MmuINT0039467 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180747941-180748148:+
Coord C1 exon
chr2:180747941-180747994
Coord A exon
chr2:180747995-180748094
Coord C2 exon
chr2:180748095-180748148
Length
100 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
CTATCTCTGTTCCCTCACAGGGC
3' ss Score
11.12
Exon sequences
Seq C1 exon
GGGCCACCAGGAGCCAAAGGAGAGAAGGGGGATCAGGGACTTTCAGGCTTGCAG
Seq A exon
GTAATGTGACAGGGCCAAGGCAGGGTGATGGCATAGGCAGGACCCTCCTTCGCCTATGACATTGGCTCTGCCCTGGTGGACTATCTCTGTTCCCTCACAG
Seq C2 exon
GGCCTCTCTGGCCAGCAAGGCATCCCTGGGAAAACTGGCCTACAGGGACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:28
Average complexity
IR-S
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(29.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(29.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCACCAGGAGCCAAAG
R:
TTTGGTCCCTGTAGGCCAGTT
Band lengths:
106-206
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: