MmuINT0040056 @ mm10
Intron Retention
Gene
ENSMUSG00000067158 | Col4a4
Description
collagen, type IV, alpha 4 [Source:MGI Symbol;Acc:MGI:104687]
Coordinates
chr1:82497154-82497934:-
Coord C1 exon
chr1:82497828-82497934
Coord A exon
chr1:82497338-82497827
Coord C2 exon
chr1:82497154-82497337
Length
490 bp
Sequences
Splice sites
5' ss Seq
CGAGTATGT
5' ss Score
6.61
3' ss Seq
ATGTAACCTAACATCCCCAGGGG
3' ss Score
4.81
Exon sequences
Seq C1 exon
GGCAAAAAGGAGAAAGAGGACTGGATGGGCCACCAGGATTTCCGGGGCCACATGGACAAGATGGTGGGGATGGACGTCCTGGAGAAAGAGGGGATCCTGGGCCACGA
Seq A exon
GTATGTGAAGTTCTGCTCTAGAATTTAATTTTCTGATACGTGCACACAAGCAAGGCAGGCAACTATAGGTCAGACTTGCACACAATAGGGGTAAAGATACGTTGTATTTGTATTTTTAACCATGGGCACAAAGGGTGGCAGAGCCTATCTGGCTGGATACCTTCTCCTAAGGCTATAAGAAGCTGACTTCACACAAAACACTCATTTGAGTTTTTCATTTGTGTGTGGATCTACCAATTGAATTACTTATTTTATATGTTATATCTGATGTTAGTGCATCTACACATAAGTTTCTATTCTGTACCTTAGGTATAATACAATTCATTTTCTGTGTTTGAGGCATAGTATAACACATCCATATCCTATATATATATATAAGCATACACTCGCTGCATCTGTCTTTTCAAATCTGGGATTTTAAACATGTAGACTGCCTTGAATACATGGGCTTTGAAAGATCAATAATAGACATGTAACCTAACATCCCCAG
Seq C2 exon
GGGGACCATAAGGATGCAGCCCCGGGTGAGAGAGGGCTTCCCGGACTGCCAGGCCCTCCAGGAAGAACAGGACCTGAGGGGCCTCCAGGCCTGGGATTTCCAGGCCCACCAGGACAGCGAGGCCTACCCGGAGAGCCCGGGCGTCCGGGCACCAGAGGCTTTGATGGCACGAAGGGGCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067158:ENSMUST00000087050:24
Average complexity
IR
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(76.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.9=8.1),PF0139113=Collagen=PU(93.5=93.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAAAAAGGAGAAAGAGGACTGGA
R:
CTTTCTGCCCCTTCGTGCC
Band lengths:
290-780
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