MmuINT0040489 @ mm10
Intron Retention
Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105698661-105702294:-
Coord C1 exon
chr9:105702198-105702294
Coord A exon
chr9:105699333-105702197
Coord C2 exon
chr9:105698661-105699332
Length
2865 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
CTAAATGACTTGGTTTGCAGATC
3' ss Score
6.35
Exon sequences
Seq C1 exon
ATTGATGACACTGGCACATTCCAAGTCATTGTGGTTCCCTCCGGGTCTGATGAAGGGCCAGCGTTAGAGAGACTCCAGCGGTGCACTTTCTGCTATG
Seq A exon
GTGAGACCCACGGGAAGAAGTGAATTTGATCAGGCCTGCTCAATGTGTTGAGTCAACTTTGGCAGGAGCAGCTGGAACTTGGCCGTAGGGATAGGCACGGCCTAGGGCAGGTCTCACTGGGGTTCGGGACACATACTGGATCTTCCACACATGGAACCTCTCAGCTCAGCCTGTAGGGCCCTTCCAATGCACCCCAGCAGGAAGCTTATACTCCTGGCCCTTCTACTTTAGTGCAGCTTCCAGGAAACAATAATAATTGAAAAACAAAACAAAAACCTTAGCCTGTCTCCTTGCCAAGTTTTTCCATGCTATAAAGGATTTTATATGTTTTCTAAATCTCAAATGTACACATACACACACACACACACACACACACACACACACACACACACACACACACACCTGGCCCCAAAGGCTTTGGAGCAACCTGGCACCTCCCTTCCTGGTCGGGAACTGTTTTTCAGTGCAGTGGGAGCGGAAGACAGCAACTCAGACATCCTCATCCAGGAGTCTTCATAGGCTCCCAAGAGTTAGGCAACAAAAAGATTTGCAGTATTGACTGTGGCGCACAGTCTGTTGGTCTAGCTGGGAAACAGCCTCTCTCCTCCTCCATCTGATGTTCCATAACCATGTGGGAGCCACTGGGGTTGCAGGTAGTCATGACAGCAGGCAGTTCCCCCCGTGTCTGCTCTAGTCTGTCCACTGCTCTCATTATTCTGCCTGATGCTGGCTCTTGTGGTGACAGTTCAAACTTAAGCTACTGGGCTTCTTATGCTCTCAGCACGGTTTTAATTGGTTTACATACACTGTGTCCATCTAGGCTTATAACCACACTGAAGTGTTTGAACTATTATTAGTAACATTGTACAGATGAGGGAGATGAAATCGAGAGAGATGTGATATTCTCCTCAGGGTCCCACAACCAGATCAAACCCAGGGAAGCTGGCTCCAGAGTGCCTTTAATTTTCGCAGACTAAGAGTCTCATTCTATTCCCTGAAACTCTCCCTTTAGACCTGGAGAAAGACCGTATGAGACCTTCTCCATGCACAGTAGTAGGATGCTGGGGTTTGCTGTGTAGATGACCTCACCTGGAGAGAGTGATTCTGAGAAGGGAGCAGACGTTCCCAGATTCCCCCTCTACAGCCCTGGATTCAAGCTCTCTGCTCACACCCTCCAGCCCTGTGGATTGTACTGGGAAGTTTTGGATCCGAGCACTCTCCTTCCTTCACATAAACTGGTGGAGTGCTAGGATCCAGCCTATACGCTCTTAGCTGCGCCCCTGGACATGTCAGCTCCAACAGTGTGCTGATGTGTTGCACGGTCATTAACTGCACATATGTGACAGGGGATAGGCTTTTGGCTCTGAGTCTTGGCTTAAACCCTTGCTTTGTCTCACAGGCATATAATGGAAGATATTTTGGCTGTCATTTCCTGCAATTAAAAACCCCACAGAACAGAGCAAATGGGCAGCCTGCTGTCCCTGATTTAAGAAACGGCTCTGCACACAGGTGACTATTCCGTCATCTGACCACTATTCAGAGTCATAAAATGTCACTAAGCTTCAGTAAGGGACTTCAGCTGAGCCATCTTTATTGATTCCATGAAAAAGCATGAAGATGGAAAGTTTGCTACACCCACAGGATCCACATGCTAGCCATTAGATTGTTCACTTAATAGTTGGTATTTATGGTCCATGCTGATATCTAATTTCCATCTGCATGCTTGTTACTCCATTTCTAACTTCCCCTTTGGTTTCTAAGGAACCCATTCTTACCCTCAGTCATCTACTAACAAACTAGACAGACCCTCAGCATCTGGGTCAGCCTGATGCCCAGTTAGTCACAATCAGTCATACAGAGGCCACTCGGTGGCTTGTTCAGAGGTGACGTCATGTTAGTTATGTGATAAGACCAGAACCTGGACATCCCAGCTCTCAGGTGAAGGGACCACCTTATACCTCATGTGTCCTTATCTCTAACGATAAGAAACTGCAATCTAGCTCAGGGGGTAAAGGGGCCCGTCTCCAAACATGACGATTTGAGTTCAACCCCTAGGACTCACGTGGAAGGAGGAAACTGACTCTCGAAAGTCCTCCTTTGCCTCCACACACATGCTGGGCTATGTGTACCCATGTATAAAACAAGTAAGTAAGTGTCAGAAACACCATTGACAGAAACTTCTAAAAATATAGTGCCTCCATTATGAATGTACTCCCCTGCTTCAGTGGGTTCCATGAAAATAGATGAAATGAATTCTAGAATCCTCTCATTTCTAATTTATCATACCCCCCCCCCATTCATTTATTGTGGTCACATTCAATAAAATCCACTCTCTGTTTTTTCCTTATGGTATGCATGCATAATGAGAGAGGCATATTTATAAAAATGACTTCACTTTATGGAAGAACACTTTTTATAAGGGGTATGAAGTTATGAACTCTTACTTAAATTGAAATAAAAGATGCATTGCCTTTTAAAGCTTAATTTTGAAAGCAGATGAGCTTTTCACAGCTAGTGTCGTGATTAAGGCCCGTAGTTTAGCCTGCACACTGTCAGCACTAGAAGTTCTCTCACAGTGTGTTCTTACACCAGAGGACGAATTGCTCACTTCAAACTTTATACACACAACAGTCAAAATTAAACTTCAATAGAACACAATTTAAAAACTGGTAGCATGGAGTCAAGGACTCACAGCCTGGTATCAGATCTGGACATCTTGGTGATAAACTCTCACTCTTGGTGTCAGAGATATAACTATTTTATGAGCAAAATCTATGTAGTGCCTGCATGCTCAAATAGCTGAGGTAGAACCTTCCTACTCTTTGTCTCGATCTGCTTAGTAACTCTAAATGACTTGGTTTGCAG
Seq C2 exon
ATCTATGCAAGCCGGATGCTTCGTGTGACCAAGCCAAACCACCCCCCATTCAGTCCTACCTGGACACTGCATTCCTACTGGATGGCTCTCGGCACGTGGGAAGTGCAGAGTTTGAAGACATGAGAGACTTTCTAGAGGCACTGCTAGATCACTTCGAAATCACTTCGGAGCCAGAGACATCTGTCACTGGAGACAGGGTGGCCCTGCTGAGCCATGCCCCCCTCGACTTCCTACCCAACACCCAGAGGAGTCCGGTTAGAACTGAGTTCAACCTAACCAGCTATAGCAGTAAGCGCCTCATGAAGAGACACGTGGATCAGGCAGTCCAGCAGCTGCATGGAGATGCTTTTCTTGGCCATGCCCTCGGGTGGGCACTGGACAACGTCTTTTTAAACACCCCCAATTTGAGACGAAACAAAGTCATATTTGTGATATCTGCTGGGGAAACCAGCCACCTGGATGCGGAAACCTTAAAGAAAGAGTCCCTACGAGCCAAATGTCATGGGTATGCCCTCTTTGTCTTTTCCTTGGGCCCTGACTGGGATGACAAGGAACTGGAAGACCTGGCCAGCCACCCCGTAGACCAGCACTTGATCCAGCTTGGCCGAATTCATAAACCTGACCACGGATACAGTGTGAAGTTTGTGAAGTCTTTTATAAACTCCATCAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719:ENSMUST00000098441:34
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=0.013
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(6.6=33.3)
A:
NA
C2:
PF0009223=VWA=WD(100=80.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
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