MmuINT0039780 @ mm9
Intron Retention
Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97819379-97819815:-
Coord C1 exon
chr15:97819717-97819815
Coord A exon
chr15:97819424-97819716
Coord C2 exon
chr15:97819379-97819423
Length
293 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
CTATACCATCTTCTTGTCAGGGT
3' ss Score
5.66
Exon sequences
Seq C1 exon
GGCGAAGCTGGTCCCACTGGTGCTCGCGGTCCTGAAGGTGCTCAAGGTTCTCGTGGCGAGCCTGGCAATCCTGGGTCCCCTGGGCCTGCAGGTGCTTCT
Seq A exon
GTAAGTTCATCTCTTTGGCCTGGAAGGCATGGCATGTGTGGCCTTGTCACAAATGTACATGTCACCTGGAGTCCCAGTCACTGGGACCACTAAATGGTCATGCTGGCCAAACACCTCCCCCTGACATCCACGACTGTCTCCCTTCACCCGTAGTCCACCCCATGAGACAGGCAGGAGGGATGCCCCTGAAGCAGACAGCACTTGTCCCTGACCCCTAGACTGGGGCCCAATGGGCCGAATGGTTGGGTTGTTTCTTTGCTGTTTATTTTATCGCTATACCATCTTCTTGTCAG
Seq C2 exon
GGTAACCCAGGGACTGATGGTATTCCTGGAGCCAAAGGATCCGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483-Col2a1:NM_031163:19
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(2.5=6.1),PF0139113=Collagen=FE(36.8=100),PF0139113=Collagen=PU(15.2=36.4)
A:
NA
C2:
PF0139113=Collagen=FE(16.1=100),PF0139113=Collagen=FE(17.7=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:
CGAAGCTGGTCCCACTGGT
R:
CGGATCCTTTGGCTCCAGGAA
Band lengths:
140-433
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: