MmuINT0039473 @ mm10
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:181015543-181015857:+
Coord C1 exon
chr2:181015543-181015609
Coord A exon
chr2:181015610-181015689
Coord C2 exon
chr2:181015690-181015857
Length
80 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGT
5' ss Score
6.05
3' ss Seq
TCTGATGTCTCCTTCCCCAGCAC
3' ss Score
8
Exon sequences
Seq C1 exon
GGAGAGCCACAGTCCCTTGCCACCATCTTCCAGCTGGTGAGCCAGGCCTGCGAGTCAGCCATACGGA
Seq A exon
GTGAGTGAAACCCACCCTGCCCAGCCTCATCCTTGCGGATGAGAAATCAGCTGGGCCCCATCTGATGTCTCCTTCCCCAG
Seq C2 exon
CACATGTGCTGAAGCTGAATTCCTTCCTCCATGAGAATGCCCGTCCCCCAATGCCCTTCATGGCAGAGACAGCTAAGCTAGGCAGACCCAGATCTATAGATCCTGGATTACACAACGAGGCTCTACTTCCTGGAGACTGGGGACATATCCTCCGCCCTGAGGACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356:ENSMUST00000108856:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.511 A=NA C2=0.912
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(6.8=17.4)
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:
CAGTCCCTTGCCACCATCTTC
R:
GCCTCGTTGTGTAATCCAGGA
Band lengths:
179-259
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