MmuINT0038935 @ mm9
Intron Retention
Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34200809-34201236:+
Coord C1 exon
chr17:34200809-34200862
Coord A exon
chr17:34200863-34200968
Coord C2 exon
chr17:34200969-34201236
Length
106 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CCCTCCCTGTCTCCACCCAGGGC
3' ss Score
10.86
Exon sequences
Seq C1 exon
GGCCCAGCTGGACCCAAGGGAGAGAAGGGTGTCCAGGGCCCTCCAGGACACCCG
Seq A exon
GTGAGTGAGGAGCGAGTGGTACCTGCTGCTCTGGCTGTAAGCAACCCATCGTACCTACCCTTTACTCTCACTGGGACCTCACTGTACCCTCCCTGTCTCCACCCAG
Seq C2 exon
GGCCCCCCGGGAGAGGTGATCCAGCCACTGCCCATCCAGATGCCCAAGAAGACCCGCCGTTCCGTGGACGGAAGCAAACTGATACAGGATGAGGAGGCTGTGCCCACTGGCGGTGCTCCGGGCAGTCCTGCGGGGCTGGAGGAGATCTTTGGCTCACTGGACTCTCTGCGGGAGGAGATCGAGCAGATGAGGAGGCCGGCGGGGACCCAGGACAGCCCTGCTCGCACCTGCCAGGACTTGAAGCTGTGCCACCCGGAGCTTCCTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330-Col11a2:NM_009926:60
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=0.933
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=8.9),PF0141013=COLFI=PU(41.5=30.0)
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:
CTGGACCCAAGGGAGAGAAGG
R:
GCCTCCTCATCTGCTCGATCT
Band lengths:
243-349
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: