MmuINT0040490 @ mm10
Intron Retention
Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105695713-105699332:-
Coord C1 exon
chr9:105698661-105699332
Coord A exon
chr9:105695807-105698660
Coord C2 exon
chr9:105695713-105695806
Length
2854 bp
Sequences
Splice sites
5' ss Seq
GGCGTAAGT
5' ss Score
9.39
3' ss Seq
GGAGCCTTTTCTCTTTCTAGATG
3' ss Score
8.48
Exon sequences
Seq C1 exon
ATCTATGCAAGCCGGATGCTTCGTGTGACCAAGCCAAACCACCCCCCATTCAGTCCTACCTGGACACTGCATTCCTACTGGATGGCTCTCGGCACGTGGGAAGTGCAGAGTTTGAAGACATGAGAGACTTTCTAGAGGCACTGCTAGATCACTTCGAAATCACTTCGGAGCCAGAGACATCTGTCACTGGAGACAGGGTGGCCCTGCTGAGCCATGCCCCCCTCGACTTCCTACCCAACACCCAGAGGAGTCCGGTTAGAACTGAGTTCAACCTAACCAGCTATAGCAGTAAGCGCCTCATGAAGAGACACGTGGATCAGGCAGTCCAGCAGCTGCATGGAGATGCTTTTCTTGGCCATGCCCTCGGGTGGGCACTGGACAACGTCTTTTTAAACACCCCCAATTTGAGACGAAACAAAGTCATATTTGTGATATCTGCTGGGGAAACCAGCCACCTGGATGCGGAAACCTTAAAGAAAGAGTCCCTACGAGCCAAATGTCATGGGTATGCCCTCTTTGTCTTTTCCTTGGGCCCTGACTGGGATGACAAGGAACTGGAAGACCTGGCCAGCCACCCCGTAGACCAGCACTTGATCCAGCTTGGCCGAATTCATAAACCTGACCACGGATACAGTGTGAAGTTTGTGAAGTCTTTTATAAACTCCATCAGGC
Seq A exon
GTAAGTCAGAAAACTGTTCCTGTACATAAGAGCCTGCTCCGTAATTCCCCAGAAGGGCAATGTGCTGGCGTGCATGCTTGGACACCTCTTGTTTGTCTTCAAGGGCATTGCAGGGTCAGAGAGGAAAATATGTAATAATGGATGGTGGAAGGGAGGACACTCTGGTTCCTAAGCATTTAATTTTCTGGCTCATCATATTTTTTTTTTATGCCTCTGGTTCCTATGGAGAAGCAATCATAACAAGCAGCTGTCCACACATCTGTCTGCACAGAGAGGTGTAGTCTGGGGGGTGTGAAATCACAGCCTGGACTCGGGCTCCCTTGCCATGTAACCCTAACAAGCTACCCTTTGGTAAGAGGTTTCTGCAGTTAACACAGAGAGAGAGAGAGAGAAGCCAGAGAAAAACAGAAACAATTCTTGGCTTTGCTTGGACAAGTTCCAAAGTCTGAGCTGGGAGTGTTAAAGAGATATCGTTTTTTATCGGTCAGAATGAAAGGCATGGCTTTGTATAACTTTCTCCCAACTCCATGACCTTGTAGGATTCACTCACGAGAATAACTGTGCCTGTAAGGAGACAAGCATGGGCTGTTTTTCTTGGCTGGGCGTCCTGAGAAATCTGCAGTCCATTTTGGATGCAGCAGGGATGGCCGAGGAGCCGTGTCCAGATATGAGGCTGAAGGCAGACAGGCAGTGGGTAACTATATCTGTTTTCAGAGCCTGCTGACTCTTGTCCAAGGGAGTGCAGATAAGGAGACAGGCATGCACAGGTTGAAGAAGGCATGTGCGAGTGCCTGGCTAATTCCTAAAGCTGTCATCGTATTGAAGAGTGAGGTGGGATGAGCCTGCAGATGTGCTGAGCAGTGCAGAGAGACTGCTGGTGGGGTTGATGGCAAATCCTACTCAGTGTGAGTCTAGGACCAGCACCAACTACCAGCTGGGGCTGGTTAGACGCAGGCTTCAGCCCCACCCGATGATGTATCTTACCCGAGCTCCCAGGATACACATATACAAGGTTTTAGAAACACGGGTATGGGAATAGTGAGCCCCCCAGAGTGAGATTCATTTCCATAGATTCTGGAACTGAAACCCCAAAGAGGAGTTTTGGGCAAGGGGTCACCCTGAAGGAAGTCTTTTATAAGGGTTGACCAAAAGACCACTTGGTAAGTCTCTGGTAAACTCGAAAAGAAGCTTGCTTGATGGCCCACAAGTGTGGGGGAGAGAGGGTAAGACTTGCCCTGAAATTTCCTTCCTGGTATTCCAGAATTCTTCCTGCTCTTCCCTGCCTGGGCATCCAGTCACATGATCAGATGCCAGTCACATGATCAGATGAGGCAGCCCCTCCCTCTTAGGACAAAAGCAGAAATGTTTTAAGCTAAGAGCAGGTGGGACTCACGGGAGACACAGAGAGTGTTCTGAACACTGAGCGTGATACAGCCGCCTACTCCATTTCCAAAGCTGTGATATCTAGAAAGTGCCATCTTTAAAACACAGCTGCAGGAAGTGAATTCTACCACAGGCCCATGGTCATGCCCATTCAACACAGTGTTCATTGCTGATCATCTACTCTGAGCCACTGGCTGCACCAGTGCTAGGCTTAAAGAATAGACTTGGCCAGATGCCCTCTGAAGCTTCGGATGCCTTCAAAGTGTCTGTGACTCATTTGGCGCACGACCACAAAGCAGACAGCAGGACATGGTCCACTTCAGAGCAGCACATTCCCTAAGGGAGGCAAAGCTGCTGAGTCAGCAACCTTCTACATACTGTTCAAATAAGAAAAGAAAACCCCAAGCCAGATCTGGTGGGCCCAGCACACACCTGTAATGTTTGCTTTGGAGAGGCAGAGACAGGAGGATTGCTGTAAGCCAGCCCAAGCCACTTAGTAAGACCCTACCTCAAAACAAAACTCCTATGTAAGACAAAAACCCTGAAGGCCATATGGTAGAGCATACTGCCCTTCTTGTAAGAGCAGTTTTGAACATATGCCCTGTTGTAGTCCAGGACATGCCTGTTAGTTGGAAGAACCTACTCAACCAGCAAGAGGCTCTGTGTGTGTGTGTGTGTGTTTGCGCGCGCGCGCGCGCATGTGTGCATGCATGTGCCACATGTACATGTGTGAGCCAGAGGACAGCCTCAGGTGTCACTCCTCAGGCACCGTCCTTTGGAGACAGAGATTCCCAGTGATGCAGAACTTGTCCAGCAGGCTAGGCTGGCTGGCCAGTATAACCCAGCATCACCAGTAAATCCTATCTTTTTGTCACCTCCCCAGTGCCAGGATTGTAAGTACTTGACACCAGGCCTGGCTTTTCCAGAAAGGTATTTGCTTAACAAATCTTTTTGACTTCACGCTTTCAGGCATGCATAACACATTTAAAAATTTTTCTCTGTTAAAAAAAAAAAGCTTTGCATTTTCAAATGGATTAAAGCATGCTTTATTGTTATGAAAAATTAATACTCTTCCAAATGAAGTGAATCGGTGAATTGAACCCAAAGGCATGTAGTGTGTTGCTAACATAAAGACCATAAAGGGACTACCCTGTTCCCTTCGCACTTGGATATGCCACAAAAACAAAAAATAAACTCTAATGAGCTCCTATCAAAGGCAAGAGCGTTATTAGGACTGCCTGCGTTTCATAATGGCTGACGACGTTAGGAGCTACAGGCATTTTAATGAAAAGTTGTTTGAATTCACCAACATATTCACTAGAGACTTCTTTCCCAAACTTGGTTTGGGGACTTCTCTGGGACATTTCTCATGCCCTGTGACCATCTTTGGATGGACATTGGCAACTGCTGTGGTACTGTACAGAACAGACAGACCAACGGAGAGCTTTATCGGAGCCTTTTCTCTTTCTAG
Seq C2 exon
ATGGGATAAACAAGTATCCACCGGTCAACCTCAAAGCCAAGTGCAACAGACTCGGCTCTAGGGATCTGAAGCCGCCCCCACGCCAGTTTCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719:ENSMUST00000098441:35
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.406
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=80.4)
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:
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