MmuINT0039799 @ mm10
Intron Retention
Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97983238-97983705:-
Coord C1 exon
chr15:97983652-97983705
Coord A exon
chr15:97983292-97983651
Coord C2 exon
chr15:97983238-97983291
Length
360 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CCTACCTTCTTAACTCCTAGGGA
3' ss Score
9.3
Exon sequences
Seq C1 exon
GGTCTGACTGGGCCCATCGGACCCCCAGGCCCAGCAGGGGCCAACGGCGAGAAG
Seq A exon
GTGAGTTGCAGCTGGCCTTTGTCCCTCTGTCTGACCTTCATCCCTCTGTCCACCTCCCCAGAATGTCTTCCCCTTACCTCCTGCCAGACAGTCAAATTTCACTCATTGGCCATTGCCTACCATGGTGGTGGTAGAAGTATAGGGTGGAGGTCCAGTTAACGTGTGACTTGTGTGGCAGTTGGCCTGGTAGAAGGGTGCCATTGGCCAAGGCCTTGAAGAGATAGATGGGACAGCTGGGACTGGGAAGAAACCTAATGTGGAATGGGGTCTAGGGACCCAGAGTCCTCTTCCCAACATCATGGCTTCCTGGTACACTTGGGTCCTCGGGCCCACTCTAATCCCTACCTTCTTAACTCCTAG
Seq C2 exon
GGAGAAGTCGGACCTCCTGGCCCGTCAGGAAGTACCGGAGCTCGAGGTGCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483:ENSMUST00000023123:36
Average complexity
IR
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:
NO
A:
NA
C2:
NO
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:
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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types