MmuINT0040461 @ mm10
Intron Retention
Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:106066652-106068392:-
Coord C1 exon
chr9:106067847-106068392
Coord A exon
chr9:106067207-106067846
Coord C2 exon
chr9:106066652-106067206
Length
640 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGA
5' ss Score
5.73
3' ss Seq
CCTACCCCCCCGCCCCCCAGACT
3' ss Score
8.47
Exon sequences
Seq C1 exon
GCTGCGAGAGTGTGGAGAAGGCAGACATTTACTTCCTTATTGATGGATCTGGCAGCATCAAACCCAACGACTTCATTGAAATGAAGGACTTCATGAAGGAGGTGATAAAGATGTTCCACATTGGGCCCGACAGAGTACGATTTGGAGTCGTTCAGTACTCAGACAAAATTATAAGCCAGTTTTTCCTCACCCAGTATGCCAGCATGGCAGGACTGAGCGCAGCCATTGACAACATCCAACAGGTGGGAGGTGGTACCACCACTGGCAAGGCCTTAAGCAAAATGGTACCAGTCTTCCAAAACACTGCCAGAATCGACGTTGCCCGATACCTCATTGTCATCACTGATGGTCAGTCTACCGACCCGGTGGCTGAGGCTGCGCAGGGATTGAGGGACATCGGAGTCAATATTTATGCCATTGGAGTAAGGGATGCTAATACGACTGAGCTTGAGGAAATAGCAAGCAAAAAGATGTTTTTCATATATGAGTTTGATTCCTTGAAGTCCATCCACCAGGAAGTCATTCGGGACATCTGCTCCTCAGAGA
Seq A exon
GTAAGAACTAACAAGTGATCATATATTAATTATGCATGATAATCGGCTTTCATTATATTCTATGTGTATATATATATATCATCTTCATCCCTTTAGTCTCTCTTGCTCCCTCTTCTTTCTGCTGATCCCTGTTTTCCTTTCTAACTGCCCCTTCTATTTTTTGTAGTTTTTTTTCTCTCTTTTTCTTTTTGTTTTTCCTTTTCCTCTGTTTGCAACCCAGTGAATTCTGGGAACACGGGTGAGAGGTTACTTACAGGAGCACAGGCCCCTCGCCATGGCCTTTACTGCTGATCGAGTAAGATTTAAAAAAAAATCTATTTAGTGGATCTTTAATTACGTGAATGGTCTTTATTCTCTTACGTAATCCACTGGCTGGTGAGTGAATTTTGAGCACAGAGTGACAGTGACCTGGCCTAAACCAAGCTGGTCAAATTTTATGTCTCTATCCCACGCCTGTGTCTTATATTGAGACTCCTTTGTGCTGAGTTGCAGAAAATTTATTGACTACCCCTCATTCCCTTTGAAAATATTTTTGCGCTGTGTATCTGCTCCCTTGGTTGTCCGTGGGGACTTGTAACCCACTGGTTCCAGGTTCTGACCAAATGTCCTCTCGTGTTGCCCCTACCCCCCCGCCCCCCAG
Seq C2 exon
ACTGTAAGAGCCAGAAAGCTGACATCATCTTCTTGATTGATGGCTCAGAATCCATCGCTCCTAAAGACTTTGAAAAGATGAAGGACTTCATGGAGAGGATGGTGAACCAGTCTAATATCGGTGCTGATGAAATTCAGATTGGCCTTCTGCAGTTCAGCTCCAATCCCCAGGAAGAATTCAGGCTTAACCGGTACTCCTCAAAGGTGGACATGTGCAGAGCCATCTTGAGTGTCCAACAGATGAGTGATGGTACCCATACTGGGAAAGCCTTGAATTTCACTCTGCCCTTTTTTGACAGTTCAAGAGGAGGGAGACCCAGAGTTCATCAGTATTTGATTGTGATCACCGACGGGGTCTCCCAGGATAATGTAGCTCCCCCAGCCAAAGCCCTCAGGGACAGAAACATAATTATTTTTGCTATCGGGGTGGGAAATGTTCAAAGAGCCCAGCTTTTGGAGATCACCAATGACCAGGACAAAGTATTCCAGGAGGAAAATTTTGAGTCCCTGCAGAGCCTGGAAAAGGAAATTCTTTCTGAGGTCTGTAGTTCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572:ENSMUST00000121963:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.005 A=NA C2=0.011
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=92.3)
A:
NA
C2:
PF0009223=VWA=WD(100=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTCGGGACATCTGCTCCTCA
R:
CTCTGGGTCTCCCTCCTCTTG
Band lengths:
346-986
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