MmuINT0038823 @ mm9
Intron Retention
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:113816469-113816680:+
Coord C1 exon
chr3:113816469-113816522
Coord A exon
chr3:113816523-113816635
Coord C2 exon
chr3:113816636-113816680
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-Col11a1:NM_007729:19
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(25.0=100),PF0139113=Collagen=PU(23.6=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(19.1=86.7),PF0139113=Collagen=FE(19.4=100),PF0139113=Collagen=PU(18.9=93.3)
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:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: