MmuINT0039466 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180747772-180747994:+
Coord C1 exon
chr2:180747772-180747867
Coord A exon
chr2:180747868-180747940
Coord C2 exon
chr2:180747941-180747994
Length
73 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
CAGTCCATCTTCCCCTCCAGGGG
3' ss Score
8.61
Exon sequences
Seq C1 exon
GGGGAGCCGGGCCCACCTGGACAAACAGGACCTGAAGGCCCTGGAGGTCAGCAGGGGTCACCAGGGACCCAGGGCCGCGCAGTCCAGGGACCCATG
Seq A exon
GTAAGTGCTGCTCTGCACGCGTCTTCTTCCCTTCTGTCTTTGTTCCCACCTCTCAGTCCATCTTCCCCTCCAG
Seq C2 exon
GGGCCACCAGGAGCCAAAGGAGAGAAGGGGGATCAGGGACTTTCAGGCTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:27
Average complexity
IR-C
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=PD(47.5=87.5),PF0139113=Collagen=PU(10.5=18.8)
A:
NA
C2:
PF0139113=Collagen=FE(29.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCCACCTGGACAAACAG
R:
GCAAGCCTGAAAGTCCCTGAT
Band lengths:
139-212
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: