MmuEX6073556 @ mm9
Exon Skipping
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:113888414-113889499:+
Coord C1 exon
chr3:113888414-113888521
Coord A exon
chr3:113888800-113888853
Coord C2 exon
chr3:113889446-113889499
Length
54 bp
Sequences
Splice sites
3' ss Seq
CCTTTTTTTCATCTCTCTAGGGA
3' ss Score
12.08
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
Exon sequences
Seq C1 exon
GGTCTCAAAGGAGAGAGAGGAGAGAAAGGAGAAGCTGGGCCCCCTGGTGCTGCAGGTCCTGCTGGTATTAAGGGGCCACCAGGTGATGATGGGCCCAAGGGGAACCCG
Seq A exon
GGACCCGTTGGGTTTCCTGGAGATCCTGGTCCACCTGGAGAACCTGGTCCTGCA
Seq C2 exon
GGGCAAGATGGTGTTGGAGGTGACAAGGGTGAAGATGGAGATCCAGGACAACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966-'55-55,'55-54,56-55=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=PD(10.9=27.8),PF0139113=Collagen=FE(38.5=100)
A:
PF0139113=Collagen=FE(18.7=100)
C2:
PF0139113=Collagen=PD(9.9=50.0)
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:
GAGAGAAAGGAGAAGCTGGGC
R:
CCTGGATCTCCATCTTCACCCT
Band lengths:
136-190
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: