MmuINT0040497 @ mm9
Intron Retention
Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105682944-105684795:-
Coord C1 exon
chr9:105684235-105684795
Coord A exon
chr9:105683502-105684234
Coord C2 exon
chr9:105682944-105683501
Length
733 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
TCCTAATTTCTCCCACACAGCCT
3' ss Score
7.26
Exon sequences
Seq C1 exon
CCTGTGTGGACACAGAGGAAGCCGATATCTATCTACTCATTGATGGTTCAGGGAGCACCCAGCCCACAGACTTCCATGAAATGAAGACCTTCCTGTCAGAGGTGGTAGGCATGTTCAACATTGCTCCCCACAAGGTGCGAGTAGGGGCCGTGCAGTACGCCGACACCTGGGACTTGGAATTTGAGATCTCTAAGTATAGTAACAAGCCTGACTTGGGAAAGGCCATCGAGAATATCAGGCAGATGGGTGGGAATACCAACACAGGGGCGGCTTTGAACTTCACACTGAAGCTGTTGCAAAGAGCAAAGAAGGAACGAGGAAGCAAAGTGCCGTGTCACCTGGTGGTTCTGACCAATGGCATGTCTCGGGACAGCGTCCTGGGGCCTGCCCATAAGCTGAGAGAGGAAAACATCAGAGTGCATGCGATCGGTGTCAAGGAAGCCAACCAAACGCAGCTTCGGGAGATAGCGGGAGAGGAAAAGCGAGTTTACTACGTCCATGAGTTCGATGCCTTGAGGAACATAAGGAACCAAGTGGTTCAGGAGATCTGTGCTGAAGAAG
Seq A exon
GTAGGAGGTGACATGGCTTGACCTTCGGACAGCAGCTTACAGAGGGACACTTGCTGTTAGTCTAGATGGATGACCCACATTTCTAGGTTGAGATTGTTGACCTGTGTGGTATTTTCTCTCCAGAACAAAGCAAAACCCCATTATAGTATAAATTAATATCTGAAGAATGACAGAGCTATTTGGAGGATTTCACTCAAATGAGTACTAATTGGCCTCTCCCCACAGACTACTGCTAAGTGTATTATTAGGTGTCAGATGTATACTACAATCAAAAGTGTTCTGAGAGGGGCATGGCTATCTGATGAACGTTTCATTTTATAAATGAACTTGTCTAAATTTCTCTGGAGCGCTGTATCAGTAATTTTGCAGCCATGGCTTTTACTGCCTGAGAGTATTTGGTAACTTGTAGATACATTTCTGGCGTCTTAAGTGGGGATCTCTCTTAGAAGCCAGGATATTTGCTAACCATCTTACAGATAGACAATTCAGAGTACTGCTACAGTAAAAATGACCTGGCCTCAGATAGCTCCGAAATTGAGCTGCTTAAGCCAATTAGCAAGGAACAGAATAGTCTTGGCTTTTATTGCTGGCGATTCTTTCTTTGCCTAACTATCTTTATGATGCACACCCTGGGCTTGAACACAGAATTATTTGTGACATGGGTTTTCCTGTGAATTCTTAATTTTTTTTATATGCAGTGATGTACATAAGCATCCTAATTTCTCCCACACAG
Seq C2 exon
CCTGCAGAGACATGAAAGCGGACATCATGTTTCTGGTGGACAGCTCTGGCAGCATCGGACCTGAAAACTTCAGCAAGATGAAGATGTTTATGAAGAACCTGGTGAGCAAATCCCAGATCGGGGCTGACCGGGTGCAAATTGGCGTGGTCCAGTTCAGCCACGAAAACAAGGAGGAGTTTCAGCTCAACACGTTCATGTCTCAAAGTGACATCGCCAACGCCATTGACCGAATGACTCACATTGGAGAAACAACCTTGACGGGCAGTGCCCTGACCTTTGTGTCTCAGTACTTCAGTCCCGATAAGGGGGCCAGGCCCAATGTCAGGAAGTTCCTCATTCTTATCACGGATGGTGAGGCTCAGGACATAGTAAGGGACCCAGCGATCGCCCTTCGAAAAGAAGGTGTGATTATCTATTCTGTGGGAGTATTCGGCTCCAATGTCACCCAGCTTGAGGAGATCAGTGGAAAGCCAGAGATGGTTTTCTATGTTGAGAATTTTGACATTCTGCAGCATATCGAAGATGACCTCGTTCTGGGGATCTGCAGTCCCCGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719-Col6a6:NM_172927:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=91.0)
A:
NA
C2:
PF0009223=VWA=WD(100=90.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAACGCAGCTTCGGGAGATA
R:
TGAGTCATTCGGTCAATGGCG
Band lengths:
353-1086
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: