MmuINT0039800 @ mm9
Intron Retention
Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97813347-97813722:-
Coord C1 exon
chr15:97813669-97813722
Coord A exon
chr15:97813401-97813668
Coord C2 exon
chr15:97813347-97813400
Length
268 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
ACTTCCTGGTCATCTTACAGGGT
3' ss Score
8.83
Exon sequences
Seq C1 exon
GGAGAAGTCGGACCTCCTGGCCCGTCAGGAAGTACCGGAGCTCGAGGTGCCCCG
Seq A exon
GTGAGTGTGTCTCTCTAAATTAGGCTTTCCCTGGCCCCAGGAGTGAGGAAACCAGCCATGCCCTTCAGGTTAGGGGTGGGAGGAGAGAAGTCATGAAAGGCAGAGGTCACAGGCCCAGGCATGACCAGTGCTCTGACTCCCCGGGACCTAGGCCACTCAGACGCCTTCTCTCTGGGAGGGGTTGAGCATGAGGCTGGGCAGTGGGTTCCCAGTCTGAGGCGAGCACAGAGGCAGGCGACGGACATGACACTTCCTGGTCATCTTACAG
Seq C2 exon
GGTGAACGCGGAGAGACCGGGCCACCTGGACCTGCTGGATTCGCTGGCCCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483-Col2a1:NM_031163:37
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=PD(4.3=16.7),PF0139113=Collagen=FE(21.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.8=100),PF0139113=Collagen=PU(15.2=77.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: