MmuINT0038881 @ mm10
Intron Retention
Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34050957-34051318:+
Coord C1 exon
chr17:34050957-34051043
Coord A exon
chr17:34051044-34051261
Coord C2 exon
chr17:34051262-34051318
Length
218 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGC
5' ss Score
8.19
3' ss Seq
TGTCCCTCCTGCTCCTCTAGCTG
3' ss Score
10.08
Exon sequences
Seq C1 exon
TTCCGGTTTGGCAGTAGTGGGGGTGACAAGGGCCCCGTGGTGGCAGCCCAGGAGGCCCAGGCCCAGGCGATTCTGCAGCAGGCACGG
Seq A exon
GTGAGCAGGGGCAGGGCAGGGGTGCGGACTGGTAGAGGGAGGTATGTGGTGGAAAGGGAAGACCGGTGTGGAAAGAGAGTGGGTTTTCTGAGGCCGAGGGGAGATGGAGGAGAGTAAAGGTTACAGGGAGATTAGAGCGAGGATGGGCAAATCTGGGGTTGTTGGGATTCTGTCACATTGCCTCCCTCTCACCCCTTCTGTCCCTCCTGCTCCTCTAG
Seq C2 exon
CTGGCACTCCGTGGGCCCCCTGGCCCCATGGGTTACACGGGCCGCCCTGGACCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330:ENSMUST00000087497:11
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:
PF0139113=Collagen=PU(25.8=84.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCGGTTTGGCAGTAGTGGG
R:
GCGGCCCGTGTAACCCAT
Band lengths:
132-350
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