCCGATCAGTTTGTTTATAAAACACGGCCTCCCAGGGAGCGGCCTGACGCATTCCCTGATGTGATGATGAATAGCTACTTAGGTTTGTGACCTCTGAGATGACAAATGAATTATTGCCTTGCTCATGGTCATTTCAAAATTGTTTTGGTCCATACAGAGCATAAATCTTCTTATTTTCTATTTCATTTCCAGTGAAACACATAGAAAAAGCATGCTCAGTGGCCAGATGGTTTTCAGCACTGGGTCAGCCATGTCTCCCGGCTCTAAACTTGGGGCTCATCATATTTTCAATTCACCTCACAATTTGAGAACTGCGACAGTAGTGGTGACGCTTTTTATAAATAAAACCCAACAAAAAGGGTGAAGTTAATGTTATTCTGCACCAGCTGCTTTTATACAGAGAGCGAGATGGATTCATTTGAAGAGTTTTGGCAATGGATAGTTCTATCTGCTTTTCTAGCAGACCTTAGAGTCACCCCAAGTGCATTATAATTGGACATTCCAATGTTGTCTGCCCTTTGAACAATATGTCACTGATCCAAATGACAGTTCACTCACCTCTATTGTTGATGCGAGGTTCTCAAATGACTGAATCACCATGCATGGTTTGTTTGCATGTTTGTGCCTGAGAACTGACTTGGTCCAAAGTAATGAGATGCTACTTACCGTATGTATTAGTATTTGCTCTTACCCGATTACCAAGCAGACTGGAAAGCATAGATGCTGTTCATGTAAGTCACTGGTCAGTGAAGAACCCTGTAACTTACACTCTGTAATGAGCACTACGATGTAGCATTCCTAGGCACTCCAGTATCTGGCTTGCTCTTCCTTTGTCATAGTTTTAATATCAGAATAGGATTTGATTTGATTCTTAAGATGGGTGAGTAGTTCACAATTCAAGCTATACCAGTGCTAAATAGCATAAAAGTGGTTTTTTAAAGTCTTTATAGAAAGCAGTAAAAGTGGTGTAGCCCTTTGCCTTTGACCTGTCAAGTCCTTTAGCACTATGACTCCTGTAGTAAATGTGGAAGTAGAGGGACGGATGGTGTGGAGAGGTGTGTGAGGATGCAGAGGGAAAGGTTATAGTGGAATTAGCACTTCAGTGTCCTCCCAAAGGTCAGGGTTGATGCGGCTCTGTATTGTTTTTCTAG
Seq C2 exon
GCTTTTCACTGGACTCAGGGAAGGGTATTGTTTCTAAAGATGACATCACTTTTGTGTCTGGTGCTCCAAGAGCCAATCACAGTGGGGCTGTAGTTTTGCTAAAAAGAGACATGAAGTCCGCGCATCTGCTCCCTGAGTATATATTTGACGGAGAAGGCCTGGCTTCCTCGTTTGGCTATGATGTGGCAGTGGTGGACCTCAATGCAGATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027111:ENSMUST00000028522:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF135171=VCBS=PU(6.8=7.0)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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