RnoALTD0007426-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117708865-117709052:+
Coord C1 exon
chr8:117708865-117708924
Coord A exon
chr8:117708925-117708946
Coord C2 exon
chr8:117709017-117709052
Length
22 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGT
5' ss Score
7.48
3' ss Seq
TCCCCTTCTTGCTTTCTCAGGGT
3' ss Score
11.54
Exon sequences
Seq C1 exon
GGTGCACCTGGGTTGGCTCTTCCTGGAGACCCTGGCCCCAAAGGAGACCCTGGAGACAGA
Seq A exon
GTGACTAAATATGGGACTGGGG
Seq C2 exon
GGTCCCATTGGCCTCACTGGCAGGGCAGGACCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579-54-51,55-51-2/2
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=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(15.5=65.0)
A:
NA
C2:
PF0139113=Collagen=FE(13.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
CACCTGGGTTGGCTCTTCCT
R:
TCCTGCCCTGCCAGTGAG
Band lengths:
86-108
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]