MmuINT0038910 @ mm10
Intron Retention
Gene
ENSMUSG00000024330 | Col11a2
Description
collagen, type XI, alpha 2 [Source:MGI Symbol;Acc:MGI:88447]
Coordinates
chr17:34058278-34058609:+
Coord C1 exon
chr17:34058278-34058367
Coord A exon
chr17:34058368-34058555
Coord C2 exon
chr17:34058556-34058609
Length
188 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
ACCCTAAATCTGGTTCATAGGGT
3' ss Score
6.37
Exon sequences
Seq C1 exon
GGTGACCCTGGTCCTCCTGGGGCCCCAGGGAAGGATGGTCCTGCTGGTCTGAGAGGCTTCCCAGGAGAGCGAGGCCTTCCAGGCACTGCT
Seq A exon
GTGAGTGTGACCCCCAAAGCTAACAGCCTATGAATATGGTCACTCATCACCTGGTCCCCTTGATATTATACCCCGCTTTGGGGGCCTACATCTCCCCAAAGCCCACACTTCCCAGGATGTCTTTTGGGGCCCCATGCCTGTGAAGGCTTGCCTTCTCACTCACCACTTACCCTAAATCTGGTTCATAG
Seq C2 exon
GGTGGACCCGGCTTGAAAGGAAATGAAGGTCCAGCTGGCCCTCCTGGCCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024330:ENSMUST00000087497:38
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=PU(43.9=96.7),PF0139113=Collagen=PU(6.9=16.7)
A:
NA
C2:
PF0139113=Collagen=FE(26.2=100),PF0139113=Collagen=PU(19.8=94.4)
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:
GGTGACCCTGGTCCTCCTG
R:
GGCCAGCTGGACCTTCATTTC
Band lengths:
130-318
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