GgaINT0022883 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9073061-9073222:+
Coord C1 exon
chr12:9073061-9073096
Coord A exon
chr12:9073097-9073177
Coord C2 exon
chr12:9073178-9073222
Length
81 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
CTCTTCCTCTCCTCCTCCAGGGC
3' ss Score
12.43
Exon sequences
Seq C1 exon
GGAGACCGCGGTGCACCTGGCCCCGAGGGTGAGAAG
Seq A exon
GTAGGTGGGCACTCATGGCCATGGTCATGACCTTCCTAGGAGCACCTTCTTCTTCCTCTTCCTCTTCCTCTCCTCCTCCAG
Seq C2 exon
GGCGAGACAGGAGCTCCAGGACGGCCAGGGCCATCGGGCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:41
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(16.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCCCCGAGGGTGAGAA
R:
CTGGCCGTCCTGGAGCTC
Band lengths:
47-128
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]