MmuINT0040488 @ mm9
Intron Retention
Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105604528-105611914:-
Coord C1 exon
chr9:105611421-105611914
Coord A exon
chr9:105604625-105611420
Coord C2 exon
chr9:105604528-105604624
Length
6796 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGC
5' ss Score
5.59
3' ss Seq
TCACTTCTGCCTTCTTCCAGATT
3' ss Score
11.4
Exon sequences
Seq C1 exon
GAAAACCTGAGTGCCCAGTGCATCCAACTGAGTTGGTGTTTGTCCTGGACCAGTCCCGGGATGTCACAGAGCAGGACTTTGAGCGAATGAAGGGGATGATGGTCTCCCTAGTTAGGGATGTCAAGGTTAGGGAGGCCAACTGCCCCGTGGGTGCCCGCGTTGCCATCCTAGCCTACAACTCCCACACCAGGCACCTCATCCGCTTCTCAGATGCCTACAGGAAGGACCAGCTGCTCACGGCGATTAAAGCTCTTCCTTATGAGAGATCCTCCGACAGCAGGGAGATTGGCAAAGCCATGAGGTTCATCTCCAGGAATGTCTTCAAGAGAACCCTTCCAGGGGCTCATGTGAGAAGAATCGCCACGTTCTTTAGCAGTGGTCCATCGGCCGACGCCCAGACCATTACCACAGCCGCCATGGAGTTCAGTGCCCTGGACATTGTACCTGTGGTGATTGCGTTCAGCAACGTGCCCTCGGTCAAGCGCGCCTTTTCA
Seq A exon
GTAAGCACTGCATAAAGCCCTTTTTATCCCTGTATTTCACCAATCTTCAGAAACATCATAAGAAAATACATAGCTATATTTTCTTGCCTTTCAGAACAAGGTCATTCCAGTTAGCTAAATACAAGGGTAGGTGCTTCATTGCTATTTACCAAGCACTGTTCATTATCCTGTTCATTATCCTGTTGAATTCTCACAACTACTGTGCAAAGATGAAGATAGGGGTTTTGTTTTTCTTTCTCATTTTGTAAATGAAAGGCTGAGCCTAGACAAGGCCCACTTCTGGTCCAGGTTCCACAGTTGTCAGAGCAGAGTGGTGATGTTAGGGTTTGATGCTAAGTTTGCTTCGCCACAGCTTTCCCAGCTGCTTACTGCATGGCCTCTGCCTCCAAAGATACTAAACTCAGGAGGTTAGTAAACAGATAGGAGTGTCCTTGAGATGGTCATGATAGTGGTCATTGCTGTGTGGTTTTGAAAAGCTAGCACACCCCTGTAATCCCAGCACTTGGGAGGCAGAGTACGAGAATCAGAAGTTCAGGGGCTTCCTTACCTACCTGGTGAGTTCAAGGCTGGTTTGGGGCTATATGAAAAATCTGTCTCAAAACCTCTTCTATGGGTGTGTGGAAACAGCTCAGGAAAGTGCATTAGGACCTGAATTTCAGGTCCCTAGCACCCACACAATGGCTAAGCATGAAAGTGTACAGTTGTAAGCCCAACGCTGGGCAGCGACAGATGGCACCCTGGAGCTCACTGGCCAGCCAGCCCGAAAGAGTGGCTGAGCCCTAGATTCATCTATCTCAAAAATCAAGATAGAGAGTGACTAAGTAGTGAGAAAGACATCTGGATAGCCCTTGGCTTCCCCATGCATGTCATACGCATGTACAAATACACAAAAGATCCATGTATCACACAGCCACATGAAAGCAAAGTAAATAAACAGAGAGGCTAATTTTTTTTAAACTTCATTTATGTAAAAGTCCCCAGCTTATAAAAGAAAAGCCAGTCCAACTAAAGCGTCTTCCATTAAGGATTAAACCTAGCTTGTAGCATCCCTCAGTAAACCACCTGGGATGGAGACATCCACCCCTTGCCATCCTTAATCGAAAAAGACACACTGGCCCCAACAAAGTATCCTTCCAGTGGGTACTGCCCCAGTGTGATGTTGGGCTCCCCCGTTTATAGCGAGCTCCAGACAGCAGGACCAGAGTATTAGGGAATACATGGGAAATAAGTCTCAACGTTTGACAGTTCATGTAAAGAGTAAATGTCTCACTGCTGTGCCTTGGGACCCAGAACATCCTAGCAAGCACAAGGGCGATTAGCTTTGCCCTTTTTAGTAGCTTGATGCTGTTTAATACTAATGGGACTGGTGTAGCACAGGAGATGGCTATTAGCATCAGTGGACTCCGAATTATATAAACAAAAAAGGACTGATTCGTCCAAAGGATACTGTAGGTAGATTAGGAAAGGCTGGGTCTAAGCCATGCAAACAAAGCCTCGAAATTCTGTAAGTGATTTTGGTGAGAGCGCCCTTGCAAGTTTAGTCATAAAGGACAACTTCATACCCTGACAAAAACACTTGGTGGTATTTGTGACACGTACCCACTCAGAAAGTACAGTGTATGAAAGGTATTGTGGTTTGGGGTTAGGTGTTTGGGTTGGGAGTTTATCAACCTTTTGCTGTGAACATCCACAAAGACAGTTTCTCGATTCTACCTAAATTGCCTAGAGATTCTCTAAGTAATGCTCGATTTCCAAAAATCGGGTCTTGTGGAGCAGAGAAGACAGCCCAGGAGTGAAGCACTTTGCCTGGGATCCAGTGTTTGAGTCTCCAGAATCCATGTAAACTCAGTGCAGTCGTGAGTCTGCAATCCCAGCACTTCCTCACAGGGATGGGGCAAAGAGAGGATCCGCTGTAGTTCATGGGCTAGGCTGAAACGCACAGCAGCGAACAACCCCTGCCTCACCTACGGTGGAAGGCAAGGACCAACACGCAGTGCTGTCCTCTGACACATGTCAAGATCATCCAAAGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTCCTCCTGCTCCTGCTCCTGCTCCTGCTCCTGCTCCTGCTCCTGCTCCTGCTCCTCCTCCTCCTCCTCCTGCTCCTCCTCCTGCTCCTGCTCCTGCTCCTCCTCCTCCTGCTCCTCCTCCTGCTCCTGCTCCTGCTCCTCCTCCTCCTGCTCCTGCTCCTCCTCCTGCTCCTCCTCCTGCTCCTCCTCCTGCTCCTGCTGCTGCTCCTGCTCCTGCTCCTGCTGCTGCTCCTGCTCCTGCTCCTGCTCCTCCTCCTCCTCCTGCTCCTGCTCCTCCTCCTGCTCCTCCTCCTGCTCCTGCTCCTCCTCCTCCTCCTCCTCCTGCTCCTCCTCCTGCTCCTGCTCCTCCTCCTGCTCCTGCTCCTCCTCCTGCTCCTGCTCCTGCTCCTGCTCCTGCTGCTGCTCCTGCTCCTGCTCCTGCTCCTGCTCCTCCTCCTTCACCTTCACCACCACACTCAGTCCCACTCAAAGATTCTTAATTTGTTTATTATTTATTTTTAAACAACAACAAACCTCAAAAATGTGGGCAGCAGCAAGTGAAGGATCTGAGGCCAGACTCGGCCCCAGGTTCATTACGGTGTCAAATGTTCAGCCCCGAGTTTGCCAGAGCTGTTCTGGGCTCTGGGAGTATAAGGAGGAGCTTATATCTGCCCTTGAGGGGCCTAGGCTTGCTGTCTAGGGGGCTTTAGACAGAGGCCAGCATGCCAGCTGGTTAGAACCGGATGCCTGATATGGTTAGCTTTAAACAGAGGCAAGCATGCCAGCTGGTTAGGACCGGATGCCTGATATGGTTAGCTTTAAACAGAGGCCAGCATGCCAACAGGTTAGAGCCGGATGCCTGACACAGTTCGTGGAAAGTCGCTTTGCTCTATTTCTGCCTTTTTGTTTCTTGTGACCATTTTTACATCCTGTGCCTTCCCTGGACTTAAACCATTAGTTGTTATCATTATGATTTTGTTGTGGTTGTTTTGGTCTTGGGATGGGGTTTGGGGGGGGGGTTGGGGGGTGTTGTTTTGTCTTAGGGACTTTCTATCTCTGGCTGGCCTAGAACTCTGAGAGATCTGCCTGTCCTGCCCCCTGAGTACTTAGGCATTATTAAATTTTACTTTTAAGAACAGAACCCTAAACTCAAGTAGCACAGTATCTGAGGGTCATATTTTAAAATGCCCTTCACATTTATCATGGCTTCTCTAGATCTCCATTCACCTGAGAGCTGAAAAGGCACAGCTGAAATCTGGTACCTGTGCAGTTGTGTCAGGGTCTCTAAAGCTCCAGTCACCCTTGGGGTTTCAAGTGCTGTGACGAAACACCATGGCCAAAAGCAACTTGGCAAGGAACACGTTTATTCTGTTTACAGTTTCCCATTCTAATCCATCACTGAAGGAAGTCAGGGCAGAAACCACATTGGCAGGAACCTGGAGGCAGAAGTTGACCCAGAGGCCATGGAGGAGAGCTGCTTACTGTCTTGCTCCCTGTGGGTTGTTCTGTCTGATTTCTTAGAGCACCCAGATCTACCTGTCCAGGGGTGGCACCACTCCTTGTGGGATGGGCCTTTTCACATCAGCCGTCAATCAAGGCATTACCCCTGCGAACTTGCCTCTAGAGAGCATTTTCTCAACTGTGGGTCCCATGTCTCACAGAGCACTAGCTGTGTCAAGTGGATATAAGTCTTGCTAGCACAACTGACCTTCCCAACCCTCTCTGTGCATTCTAAAGGAAGACAACTTTCCAGTCTAGTAGAATGCCATCTCTTTCTTATGTGCCATCTTACGGAGTCCTGTGATGACTATGAGAGAAAAATCACCCAACCACCCAGGAATGCCCACACTTCATCTGCAGCCTTGTTAGCTGTACTCTCAGCCTTGCTGGCACATCTTTGCATTTTTTTCAAGAAAACAAGCAATAAGAGAAACACAGAAACTTACCATTTTAAATCCCCAGCTGACATTCAGTTCAGGGATTTCTGGGGTTTTTTTTCTTTTTTTGTTTTTTTTAATACTACAGCACCCCCATGCTAAGCAATAGGATCAGTGATCCCTAAAACAACATCTTCCAAACTGTATGAAGAGATTACTCGCTGGGGTGTCGGGAGTATGCAGGTCGCCAGTGAACTCTTCCTAATGGAGCAGCTCATTAGAATCAGTGAGGAAGACCTGTGTCCCGTTTTATATCCTTGTGCGGATACATGATTAAATGTGAGCATCCATTATTAGGCAGGGTCATTGCCAGAAATGTGGAAGTTGTTACACCGTAGACACATAGAACACAAAGCTAGTTAGCAGATGACAACATTCCCTGGACAATCTCCCGAGAAACATCACTCTTAATTACGTAAGGACCCGCTGATGCACAGCTAAGGCATAAAAGCAGCTAGAGCATGGAAGCTGGTCCTTGTGAGGGAAGAGCAAACCCGGTGCTGAAGCCTTCTGGACCCCACGCCTATCCTGGGCTCGCTTTCCTTGCCTGTAAAGCAATGAAGCTGGCTTATGTGGTCTCTAAATTTTCTTCAGGCTTATTATGAATCATGATGGGCAGCAAGAAAAATCCTTGTGGCCCACTCCGGCCCTGGATGTCCTTCCCACCCTCTCTGAGCTGACTGGCTGGGTTTCTTGTCACTCTTTACGAGAAGACATTTGCACGGTCCATGAGTGACGCAGATGCTACTGAAGATGGCGAGAGGAGGCCAAGCATTGTGTTCCACTGCACGGCGTCCCATTGGTGTCACTACAGCTCCTGTGCCCCTCCCTGCCCAACCTCCATGGCTGTCCCCTTGGGACACATCATGCTTGCTTTTATTGTTTTCTGCTGCTTCGCCCAACTATGGAGCACTCTGCTCCTTTCTCCATGGACTCGGGTCTAGAAATATAACCCACACCTTCAGTTCTCACAGGCGCTCTAAGCCTTTACCTCTAACCCAGGAAGAATATCAAGGAAAAGCAGTGGGCAGCTTGAGGGGAAGCTGATGAGCGCAGACCCCTCCATCTGCTCTGTGTGAGATAAAAGAAAAACAAACAAACAAACGGGCAGAGATAGGGCTAAGTCTTGGGGAGATGCCCTCCTCCATTCTTCTATTTTCCCTCATTCCTTGAGCCACCAGAATATAAGCAAAGTGACAACCAAAATTAGTGGTGACACTGTTTAATGTTTTCTTGTGAGCTAGGTATCACAGAAGCAGGCTCAGGCCCAGGCCTAGGTGGCTTTCTTTCCTGAAACACCCCAGTCCCTCCACAGTGGCAGCACATCATAGCCCATCTAGGAAGCTAGAGGATGAAGTCTTGACTCTGCCCTAGCAGGTAAGACTCTGCACTGTTGGTGGTTTTGAGAGGCATCCACAGTGTTTCAAGTGAACCACACCTTTGGCTCACCTGAACAGTGATGAGTGACTGGTGAGGAAGCCTGGGCCCCCTCAGAGAGCACGAAGAGCAGATAAGGATTCGACCACTGACCAAGATTAGCAAACTTGCCCGTCAACTGTGAGATGACTGATAGGTGAAGAAAAATTATAGTGATACTATCCTGTGGCTAAGATGGGTCAGACGATGTTTGTTTGTTTCCAGGGAATCATTCCTAGACTATCAAGTAAAATAGCTCTCCTCTCTCCCTAGTGAGCCTCAATCCCATACTTAATCCATAGAGGTGTAATCACAGAGGTCCTAGCTACTTAGGGTTACACCATTTCTCTGACCAGAGACAACTGAACCATGGCAGAGAATCTGAACTGTTCTTTTAGGGGTTGAGAATCGGAGTCCCAAGGGATGCCAGGCTGTCTAGAGCAGCAGTTCTCAACCTTCCTAGTGCTTCGACCCTTTTAATACAGCTCCTCATGTTGGGGTGACGCTCAACCATAAAATTATCTCTGTTGCTACTTCACAGCTACATTTTTGCTACTGTTATGAAACATAATGTAAATACCCACTTAATAGTCTTAGACAGCCACTGTAAAAGGATCATTCAACCCCCAAAAGGGTCTTGACTCATAGGTTGTGAACCAATGATCTAGAATTAACCACCTGCAGTTACACAGTGGGCTATATTCTATATTCTATGTTCTCCAACAGTGCAGAGTCTCTCCTGCTAGGGCAGAGTCAAGACTGCATCCTCTAGCTTCCTAGATGGGCTATGATGTGCTGCAGCTGTGGAGGGACTGGGACGTTTCAGGAAAGAAAGCCACCTAGGCCTGGGCCTGAGCCTGCTTCTGTGATACCTAGCTCACAAGAGAATGTTAAAACAGTGTCACCACTAATTTTGGTTGTCACTTTGCCTGCATTATAAAGAGCAGCCCTTGGTTTCCTGGTTCCCTGGGACTCGTTGTGAGGTGCAGGAGTGGGAGGGTAGAGGGCAGGAGTGGGGGGGGGCTCATTCTTTTCCATAACTGACTTGAGTGTAGGCAGTCTCTCTTGACCAGTGTTAGTATTTCTCTGAGCTTCAGTTGCTCTATATGAAGAATAAGGATGGGGAATTCCCCCCAGATGGCTGGGTGACATGAATAGGAAATGCTTTATGCGCTCTGCTCACCCATGCCACCCACTGTGTGCCACTGACTGGGACATTCTATTAGATCGAGTAATAGAATTCCCCTTTGACAGCTCAAGGAAGAGTCAAGAGTTAGAACCAGCTGGACCACCTCCCAGCATCCTTGTGGGGTTGCCCTCCCCTGACCTCAGCTCTCAAATAAAGCTGGAAGGCTCCTCCATCCCAACGCGCTAAGCAGTTCTTTCTCTCACTTCTGCCTTCTTCCAG
Seq C2 exon
ATTGATGACACTGGCACATTCCAAGTCATTGTGGTTCCCTCCGGGTCTGATGAAGGGCCAGCGTTAGAGAGACTCCAGCGGTGCACTTTCTGCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719-Col6a6:NM_001102607:33
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(92.2=93.3)
A:
NA
C2:
PF0009223=VWA=PD(6.6=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: