MmuINT0039469 @ mm10
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180992434-180993008:+
Coord C1 exon
chr2:180992434-180992577
Coord A exon
chr2:180992578-180992852
Coord C2 exon
chr2:180992853-180993008
Length
275 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
AGTCCTTCCTCTCTCTGCAGTTG
3' ss Score
10.43
Exon sequences
Seq C1 exon
GGGACTTGGAGCAGGAGCTGATACTGACCACCAAGACCCCCAAGGCCACTGTGGGTGGCCTGAACCCTTCCAAGAGCTACACCTTGCAGATCTTTGAGCTCACTGACTCGGGGCCTATCCTGCTGGCACGAAGGGAGTTTGTGA
Seq A exon
GTAAGTCCTCCTGTACCCAGATGGGTGGATTTGGTTGGAAGGCCTCTGGCTTGTGCCCTGAAGCACTTTGCCTGTGAAGTACTTGGGTTTTTGTTGTTGTTGTTGTTGGTTTTTTTTTTTTTAACCTGTTTCTGACATTGCTGCTCATCTTCCATGAGGCAGACAGCAAGTCTGTGGGGTTGCCTTCCAGGAAGTGTACAGATCCCTAAGCTCCAAGCCCCTGTTCCTGCTTTGGGCTGGTGTCCTGGGCCTGACAGTCCTTCCTCTCTCTGCAG
Seq C2 exon
TTGAGGATCTGAAGAGCCAATCTTTGGGCAGAGGCAGCCGGAGGCTGGCTGGAGCCACCCTGGAGCCTACCTCCTTGCCTCTGAGGGGCCCAGACTCTGAGAAAACATCTGAGCCCAGCATTGCCTTTACCTTAAGCAGGGACCTGCCCATTCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356:ENSMUST00000108856:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.440
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(50.6=79.6)
A:
NA
C2:
NO
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:
GGGACTTGGAGCAGGAGC
R:
GGTCCCTGCTTAAGGTAAAGGC
Band lengths:
288-563
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