MmuINT0038898 @ mm10
Intron Retention
Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34054837-34055325:+
Coord C1 exon
chr17:34054837-34054890
Coord A exon
chr17:34054891-34055217
Coord C2 exon
chr17:34055218-34055325
Length
327 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
ACCTCCCACTTTCCTCTCAGGGC
3' ss Score
10.88
Exon sequences
Seq C1 exon
GGCGAGGACGGCTTTCCTGGGTTCAAAGGTGACATAGGAGTGAAAGGAGACAGG
Seq A exon
GTGAGTAGATGTCTGACTGTCCGTCCACCCATCCCCATCCGATTCCCCATCTCCTATCCTACCACTCTCCATTTTGAGCCATCCTGGGCTCCCTTGAAATGGAAGCTTTCCCTCCATTGCCCCGCCCCCTTTAGAGCTGGGCCCCAGGGAGATGGCAGCCTTAGCCAGCCACAGTGCTCCCCCCAGTCACTGTCTCTGTGCATCTCTGCTGTCCTGCAGTGTCTTCTCAGACACCTGCCAATCCCAGCCGGCCTTGCTGGGGCCCACCTCTCTACAGAGGGCCTAGACCCATCTCTCCCTAACACTCACCTCCCACTTTCCTCTCAG
Seq C2 exon
GGCGAGGTTGGAGTCCCTGGTTCCAGGGGCGAAGACGGCCCTGAAGGGCCAAAAGGGCGCACTGGACCTACAGGAGACCCTGGACCCACTGGGCTCATGGGCGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330:ENSMUST00000087497:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(20.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(7.1=16.7)
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