MmuINT0039453 @ mm10
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:181000033-181000497:+
Coord C1 exon
chr2:181000033-181000175
Coord A exon
chr2:181000176-181000364
Coord C2 exon
chr2:181000365-181000497
Length
189 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
GGACCCCTGCCTTTCTCTAGATC
3' ss Score
8.11
Exon sequences
Seq C1 exon
AGAAAGCTCCTAGCCCTGGCCAGCTGTCTGTGATGGAGCTCCCGGGAGATGCAGTAAAGCTGTCATGGCTGGCCACTGCCTTGTCTGGTGTACTTGTTTATCAGATCAAGTGGATGCCCTTGGGAGAAGGGAAGGCCCGTGAG
Seq A exon
GTAAGGACACGGGGCAGGCGACCTTTCAGAGAAATTCCTATGGCCCCAGATCCCAAGGCCAAGTGAGGCTTAGACTCTGTGCCCATCCCAGTCCTGTATCTTGAGACAATCTGTCTGCCCATAGCCTGTGAGTCTGTCTCTTGGAGGTGAGGCTTCCTGTGACCCAGGTGGACCCCTGCCTTTCTCTAG
Seq C2 exon
ATCTCTGTCCCAGGGACCCTTGGCACAGCCACCTTGCCTGGCCTGATGAAACATGTGGAATATGAGATCACCATCCTTGCCTACTACAGGGACGGCACTCGCAGCGACCCCGTGTCCCTCCGCTACACCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356:ENSMUST00000108856:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.146 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.7=91.7)
A:
NA
C2:
PF0004116=fn3=PD(43.9=80.0)
Main Inclusion Isoform:
NA
Other Inclusion 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:
AGAAAGCTCCTAGCCCTGGC
R:
GAGTGCCGTCCCTGTAGTAGG
Band lengths:
243-432
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