MmuEX6099956 @ mm10
Exon Skipping
Gene
ENSMUSG00000026837 | Col5a1
Description
collagen, type V, alpha 1 [Source:MGI Symbol;Acc:MGI:88457]
Coordinates
chr2:27929379-27950758:+
Coord C1 exon
chr2:27929379-27929541
Coord A exon
chr2:27949627-27949758
Coord C2 exon
chr2:27950627-27950758
Length
132 bp
Sequences
Splice sites
3' ss Seq
GAGCTCTTGTCTGTTTGCAGGGT
3' ss Score
8.46
5' ss Seq
TATGTGAGT
5' ss Score
5.56
Exon sequences
Seq C1 exon
GTGGCACCGAATTGCTCTCAGTGTCTACAAGAAAAATGTCACCTTGATCCTCGACTGTAAGAAGAAGATTACGAAGTTCCTCAGCCGCAGTGACCACCCCATAATAGACACCAATGGGATTGTCATGTTTGGCTCCCGGATTCTGGATGATGAAATATTTGAG
Seq A exon
GGTGACATCCAACAGTTGCTTTTCGTCTCTGACAACCGAGCTGCCTATGACTACTGTGAGCACTACAGCCCCGACTGTGACACTGCGGTCCCTGACACACCTCAGTCACAGGACCCTAACCCGGATGAATAT
Seq C2 exon
TACCCAGAAGGAGAGGGTGAGACCTATTACTATGAGTATCCATATTATGAAGACCCTGAAGACCCGGGAAAGGAGCCTGCCCCTACTCAGAAGCCAGTGGAAGCTGCCAGAGAAACCACAGAGGTTCCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026837-'4-11,'4-4,11-11=AN
Average complexity
A_S
Mappability confidence:
NA
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 Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCGAATTGCTCTCAGTGT
R:
CTTCTGAGTAGGGGCAGGCTC
Band lengths:
253-385
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]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types