RnoALTD0007286-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000031475 | Col16a1
Description
collagen type XVI alpha 1 chain [Source:RGD Symbol;Acc:1310982]
Coordinates
chr5:148292582-148294369:+
Coord C1 exon
chr5:148292582-148292626
Coord A exon
chr5:148292627-148292668
Coord C2 exon
chr5:148294316-148294369
Length
42 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTCT
5' ss Score
1.07
3' ss Seq
TCATGGTTTCTCTCTCTAAGGGT
3' ss Score
8.41
Exon sequences
Seq C1 exon
GGCCCCCCAGGTTTTCCTGGTGCTGTTGGCTCCCCCGGATTGCCT
Seq A exon
GTAAGAACCTAGCAGCACTCCGTCCCCTTTCCTGCCAGCCAG
Seq C2 exon
GGTCTTCAAGGGGAGCGAGGCCCCACAGGCCTGACTGGAGACAAGGGAGAACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000031475-69-70,70-70-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.789 A=NA C2=0.945
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(22.6=100),PF0139113=Collagen=PU(13.2=60.0)
A:
NA
C2:
PF0139113=Collagen=PD(3.2=11.1),PF0139113=Collagen=FE(25.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTCCTGGTGCTGTTGGCTC
R:
CGGTTCTCCCTTGTCTCCAGT
Band lengths:
88-130
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]