MmuEX6073567 @ mm9
Exon Skipping
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:113856017-113861110:+
Coord C1 exon
chr3:113856017-113856106
Coord A exon
chr3:113856559-113856612
Coord C2 exon
chr3:113861003-113861110
Length
54 bp
Sequences
Splice sites
3' ss Seq
TTGTGTTCTCACTTTTTCAGGGT
3' ss Score
12.09
5' ss Seq
GTTGTAAGT
5' ss Score
8.3
Exon sequences
Seq C1 exon
GGTGATCCCGGGCCTCAAGGTATCTCAGGAAAAGATGGACCAGCAGGAATACGCGGTTTCCCAGGTGAAAGAGGCCTTCCTGGAGCCCAG
Seq A exon
GGTGCACCTGGGCTGAAAGGAGGAGAAGGTCCCCAGGGCCCACAGGGTCCAGTT
Seq C2 exon
GGCTCTCCTGGAGAGCGAGGCTCAGCAGGCACAGCAGGCCCAATTGGTTTGCCAGGACGTCCAGGCCCCCAGGGTCCTCCTGGTCCAGCTGGAGAAAAAGGTGCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966-'43-43,'43-42,44-43=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(41.4=96.7)
A:
PF0139113=Collagen=FE(24.3=100)
C2:
PF0139113=Collagen=PD(30.0=58.3)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGTTTCCCAGGTGAAAGAGG
R:
TTTTCTCCAGCTGGACCAGGA
Band lengths:
135-189
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: