GgaALTA0002978-2/2 @ galGal4
Alternative 3'ss
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9068607-9068986:+
Coord C1 exon
chr12:9068607-9068753
Coord A exon
chr12:9068859-9068861
Coord C2 exon
chr12:9068862-9068986
Length
3 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGG
5' ss Score
10.19
3' ss Seq
AGCACCCTATTTCCCCTCAGCAG
3' ss Score
5.09
Exon sequences
Seq C1 exon
GTGGTCCCCAGCGCAGCCAGCAGCTTCCAGCCACCGCCAACTCCTATGACCTGGGAGGGCTGGAGCCGGGCCGGCGCTACCACATCAGCATCACCAGCATGGTGGGCAGCCGGGAGAGCGCTCCAGTCACCGTCACTACTGCCACCG
Seq A exon
CAG
Seq C2 exon
CCTCCCCGAGCCACGCCACCAGCCTGCGAGTGACGGAGGTGCAGAGAGATTCCGTGTCGCTCTCCTGGACCCCTGTCCCCGGTGCTTCTGAATACGTCCTGTCCTGGAGCCCCCCTGCAGGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811-20-21,20-20-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.600 A=NA C2=0.465
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(51.9=82.0)
A:
NA
C2:
PF0004116=fn3=PU(44.2=88.4)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCCAGTCACCGTCACTACT
R:
GGAGAGCGACACGGAATCTCT
Band lengths:
93-96
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]