MmuINT0040428 @ mm10
Intron Retention
Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:106060324-106061560:-
Coord C1 exon
chr9:106061482-106061560
Coord A exon
chr9:106060470-106061481
Coord C2 exon
chr9:106060324-106060469
Length
1012 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
TCACCTTTGACATTTTGAAGGGC
3' ss Score
5.83
Exon sequences
Seq C1 exon
GTCCTTTTAGTGTTTACAGACGGACTTGATGAAGACCTAGAGAGGCTGAGGAGAACCTCAGAGTTCCTTCGCAGCAGAG
Seq A exon
GTAAGCACACCTCTGCATGTGTTCTGAATGGACTGGCCCCTCCCACCTAGGCTGAGTCCCTTATGCCTCAGGTGGGGATGGGCCCCAGGAAGCCACCTGCCCTAGTGGGTGGAGCAGGGTTCCAAAGGGCCGAAGCCTGGTGTCCCTTGTGTGAGTTGGGGATGTAGAGCCGTCTCCCACTCCTAGCAATTGCAATCTAAAATTTAGAAGCGCAATCTTACTGTGCATCCTCAAGAAGAGGATCAGAATATGCATAAGTAGTCATGCGATTACCAGAGTTCTCCTTCCTTCTTTCCTTACCAGGGTGATATATATAAACACACACACACACACATACACACATATATACATATATGTATATATATCTTCAATATATATTCAAATCTCAAACAAAAATAAAAAAAAAAGCATTTGAAGAAAGGCAAGATGACCATTGATAGTTTGAGGTTAGCCTGGGCTTTCTTGGAAGCACTGGGCCAGCCAGGGCTACATAAGTAGAATCTCAATGAAACAACCAACCAACCAAACCAAACAGCACCAACAGCAATGAAAAAGAAGGCTAGTTGTATTTTCCTCTTCCCCATCTCCTTCCCCTCCTCCTCCTCCCCCTCCTCTTCCTCTTCCCCCTCCTCTTCCTCTTCCCCCTCCTCTTCCTCCTCCCCTTCCTCTTCCTCCTCCCCCTCCTCTTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCTTTCTTCTTCTGTTAGAGTCTTGCTGTGTAGCTCAGTCTCAGCAGCCCAAACAGTTCCTGCAGCCCAAGCAGGCCTCGAACTCCTGACCTTCTTGCCTTCGATTGCATGTTGTGGGGCTGCAGATGTAAGCCACCTCACCTAGCCTGGGAACTTCTTTCAATTTTCACAAAAATGCAGCTTGAGACGAGACAGACTGAGGATGTGGTGATGGTGGGACCGTGAGTGACCAACTGAGGCAGAGACAGATGGGTTCTAAAGATGGGTAGTAAACCTCACCTTTGACATTTTGAAG
Seq C2 exon
GGCTCTCCGGACTGCTGCTCATCGGCCTGGGAGGTGCACATAAGTTAGAAGAGCTGCAGGAGCTGGAGTTTGGCAGAGGGTTTGCCTACAGGCAGCCTCTGAGCTCCAGTCTGCCATCCCTCCCAAGCGTCTTACTGAAGCAACTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572:ENSMUST00000121963:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
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
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCTTTTAGTGTTTACAGACGGACT
R:
TTGCTTCAGTAAGACGCTTGGG
Band lengths:
222-1234
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types