MmuINT0039449 @ mm10
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180998354-180998708:+
Coord C1 exon
chr2:180998354-180998499
Coord A exon
chr2:180998500-180998584
Coord C2 exon
chr2:180998585-180998708
Length
85 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TGTCACCATGTCCCTGCCAGGTA
3' ss Score
8.82
Exon sequences
Seq C1 exon
CACCCCTGCCTCCACCTGGGCCACTGACCCTAGCTGCAGTGACACCCAGAACTCTCCACGTCACCTGGCCGCCCTCTGCTGGGGTCACTCAGTACTTGGTGCAGTACTTGCTGGCTACCTCCACTGGGGAGGAGCAAAAGAGAGAG
Seq A exon
GTGAGAGGCAGGGAGAGAGAGATGGGGTGGGGCAGATGGTGAGGCTCAGTATAGAGAGAGTACTGTGTCACCATGTCCCTGCCAG
Seq C2 exon
GTACATGTGGGACAGCCTGAGGTACTGCTGGATGGTCTGGAGCCTGGCCAGGACTATGATGTCTCAGTGCAGAGCCTTCGGGGACCAGAGGCCAGCGAGGTCCAGAGCATCCGTGCCAGGACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356:ENSMUST00000108856:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.388 A=NA C2=0.738
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(57.0=91.8)
A:
NA
C2:
PF0004116=fn3=PD(40.5=76.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAACTCTCCACGTCACCTGG
R:
AGGCTCTGCACTGAGACATCA
Band lengths:
176-261
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