MmuINT0071354 @ mm10
Intron Retention
Gene
ENSMUSG00000091345 | Col6a5
Description
collagen, type VI, alpha 5 [Source:MGI Symbol;Acc:MGI:3648134]
Coordinates
chr9:105862749-105864835:-
Coord C1 exon
chr9:105864146-105864835
Coord A exon
chr9:105862846-105864145
Coord C2 exon
chr9:105862749-105862845
Length
1300 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGT
5' ss Score
10.93
3' ss Seq
AAGAATTCCACTGTCTCCAGGTG
3' ss Score
6.61
Exon sequences
Seq C1 exon
AACATGAAAGTCATGGCAGAGAAGAACTGGGTCTTGCTCATGAGCCTGGGGATGCTTCTCTTCAAGAATATTACATGGACGTGGCTTTCCTCATAGATGCTTCTCAACGAGTAGGAGGACGTAACGAGTTTAAGGAAGTGAGAACTTTGATAACGTCAGTACTGGATTACTTTCACATTGCCCCAGCTCCACTGACCTCTGTCTTAGGAGACAGAGTGGCTGTCCTGACCTACTCTCCCCCAGGCTATCTGCCAAACACTGAAGAGTGCCCAGTCTACCTGGAATTCGATTTGGTCACTTACAACACTGTACATCAAATGAAGCATCATCTCCAAGAGTCTCTTCAGCAGCTCAATGGTGATGTTTTTATTGGGCATGCCCTTCAGTGGACAGTTGACAATGTCTTTGTAGGAACCCCCAATCTGAGGAAAAACAAAGTTATCTTTATAGTAACTGCAGGTGAAACCAACCCTTTAGACAAAGAAGTTTTAAGGAATGCATCTCTGAGAGCCAAGTGCCAAGGCTACTCCATATTTGTATTTTCCTTTGGTCCGATACACAATGACATGGAGTTAGAAGAATTAGCAAGCCACCCTCTGGATCATCACTTAGTCCGGCTTGGCCGGGTACACAGGCCAGATTTGGACTATGTCATCAAGTTCATCAAGCCATTTGTTCATTCGATCAGAC
Seq A exon
GTAAGTCACTCAAGCCTCTCTCCTTTGTTGCTTTATTGATGTCTCTGTGTGCAGTCAATCAGCGTACTTAATCAAATGCATGTCATTTTAGTAGAGAGTGGTAGGATGTGAACAGGAGTCAGTGAGAGAATCTCAGAGAAAAGCCTGTTCATGTTGGGTACAGTTCTAGGCAGGAGATCCTCAAATAGTTGAAAGATTTTCTTTAAGCCTGACTTCTGAACATTTGCTACGTGTTTGGTTCTCTGACTGGCTACATCAGTTAATCTTCAGCATAGCCCTCAAAGGGATGAATTCAGATCCCTTTTCTATAAAGGAAAAACTAAGGTTTGAACACACTAAATACATTTCTCAAAAGCTCATAATTAATGCATGGTAAATTCTAGACTCAACCCCACACATTCTGACCCTAGGAATATATTCTTTTCTATTAAGCTGCACTTTAGTTACTAAACCCTTAACAAAGTGTACTGTTATAGTAAATAAAACCCCTACTATCACTACCTCCACTTTTCCCAAGGACATCTGGTCTACCTTGTCAGCCTTGGTTCTGAATTGAATTCTTATGATTTATAGGTATAGCTATTTTCTAGAGCCTCTCTGCAAGATCTAGCTTAAATACAACCACATAGTGATTTGAAATGTGTCTTTCTACTGTGGCTCTCTGAGAGTAGCTGCTTCAGCTTCTGACCTTGGCATTGTAATTTTAGACAGAGGTATGGAATAGGCTAAGTTTTTAGAAGTGTCAAACAAGTCCTGGCCTGTGCTAGGAATCAGGACAGAGCAAAAGTCATGCTGTGTGGTAATCTGTGGTGGCTGGGAGCTTGCTAGGGTTACCCAGGATTTTAGGAGTTCTGGCACACACACAATCCCAGGACTCGGCTTAGAGTTAGGAATCATGGAGTTCAGGCAATATATTTACTACTGAGTCAAAAACAGTGCCTTCTTTCAACCCCAAGGTAGAAACAAGGAAGACAACTTCAATGGCCAACAGAGCTTATTAAGAAGAGCCTCCATTTCTTGGGTGTGGGATGAGGGGAGAAGAGATAACAGGAGGAATGCAGAAATGTCCTTGAATTGAATCACCAAGCATGGGAACTTTTAATTCAATTATTGCTATATCTCATTGACTTGGCAAGAACAAGGTCTTTCAATGCCAGCATGCCGACTTTGCAAAGTCCCTCACAAGATTAATTTGTTTTTTTAAGAGACTTCCATCTCCAGGAAAAGATGAGTTGACTTTTTGGGTTATAGGCATTATGTGGGAAGGTAAAAACTGGACTAAGAATTCCACTGTCTCCAG
Seq C2 exon
GTGCTATCAACAAATATCCCGGCAGAGACCTGCAAGCCAAGTGTGATAATCTCACCTTCCCTGGCCCAGAGAATGCTGGCACAGAAGACAGTGCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000091345:ENSMUST00000190193:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.052 A=NA C2=0.323
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=78.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCTTCAGTGGACAGTTGAC
R:
CACTTGGCTTGCAGGTCTCTG
Band lengths:
356-1656
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