MmuINT0040495 @ mm9
Intron Retention
Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105685960-105688605:-
Coord C1 exon
chr9:105688009-105688605
Coord A exon
chr9:105686581-105688008
Coord C2 exon
chr9:105685960-105686580
Length
1428 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
ATTTCTTTTTCCCCACACAGCCT
3' ss Score
8.63
Exon sequences
Seq C1 exon
GCCCCGAGTACGCAGACGTGGTGTTTCTGGTGGACAGCTCCGATCACCTAGGGCTTAAGTCCTTTCCTCTTGTGAAAACTTTCATCCACAAGATGATCAGCAGCCTCCCCATAGAGGCCAACAAGTACCGCGTGGCCCTGGCCCAGTACAGCGATGCTCTCCACAATGAGTTCCAGCTGGGCACCTTCAAGAACAGGAACCCCATGCTGAACCACCTGAAGAAGAACTTCGGGTTCATCGGTGGCTCCCTGAAGATAGGGAACGCCCTGCAGGAGGCTCACAGGACCTATTTCTCTGCTCCCACAAATGGAAGAGACAAGAAACAGTTCCCCCCAATCCTGGTGGTGCTGGCTTCAGCAGAGTCTGAGGATGATGTGGAAGAGGCTGCGAAGGCCCTGCGGGAAGATGGGGTGAAAATCATCTCTGTGGGGGTGCAGAAGGCTTCTGAGGAAAACCTGAAGGCGATGGCCACCTCTCAGTTCCATTTCAATCTCAGGACTGCCAGAGACCTCAGCGTGTTTGCCCCAAACATGACAGAGATCATCAAGGATGTGACTCAGTACAGGGAAGGAATGGCAGATGACATTATTGTAGAAG
Seq A exon
GTGGGTGGTCTAATTTTCTTTGTATTGTTGTGATAAGACACTGGCCAAACACAGAGTAGGGAGAAAAGGGTTTATTTTAGCTTATTGGTTTACAGTCCGTTGTGGAGGGATGTTAGGACAGAGATTCAGTCAAGGACTGAAGTAGCACCTGGAAGGACACTGCTTGCTAGCTGGCTCCCTCTAGCTTACTCATCTACCTTTCTTATATACTCGCACTTGCCTAGGGATGGTGTTGCCCACAGTGGGCCAAGTCCTCCTCCATCAATTAGCAATCAAGGAAAGGCCCCAGACACATGCCCTCAGGCCAATTTGATGGAAGCAACTCTTCTAAGTGTGTCAACATGATAACAAGATTTACCAGGACAGTGAGCTAGGCTCTGTGCATAGGACCAATGTCAAAATGATTTTGAAAAATCAAGATGGGAAGAGAATTAAAGTCCTATGAATACTCCTTTCTTCCAATGGGTGGCTTTTTCAGGTATTAAATATCTCTTCATGCTCAAGAAGATACAGAGATTGTGGCCATTAAAAAAAGAGAAAGAAAGAAAGAAAAATGAATCCCATTAGCCTTGGGTTTTTTTCATGGCCTATTTAACCCTGGATTTAAAAATTCTGAAAAATAAGAAATCCTTGCCACCCAGGTCCCTCTCAGCCACCGCCCTAGGTTGTTCCTGCTGTGGGTTTATTGCTGGTTTAGTGAAAACAAATTTGGTTCTGGAGAAGTCTTTGCTTCAGAAACCACACAGTGTAACCACAGAATGTCAAGGCCAAAGCCAACCTCTGGTTATTCAAACCCTATTCAGAAGCAAAGAATTTATGTGGTATGCTCTGCCGCAGTGCCAAGCAGCCAGGTGTGGCCAGAGCTGGGGGAAGTCCCCTGGTTTCTAGTCAGGTAGCCTGGACCCCACATTGCTTATTCTGCTGTTGGATGCTGCATTTGCCTCTGTGTTCTCCACAGTCTGCTCCCTTGGGTAAATCAGCTTGAGATGGCCCAACTGACAACACAGAATGCTTTCCTGTGGCAACTTTTGGAGATACGGATCTTTTCTATTAGTGTCTTTCCCAAATAATTGAAGATGCGCCCTTTAGCGTTCCTTTGCAATATTTAGGTTTGAGCAGCTGAATATAATAAAGGTGGTACCTAAATGATTTTCACATTTAATTAGTGTTTGTTGAATGAACCTGGCTCCATATTAAGTATATCATTTATTTAATATCTATGCCAACTCTATGAGGTAGTTTATTTTATAAAATTATATATATATATATATGTATATATATGTATATATATATATATATATATATCCACATCATACCTCCTTTACATAGCTGAGCTCCATTGTATATTCTATATCTCTTATGATGCTCAGTAGAGGTGCTGACCTTCCTGAGATAACTGTGCTGACTCATTTCTTTTTCCCCACACAG
Seq C2 exon
CCTGCCAAGGCCCTTCTGTGGCTGATGTGGTGTTCCTGTTGGATATGGCCATCAACGGCAGCCAGGAGGACCTAGATCATCTTAAAGCATTCCTGGGCGAAAGCATCTCTGCCCTGGACATAAAGGAAAATTGCATGAGGGTTGGCCTGGTGACCTATAGCAATGAGACAAGGGTGATCAGCTCTCTGAGCACGGGTAACAACAAGACAGAAGTCTTGCAGCGCATACAGGATCTGTCCCCTCAAGTAGGGCAGGCCTACACTGGAGCTGCCCTCAGAAAGACTAGGAAGGAAATCTTCAGTGCACAGAGGGGCAGTCGGAAGAACCAAGGGGTCCCTCAGATCGCTGTGCTGGTGACCCACAGAGCATCAGAAGACAACGTGACCAAGGCAGCTGTCAACCTCCGGCGGGAGGGAGTGACCATCTTTACCATGGGCATAGAGGGGGCTAACCCAGACGAGCTGGAGAAGATCGCATCCCACCCTGCGGAGCAGTTCACCTCCAAACTGGGCAACTTCTCTGAGCTGGCCACCCACAACCAGACGTTCCTGAAGAAACTGCGGAACCAAATCACACACACGGTCTCTGTCTTCTCAGAACGGACTGAGACCCTCAAATCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719-Col6a6:NM_172927:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.035 A=NA C2=0.111
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=89.5)
A:
NA
C2:
PF0009223=VWA=WD(100=86.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATGATGTGGAAGAGGCTGC
R:
GTCCAGGGCAGAGATGCTTTC
Band lengths:
349-1777
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: