MmuINT0039783 @ mm10
Intron Retention
Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97988563-97988860:-
Coord C1 exon
chr15:97988762-97988860
Coord A exon
chr15:97988617-97988761
Coord C2 exon
chr15:97988563-97988616
Length
145 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGA
5' ss Score
9.63
3' ss Seq
TATTTCTTTCTTTCACGTAGGGT
3' ss Score
9.22
Exon sequences
Seq C1 exon
GGTGCTCCTGGAATTGCTGGTGCCCCTGGCTTCCCTGGGCCCCGTGGCCCTCCCGGTCCTCAAGGTGCAACTGGTCCCCTTGGCCCCAAAGGTCAGGCG
Seq A exon
GTAAGAGCCCAAAAAGATTGGCAGGTCCTACCTACAGGCTCCTCTTTTCTGTGCCCTCCTGCTCACCGTAGGAGGCTTCTGGGAGGAGGGTGAGCAGACTCTATGGAGAGAAGCCAGTGCGAGCATATTTCTTTCTTTCACGTAG
Seq C2 exon
GGTGAACCTGGCATTGCTGGCTTTAAAGGTGATCAAGGCCCCAAGGGAGAGACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483:ENSMUST00000023123:21
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:
PF0139113=Collagen=PD(16.1=42.4),PF0139113=Collagen=FE(40.5=100),PF0139113=Collagen=PU(37.7=78.8)
A:
NA
C2:
PF0139113=Collagen=FE(21.5=100),PF0139113=Collagen=FE(24.6=100)
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:
GTGCTCCTGGAATTGCTGGTG
R:
CTCTCCCTTGGGGCCTTGATC
Band lengths:
149-294
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