MmuINT0040483 @ mm9
Intron Retention
Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105619004-105625248:-
Coord C1 exon
chr9:105625186-105625248
Coord A exon
chr9:105619067-105625185
Coord C2 exon
chr9:105619004-105619066
Length
6119 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGC
5' ss Score
9.89
3' ss Seq
TGACTTAATTCTGCTTTGAGGTA
3' ss Score
-0.05
Exon sequences
Seq C1 exon
GGTGATATTGGGGACCCTGGTGATCCAGGAGAAGCTGGTCCCAAGGGAGCCAGAGGCAAAACG
Seq A exon
GTAAGCTATCCAGAGGGTAACTTTGGCTCGTGTGTGTGTGTGTGTGTGTGTGTGTACATGTCTGTGTGGGAGAGGAGAGAAAGAGGAAAGAGACTAGTTGGTTTTTTTATTGTGTTCATGTGTATGATGAGTGTGTGTGTGTGTGTGCGCACACATGCACGCATGCTTACACATGCTTGGTTCATGATCATGTATGTTTGTATACACACAAAGGTTAGATACCAATGATAAGTGTCTTTTTCAATTACTTGCCATCTTTTTGTTAATATTTAATAATAAAAAAAAGAAAACATTGTGTGTGAGTGTTTGCCCACATGTATCAAAGTGTAATCGTGAATGCCTGTTGCCCACAGAAACCAAAGGTGGACATCAAATCTCCTGGAACTGGAGTTACAAGTGGGTCACGGTCCTGAGCTGTTCAGGAACCAAGTCCAGGTCCCAAGCAAGAGCAAACATCTCTCTACTCCTTCCATCTTAGTGTCTAAGCCAGGGCCTCTCACTGAACCTGATACCTGCCCACTCAGCTCGACTGGCTGGCCAGCAGGCCCCAGGGATTACAGATACACACCATTGCACTCTCATCGCCCAAGGCCACCAAGAAGGCCAAGAACTGTTTTAATGAACACATTGGCCCATTCTGTTGCCAGTGTGCCTTTCTTAACCTTTGGAAGTAAGACTTTTATTAAAGGAACTTGTGTAATCCAAAGGTTTTGCACTGACAAATTACAATCAGTTCATCCAGCCTTCCTAGAAAACTGATATCCACTAACATCTTGCTTAAAAACATCTCAAAACTTTCGTGGAGCTACTTTTAATAAGATGTCTATTAAAAGGTCCTGGCCTTGCTTGCCAGGTTTCTCCTGAGCTTTGTGAGATGTCTGGATGTTAAACTGAATTATAGGAGAGTCAAGTATCACCTGACGTTTTATGTCACATAAACACGACTCTTCATCATGTGTCACAGGAATCAGCTCACCTTGGGTTACAGATGGTTAGAAATATGACAGCGCGTTCCTTTTACCAGTATTAGGAAGACATAGAAGAATCTCAAGTTCAAGGCTAGCCTGAGCTACAAAGTGAGCCCATGTCTCAGAGAACAGCAGGATAGAAAAAAGGATGGAACCTTTGCGGTTGTTGACTGTACACTTTAGATTGTGGGTAAAGGAGATTGTGTTGTGACAGGACACTCTGAAGACAAGTGTCTCTCAAAAAAAGTCTTTGCCTCTTACCCTTCTGAATAATCTTGACTGGAAAAAACTGGTCTACAACCCTGTCCATGACCAAGATCTTAGGGGGAAAAAAAAACCTTTTAGGAAAACATGTACTTGAGACAGCTTTCTGGTGTGTCTTCATAGCGAATTTTACTGTGATGTAGTTTTTCCCTACAAGCTGAATTTTACGTGTAGGGCTCATGTTTGGAGGTTGTAAGCTTCACCAGGGGCACCTCCTTCTCCAGGCTGCTCTTGAGGGGGCTGCTTCCAGCTGTAACTCTTGTGTGTGTTTTCAGATGGCAAGCCTTTATCATTTTTGCCCTCAGCAATGACGAAGACGAATATAATTAGGAAAATAATTGGGAAAGGCTTTCAAGTTAATCCAGATGTCACCCGCATAGAGACATCTCTGGATCACTTCCCTTGGCTCGTTAATGGAGCAGTTTAATTTGTACACCAGCAGCATGCTAACAAGTTCATCCATTTGTCGGGGTCCTCCCTACGACAGTCCCATTCATCAGTTTTTAGTACACTTAACTGATGGGAGACGTGTGGGCAGGTGTCTTGGCCTCTGGGGATGCGTTTTGGTTCCCCCTTTGTTGTTCTCTTGTTGGGCTGTTATAACTTACTAATTTTTCTGCCTCTAACTACTCCGTCCCCCTCCTTAACATGAGTAATATTTGGATTTGAAATGGAAGTTTAAACACTGAAAATGTCCAGGTTTTCCCCTGGAAGAGCAGCTGTTTTCTCTGGAAAGATTTAGCCTTAAATTATGAATGTCTTTTCAGGTCTCTTGGAATTATTCTATTCTTAGCTTGAGTTCACTGAGTTACAGATTTTAAAATCTATAAACCTGTTTTAGCTGTGCATATATGTATATTTGTATGTATATTTTTAAAAAGAACCAAAAAAAAAAAAAACCCCCAAAATCTTTGAACAGGTTTCAAGCAGGGATGTGGGACTTTGGCCATCTGGAGCTGAAGAGCCTTCATGGGGAGGCTGCCCGTGGGTGGTGTTGAGCGTTTAACTGCATCCATGGAGCCTTCCACTGAATTCCAGTCCTACCCAGCCTACTTCCCTAGTTAGAGCAACTAGCTATATCTCCATACGCTATCATGTGAGGTGGGAAAACTTCTCCCAGCAGGCACTTGTATTGAAAGAGTCGGGGGCAGCATATTACATTTTCTTACTTTAAAATGGCTTTTATCTTTCACCTTAAAAAAATAAATTTAAAAAGGTGATCCCAGGCTATGGTCATGGCTCACTGGTAGAGTGCTTGTCTGACATATCTTCACCACCACCCCACCCTCCCACCCCCGCCAGCACAAAAGAGAAAATGGCAGTCAATCCCATCCTCTTCTCCACCTTCCTCTTGCTTCCTTTGTCTCTGAACGCTTCTTTCATCCAAATAGAGTGTCTTGGAATTGAAAGTCTCTTTGCACTCTCTGAAGACATTTGCATATGCAACAGGCACGTCCTGAGCAGCCCTATCTGTTTTCCCTGTTGCCTGGTATCCAATAGATACCGTTCTGCAGGGACAGTGCATCTATCTGGCTGTGAGGTCTCCTCTTCTCCTCCCCTGCCAGGTTTCTCCATCTCCCTTCCACTCCCACGCCCCCTGGATTTCCCATCATGGAAAACTCTGCCAGGAACCTTGTATTCATTACTTTTCTTATCATTGTGGTAAAGTATTTGACACAAACACACTAAGGAGAAAAGAAGGATTATTCTGGCTCTCAGCATCTGAGGATCCAGTCCATGGTCATTTGGTTCATGTTTTGGGGCTCATGGGCAGAACACTACAATGGTGGGGAGCAGAGAAAAAACGGAACAGACTGGAGACAGTCTAAGTTTTAAAGCATATCTTTGGGTGAGTTATTCCTCCAGCTAAGCTCCTCTTCGTAAAGCTTCTAAAACATCCCAGAGAGGGCCAGCATCTGGACACCGAGAGTTCAGAACACAAGCCGGTGTAAGGGGAGTCTCCCATGTAAACCCTAACAAGCTGATCAGAGGAGACAGGCTCCTGGAAGGTTTGATGATACAGTGAACATCTGAAAATGACTTCTATTGCCTCCAGATGTGGCAATAGTGCGGCGAGTGTACAGCTCTGGGTTGGAATTACTTCCTTGGAACTTTTTAAGTGATTATGTTTTCCATTATTTCTGGCGGGTTTTGTTCCTTTGTAAGAATTCAGAGTCCTATTAACTAGTGTTTTCTCTCTGGAACCCCGCTGGATCACCTCTTAGATCTGCCATGGGTTTGGTTACTGGACATATGGTCCATTTTTTCCCACTTTCCTGAGAATTAGCAGGTCCCTTGACCCTGAAAATATGTCCCCTTTCATTCTGTTATTTTGCTGACCTTTGACCTTCCCCTGCAGAGCTCTCTGCTCTGTATATTGAAACATCTATCATCCAGTATAACGACAGAGTCCCTGAGTTTACTTCGTATGGTATTTATTTTATAGGTACAACCTCTCTTTGATCTTCTCCTTTCTGGGAAGGTATCTTCTTGATTCTATTTTTAATTTATGTCCCATAGTTGACCTTTGAAAAGTTGGTTGCTAAAATCTGACTGTTCTTTCTCTGTAGTGTACTGTTCTTGTCTCATGACTGAAGCATCTCATCTCTCTGAGGATATGAGTGAATATTTTTAGGTCCTCTTTGTTCAACCCAGTTTCCTCCAGGTTTGCCTTCTGTCTTGACATTCAGCTCCCATGGATCTCAAGAACAGCAGTGCATTTACACTGAGCATTGAGTACAAAGAGTCTGGTAGGAAACCCTGAAGTCAGGACCGATTTGCCAGTTATGAATTTCACTGATGGCTATCTGCTGGACCTGTGCTTGGCAACCCTTCACTATTGGTGTTCTCTCTTCTTTGATTTCCCTCTGGAAACACCTTCTACCCTTTTTTAGAGGGTTCATATCCTGATGCCAGTTTAGAGGACACTGGCAATGAGAGCAGAAGCTCAGACTCAATGTGCATATTTTGGTTGGTTCTCCTGGCTCAGTGTGGTAATATTTGTCTTCAGCTCTGCCGAGAATCCTACCCCTGATTTACCTTTGCTTTTTCCTAGTGGGGAAAAGTGTCTAACTACCTGGTGAAATTTTCCCCACTAGTCCTCCGTATTTAGCCTCTTCACTTCTGCTTCTGGGGACCTCTGGCCCCGACAAAGCCTGAGCTTTCTGGGAATGTGTGATACCAAACACACTGGTTCTTGGGTGCATCTGCTGCTGGCTCAGGGCTCAGACTCCTCGGCTCTGCCAGGTCGGCTCCACACAACACCTATGCATCTGCGTTCCAGGCTCCACAACGTTGAGGCTCCCTTTATTTCTTTTTCTTGTACTATTCATTTTTATTTTAAAATCTATTATGGAAATATTAGAAAGGGACAAAGGTATCCAAGTGGTCTCCTTTTCTTTCTCTTGAAGGTAAACATAACTTTTAAATAAAGTAAGGTCATTAAGTTATGTTTTTTAATACTGTCAATATCAATTGGGCACTGGAAGGATATTAGTGATAATTAACTTCCCCACAGGTGGTGCTTTTATAGATTAATTTTTAAATAACTTCATTTATTACTGTAAAGGATTTACAAATCCTGACACATTAAAAAAAATGTGTGTGTGTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTGGGTATGTGCGTATGAATGCAGGTGCCTCCAGAGGCTAGGGGAGGGAGCTGGACCCCCTGGAGCTGGCGTTGCAGGTGTGAACCTCTTGACATGGGTGTTAGGGACCAAATTTGGGTCCTGTGGGAAAGTAAGACGTGATTCTAACCACCAAAACATCTCTCTAGCCCTCCTCTCCTGTGGCATTTTGAATGATGAAAACAATGTTGTTTCTTAAACAACAAACACACCAACAACCCTAAGTCCTAGCTTTTTCTAGGACAAACTGTATTGTTAAATGTGCATAGAAGAATTCTTACGTACAGTAAACAAGATAACTGTTGTTTCTATGCCACTGTTGCCATCATGCCCTTCCCATTACGGAGATTTCCACCCAACCATTGACTGTGTTGTTGCTAATTTTGTGGGTTTGGTTCTGTTTTGTTCTTGGATTTTGAGCCCAGCATGTGATCATAATTTTGTATGTGTTTTTTTTTTCAATTTAGTTACCTTCATGTTCTTAAGAAATCCACACTACTTTGATCCAACAAAATTCAAAATTCTAATCTTAGTAATCTTCAATAATAATCAGAATTATATATATGTGTGTGTATATACATATAAATATATACATACATGTATACATATGTGTATATATTTATATATAATAGCATTGTTAGCAACATCAAACTTAAATGCCAACAGCAAGGACCAATTGAATAAATCATGGTATATCCACAAAGCCGTGAAATACCATGAAAAGTTATTTTGTGTATAAGAATATTTAGTTACAGAAATTTATGTGTGTGTATATGTGTGTGTATATAAATAATTTAAAACATAGCAGGGATACAAGCACAGTAGTACATACCTGTCATCCCAGAATTTGGGAACCAGAGGCAGGAGGATTATGAATTGGAGGCCAGTCAGAGCCATACAGGAAGACCTTCTATAAAAGAAACAAAACCAAAAATAGAGGCATCAGCAAAAAGTAAGGTACATACCAGTTTTTTAAAAAGACATCTTAATGCCAAAAGAACAAGAAAAGTAGCAGAAGAAAATTAACAAGTAGTTTTTTAAAAACAAATGGATTGCTGTCCCTTCATGTATTTTAGAAATCTATCCATTTTCTAAAATGAAAATGGATTTATTTTTTGCTTTGGTACTTCTACTTTTGAAATAGTGTCAATATTTCAAATTTGAATTTAAGCCATTCACACATATATAAAATATGGTTTTAAGGTGACTTAATTCTGCTTTGAG
Seq C2 exon
GTATCTGCTGGGATTCCAGGAGAGCCGGGGTCCCCCGGGGAGCCAGGACCCCCTGGACGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719-Col6a6:NM_001102607:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
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: