RnoEX6016140 @ rn6
Exon Skipping
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6472590-6493392:+
Coord C1 exon
chr3:6472590-6472752
Coord A exon
chr3:6492253-6492384
Coord C2 exon
chr3:6493261-6493392
Length
132 bp
Sequences
Splice sites
3' ss Seq
GCCTTTTATCTTTTTTGCAGGGT
3' ss Score
10.96
5' ss Seq
TATGTGAGT
5' ss Score
5.56
Exon sequences
Seq C1 exon
GTGGCACCGAATCGCTATCAGTGTATACAAGAAAAATGTCACCTTGATCCTCGACTGTAAAAAGAAGATCACGAAGTTCCTCAACCGCGGCGACCACCCCATAATAGATGTCAACGGTATCATCATGTTTGGCTCCCGGATTCTGGATGATGAAATATTTGAG
Seq A exon
GGTGACATCCAACAGTTGCTCTTCGTCTCCGACCACCGAGCTGCCTATGATTACTGTGAGCACTACAGCCCCGACTGTGACACAGCGGTCCCTGACACACCTCAGTCACAGGACCCTAACCCAGATGAATAT
Seq C2 exon
TACCCAGAAGGAGAGGGTGAGACCTATTACTATGAGTACCCATATTATGAAGACCCTGAAGACCCGGGAAAGGAGCCCGCCCCCTCTCAGAAGCCAGTGGAAGCCGCCAGAGAAACCACGGAGGTTCCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749-'11-8,'11-7,19-8=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.455 C2=1.000
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=FE(44.3=100)
A:
PF0221019=Laminin_G_2=PD(8.2=22.7)
C2:
NO
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCGAATCGCTATCAGTGT
R:
ACTGGCTTCTGAGAGGGGG
Band lengths:
258-390
Functional annotations
There are 1 annotated functions for this event
PMID: 12145749
[Not physiological]. Pro-alpha1(V) chains with abnormal N-propeptides were secreted and were incorporated into extracellular matrix, and the mutation resulted in dramatic alterations in collagen fibril structure. Note: also refers to a cryptic splice site.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]