MmuINT0039789 @ mm9
Intron Retention
Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97816739-97817271:-
Coord C1 exon
chr15:97817173-97817271
Coord A exon
chr15:97816793-97817172
Coord C2 exon
chr15:97816739-97816792
Length
380 bp
Sequences
Splice sites
5' ss Seq
AACGTAAGT
5' ss Score
10.74
3' ss Seq
CTTCTCGTCCCTCCCTTCAGGGC
3' ss Score
12.28
Exon sequences
Seq C1 exon
GGAGCCCCTGGTGAAGACGGTCGCCCTGGACCTCCTGGTCCTCAGGGAGCTCGTGGGCAGCCTGGCGTCATGGGTTTCCCTGGCCCCAAAGGTGCCAAC
Seq A exon
GTAAGTGACAGTTTGCTCTCTCATCTCCTTCGTCTTTCCCTATATCCTTCGAGGAGAAGGAGCTGGGTCCTGAGCAGAGTTAACCCAGGGTGGGTGACCAGTGGCCTCTCAATGTCATTAAGCTCTGTCCTCCATGTCCTGCAAGGAATGCATGTGACCTGGGGTAAACTTGGGTACCTTAAAACCCTAAGATATCAGCACTGCAACATTACCCATAGAGCCTTGTGCCCCGGAGGCCAGTGACTATAAAAGAAGGGGCTGATGTTCGATGGCACCTTCTCTTGTGCACCACACTGAGGCTTCAGGCCTCAGCTCTCTAGCCTACTACTTCACTCTATCCCAAATCACCCAGCTCATGGTCTTCTCGTCCCTCCCTTCAG
Seq C2 exon
GGCGAGCCTGGCAAAGCTGGTGAGAAGGGTCTGGCTGGCGCTCCTGGTCTGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483-Col2a1:NM_031163:27
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(32.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(5.0=27.8)
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: