MmuINT0040478 @ mm9
Intron Retention
Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105634543-105638740:-
Coord C1 exon
chr9:105638678-105638740
Coord A exon
chr9:105634606-105638677
Coord C2 exon
chr9:105634543-105634605
Length
4072 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGT
5' ss Score
10.65
3' ss Seq
CCATTCTTGTTTCATTCCAGGGG
3' ss Score
9.91
Exon sequences
Seq C1 exon
GGTCCAAGAGGAGAGGTCGGTGAGAAAGGAGAAAAAGGAAGTCTGGGAATGAAAGGTCCTCAG
Seq A exon
GTACGTAAGGAGAAAGCAACTACATCCATCCAACTTCGACCTTGGCTTGAAGAAGGATGCTTTAGTGGTTTCTTCCCTAAAGGTGAATGACACATTGCCTGCAGGCCAACAGTATTAAGTTTGACTTGAGTGTGAGAAGCGGCAGCTGCTTGTCTCCTGGTCCTACCCCACCCCCTGCCTCTGCACCATATAGACTGTAGTAGAGCCAGAAGATCCTCCCTAGACCTCCTTGCCTCAGCTTCTCAGCCAAGGTTAACGATTCCCTCTTTGTGCTTATGTGGATAGAATGAGCCCCCCACACAAGTCACTTGGAGTTGCCTACCCTACCTCCAGGGGGAGCTAGAGCGGAGGGTTAGTAGCCAAGAGTGCTTGCTAGTTCTTCCAGAGGACTAAAGTTCATAACCTCCTGTAACGCCAGCTTCAAAGTATCTAAAACCAAGTTTCCTGGAGGGACTAAAACATTTTGCCACCTGGGACTGTCCTCAAAACTCTTAGAACCTCTGCAGGCAAAGCTGTGGTGTTGATAATCCTGAATTCTTCCTAGCTAACACCAGGTTTTGGAATGGCCAATGTCCACACTACTCCTTGTTCTGAGTGTGCTAAGAGTGTGTTAGGATGCCGGTCCTGATCTAGTAGGTCTAGGTTGAGGTTTGGGATGCTGCATGTTCAATCAGTCTCCTCCTGATACTGATGCTGCAGATCTGGACCACACAGTGAGTAGCAAGGTCCTGTGTGATCTGTTCCCTGTCTATAGCCAGCATAATATATATGTATCTGTAGGTCTCTTTTGACATGCTGCAAGCTCCATTTATGTTAGTGCCTTGCGAGTATGCTGGATCTACAGTCCCTGGCACAACAGAGCTCAATTCCTTTATGGAATGAATCAAGCAGTAAATGAATGAATGAGACCCAGTTGGGACTTTCACCCTCTGCTAATAGCAGTACCAAGGGGAATGCATTACTTAACATGAATTAACTAAACCCTGGCAGAGGCCCAACGTTTAAGTCGTTGTGCTCATCATGAGAATATTTAACAGGCTATTTGCATAAACTTGTAAACCATGGCAAACTGTTTTAAAGTACATTAATATCTGTTCCTGACGATGTTTGTTCCTGGTTTTGATGAAAGTGCTCTTTTCGAATGCATGAAAACTCCATAATTTCATAGCAGAACTAAACCAATGATAAAAAAAAAACCAAAACCTCTTCTGCATTCACATCTTTGAATCATTAGAAGCTGGCTGGCACCACAAATGGAGATTTTTATTTTAAAAAAACACAGTAAGTACAAAGGAAAATATATATCGATCTATATCTCATCTGTTGATATCAAATATTGATGTGGGTATGTAGATGAATTGAAATCCAAAGATCTGGGGTCCAAAGTGGTATCCAAGGCTGTTACTGGAGTAGTTTTTCCATGTGCCCTGTGGGGCACCTTCATCCATGGGTCCCTTTAATCTCGCTTTGGCAAGAAGTGACCCAGTCATAAATCACCCAGCCCTTGGCATTGCCAGCTGGTCAAAGGCACCACACCCCTCCACCAGCCATTCCATTTTTCTGGCTGAAAACCCTGCTTTTCTTTCTCTGCTTGCTTTTTATGAAATACCCTTCTTGTCAGCTGTTAAAATGGAGTTTCAAAGACAAGTGGAATTTTCTGTGTTTGGGACATGATGAATAGGATCTCTAGACTGCTGTTTCTGAAGGAAATCTACAGAGACAAACACAGCCAGACACCCAGAGAGTGCTGTTCTCTATTGGCTATACGGACCCCTCGCCATAGGTCTTGTATTGTTTTATGGCACAGGAGGAACCCTTCAGTGGAACGATGTGTTTTCTTACTGCAGACTTGAAAGCTCTCCTTGGGACTTACATCTTGGAAGGGGATGTAATTTGTAATGATGGCATACCAGAGGCTTATTAACTTACACAGCACTGGGTGTTCTGCATAAATGAAAAGCACCAACCCAGCCATATGTGGTTATGACTACAAAAAAACAAAATAAAACAAAACAAAAATACAAGCTGATGTGCTATGCCCAGAAAGACATCTTTGAAAGGAATAACATCTTCTTTTGTCCTTTTTGTTGTTGTTGTTGTTGTTGCCCTTAAGAATTTCTCTAAAATCTCCAAAATGCAAGGAAACATAATAGGAAACTAGATCCAAAATACTAATTATAGAGCTGAACTTGTTCTTTGAAAATGTATGTTCCTAGCTAAATAACACTGGCAGCACACACACCATCAAGAAAGGTTAGAATTAGCCAAGCATTGGGGTGCTTCTCCCCAGGACCAGCACTCGAGAGGTAGAGGTAGGGTGAACCCCCAGACTCTACTGGAGACCCTCACATCCACAGCCACTCCAGTGGTGCTGCTTAAACTCAGCAGGTCCTGAAACAGAAAGGGACCGAGGGAAAGGGGTCTGTGGCGGGGAGGAATTGAGAGGTGGGAGGGAGGCATGAGGGGTGGGGATGAGAGTAGCCTGAGTATATCATGCACACGTACGAAATTGTCAAAGGACAAAATATGTGAATAAGTAGTATTTTTTAAAAAGAAGTAGTAGTGAGAGTGATAACGAGGGTCTCTTGGTTCTCAGGAGAGGGGTAGAAAGGAATGGGGGGAGGATCTATGTGAGCAGGCACTGGGAAGAGAAGGGAGCTGATATTGAAATGTAAGGTGAATAAATAAATTAATTAATTAATGGCAAAGAGGGAGGTAGAGGAGTAGAAGCATAGGAGTTCAAGGGTTGCCTTGAAACTTTGTTTTTTTAAAAATGTTGACAGAGTGGGGATGGAAGAGTGGAGGAGAGTCTTGGGAGGAGGGCCTAGAATCGTTCCACACAAATGTGGAGAATAGTGTAGGATTTCTGTTGTCTTCATAGATGGAGGCATAGTAGCCATAGACATTGAATCTGGAGCCAGGCTGCCTGAGTCTGATTCCAGGCTTATACCTTTACATCTTATCTATGGTACCTTGGACAATTGACTCGACAATGGACACATCTTCAGCAAAAGAGCAGTGATAGCAACTACCTCCTCGGACGTTGTGAAAAATCAGTGGTTTGATAGCTGTAGATGCTTGGGACTATTACGGGCACAGAAAGGGTTGTATAATTATTTTTATTACTATAATACTGTATCTACATTGCCTAACCAAACAGCATTTTTAATACCTTTTTATTAGTGTCAGAGTATGCACACATGTACACACCATAGTCCATGTGTAAAAGTCAGAGAGCCAGTTAGAAGACCTGGTTCTCCTCTACCATGTACATTCCAGAAATTGAACTTGGATCCCTGAGCTTGGTGGCAAGCACCACTACCCACTGAACCACCCCCTGGCCTCAGACGGGGGATCCTATGCTCTGGCTGTGGCTCGTGTGTGGAGAAGAGCTCTGCCAGGCTTAGAACAGCCTGTAAACCCACGAGTTAGCTTTTCTGCCTCCCTATCCCACGTGATTTAGGTTGGATGGTCTACGCACTCATCCCTTCTACTAATTTGACAAGTGTTTATGAGTTCTCTAGTAGTGGGCCCTGTTCTAGGACACAAAGATGACAGTTCCATTTTCTAGCAGTCTCTGATATTAACTTAAGAATCTTTATCCTGTGTTCCTTAAGACACTTCGTCACGACGCTAGTTGGTTTTAGTGAAACTCTTTGAGCTTTCTAATGTGCATCCCACACTTTGCAAATGAAGATAAACAGTCCTTGGTGCTGGTAGAAAGCATTCTTTGAAAGGCCACTGTCCTTTGGAAAGCTCGCTTTAAATACTAGACACTTCAGCGGCATCTGTTCCCTGAGCTAAGCAGTGGGAACCTCGGCTCGTTTGGACACGGAGACTCACAAAGAAAGCATAATCATTTAGGCCACATCTGGCCAGGGTTGCTTTATTAATTTTCTTTTATTTACTAGTCTTTATTTGACAGCTCCAATATTTTATTTCCCAGAGTAGGATCAGCTTAGCCTGTAACTCTTCTTCCATCTGCACTTCATTTTCCGTAGAAGACACGTAAAACTGTTGGGGGAGAGTCATACCTCATCCTGCTATATCTGCCATTCTTGTTTCATTCCAG
Seq C2 exon
GGGCCTCCAGGACCCGGAGGACAAGCTGGGAGCCAAGGCCATTTGGGAAGCCAAGGAAACAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719-Col6a6:NM_001102607:23
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:
PF0139113=Collagen=FE(25.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(25.0=100)
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
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: