RnoEX0023158 @ rn6
Exon Skipping
Gene
ENSRNOG00000058560 | Col2a1
Description
collagen type II alpha 1 chain [Source:RGD Symbol;Acc:2375]
Coordinates
chr7:139457464-139458381:-
Coord C1 exon
chr7:139458274-139458381
Coord A exon
chr7:139457982-139458035
Coord C2 exon
chr7:139457464-139457571
Length
54 bp
Sequences
Splice sites
3' ss Seq
TGTTTTCTTCTTTTCCACAGGGT
3' ss Score
11.98
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
Exon sequences
Seq C1 exon
GGCCCTCAAGGCCCCCGAGGTGACAAAGGAGAAGCTGGAGAGCCTGGCGAGAGAGGACTGAAGGGGCACCGAGGTTTCACTGGACTGCAGGGTCTGCCTGGCCCCCCG
Seq A exon
GGTCCTTCTGGAGATCAGGGTACTTCTGGCCCTGCTGGTCCTTCCGGCCCTAGA
Seq C2 exon
GGTCCACCTGGCCCTGTTGGTCCCTCTGGCAAAGATGGCTCTAATGGAATCCCTGGCCCCATCGGGCCTCCAGGTCCCCGTGGACGCTCAGGAGAAACTGGCCCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058560-'58-50,'58-49,59-50
Average complexity
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(19.5=47.2),PF0139113=Collagen=FE(42.7=100)
A:
PF0139113=Collagen=FE(20.7=100),PF0139113=Collagen=PU(12.7=44.4)
C2:
PF0139113=Collagen=PD(18.3=41.7),PF0139113=Collagen=FE(55.6=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:
GAGGTTTCACTGGACTGCAGG
R:
CAGTTTCTCCTGAGCGTCCAC
Band lengths:
138-192
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]