MmuINT0038885 @ mm10
Intron Retention
Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34051753-34052004:+
Coord C1 exon
chr17:34051753-34051806
Coord A exon
chr17:34051807-34051950
Coord C2 exon
chr17:34051951-34052004
Length
144 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGCA
5' ss Score
6.28
3' ss Seq
ATTTTCCCTCTTCTTCCTAGGGT
3' ss Score
10.1
Exon sequences
Seq C1 exon
GGCCGAGCAGGTGCTGATGGAGCCCGTGGGATGCCGGGAGAACCTGGCATGAAG
Seq A exon
GTAGCACGCTTACCCTCCTGTGACGCCTGCATCTGCCTTGCCTGCCCCCTGCCCCCCAGGGCTCAAGAGTTCCTCAGCCAGGACTGAGTAGGAAGGAATGGGACAGGGCTGGACCCTCCGTTTGATTTTCCCTCTTCTTCCTAG
Seq C2 exon
GGTGACCGAGGTTTCGACGGACTTCCAGGGCTACCTGGCGAGAAGGGACAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330:ENSMUST00000087497:15
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(12.9=44.4),PF0139113=Collagen=FE(20.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.2=100),PF0139113=Collagen=PU(10.7=44.4)
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:
CTGATGGAGCCCGTGGGAT
R:
TTTGTCCCTTCTCGCCAGGTA
Band lengths:
93-237
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