MmuINT0040702 @ mm9
Intron Retention
Gene
ENSMUSG00000027570 | Col9a3
Description
collagen, type IX, alpha 3 [Source:MGI Symbol;Acc:MGI:894686]
Coordinates
chr2:180344761-180344948:+
Coord C1 exon
chr2:180344761-180344805
Coord A exon
chr2:180344806-180344894
Coord C2 exon
chr2:180344895-180344948
Length
89 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
CTGTCTCTTCACTTGTATAGGGT
3' ss Score
8.52
Exon sequences
Seq C1 exon
GGGCTCCCTGGACGAGCAGGGTCCAAAGGCGAGAAGGGAGAACCG
Seq A exon
GTAAGTGACTGTTTTCCCCAGGAGAGAGGAGCCACAGCTGTGTGGGGAATGGAGGGAACATAGAACTCACTGTCTCTTCACTTGTATAG
Seq C2 exon
GGTAGAACTGGCGAGCTGGGTGAGGCTGGCCCCTCTGGAGAGCCAGGTATCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027570-Col9a3:NM_009936:20
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(14.3=100),PF0139113=Collagen=PU(2.6=13.3)
A:
NA
C2:
PF0139113=Collagen=FE(17.3=100),PF0139113=Collagen=FE(22.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCCTGGACGAGCAGGG
R:
CTCTCCAGAGGGGCCAGC
Band lengths:
84-173
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: