MmuINT0038823 @ mm10
Intron Retention
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:114113551-114113762:+
Coord C1 exon
chr3:114113551-114113604
Coord A exon
chr3:114113605-114113717
Coord C2 exon
chr3:114113718-114113762
Length
113 bp
Sequences
Splice sites
5' ss Seq
AGGGTATAT
5' ss Score
3.89
3' ss Seq
TCCACTTTTGTCACCCATAGGGA
3' ss Score
10.5
Exon sequences
Seq C1 exon
GGAGAAAGAGGTCCACAAGGTCCACCTGGCCTCCCTGGCGATGATGGAATGAGG
Seq A exon
GTATATTAAGAGTTTTCTTGTTTTAGACTTGTTTACAATTAATCCACAAAAGAGCAAGTGTTTTTGAAGTCACACCCCTCTAATAGGGCTCTCTCCACTTTTGTCACCCATAG
Seq C2 exon
GGAGAAGATGGGGAGATCGGGCCCAGGGGTCTTCCAGGTGAAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966:ENSMUST00000092155:19
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=FE(22.1=100),PF0139113=Collagen=PU(20.0=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(13.0=66.7),PF0139113=Collagen=FE(16.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAGGTCCACAAGGTCCACC
R:
TTCACCTGGAAGACCCCTGG
Band lengths:
91-204
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