MmuINT0039786 @ mm9
Intron Retention
Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97817916-97818152:-
Coord C1 exon
chr15:97818099-97818152
Coord A exon
chr15:97818015-97818098
Coord C2 exon
chr15:97817916-97818014
Length
84 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TCCTGTCTCCTCTGGTATAGGGT
3' ss Score
8.76
Exon sequences
Seq C1 exon
GGTGCTCCTGGCAACCGTGGATTCCCAGGTCAAGATGGTCTGGCAGGTCCCAAG
Seq A exon
GTGAGTGGAGGAGGAGAGGCCTGGTCCCTGCCTGTTTCCCTAGTTACAGAGCATCCCATGGACTTCCTGTCTCCTCTGGTATAG
Seq C2 exon
GGTGCCCCTGGAGAGCGAGGGCCCAGTGGCTTGACTGGTCCCAAGGGAGCCAACGGTGACCCGGGTCGTCCTGGAGAACCTGGTCTTCCTGGAGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483-Col2a1:NM_031163:24
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(18.9=100),PF0139113=Collagen=PU(9.0=50.0)
A:
NA
C2:
PF0139113=Collagen=PD(32.2=87.9),PF0139113=Collagen=FE(32.0=100)
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:
CTCCTGGCAACCGTGGATTC
R:
TCCAGGAAGACCAGGTTCTCC
Band lengths:
143-227
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: