RnoEX6033859 @ rn6
Exon Skipping
Gene
ENSRNOG00000058560 | Col2a1
Description
collagen type II alpha 1 chain [Source:RGD Symbol;Acc:2375]
Coordinates
chr7:139463974-139464532:-
Coord C1 exon
chr7:139464479-139464532
Coord A exon
chr7:139464217-139464261
Coord C2 exon
chr7:139463974-139464072
Length
45 bp
Sequences
Splice sites
3' ss Seq
CATCCTTTTTTGTTCTCTAGGGT
3' ss Score
11.54
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
Exon sequences
Seq C1 exon
GGACTTCCTGGCCCTCCTGGTCCCCCGGGTGAAGGTGGAAAGCAAGGTGACCAG
Seq A exon
GGTATTCCTGGTGAAGCTGGAGCCCCTGGCCTCGTTGGTCCCCGG
Seq C2 exon
GGTGAACGAGGTTTCCCAGGTGAACGTGGCTCTCCCGGTGCTCAGGGCCTCCAGGGTCCCCGAGGCCTCCCTGGCACTCCTGGTACTGATGGTCCCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058560-'41-32,'41-31,42-32=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=FE(17.5=100),PF0139113=Collagen=PU(17.7=94.4)
A:
PF0139113=Collagen=FE(14.4=100),PF0139113=Collagen=FE(14.6=100)
C2:
PF0139113=Collagen=PD(9.3=27.3),PF0139113=Collagen=FE(33.3=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACTTCCTGGCCCTCCTG
R:
ATCAGTACCAGGAGTGCCAGG
Band lengths:
144-189
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]