GgaINT1010142 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9073423-9073579:+
Coord C1 exon
chr12:9073423-9073458
Coord A exon
chr12:9073459-9073546
Coord C2 exon
chr12:9073547-9073579
Length
88 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
TCCTGCTGCTTTGTCCCCAGGCT
3' ss Score
10.11
Exon sequences
Seq C1 exon
GGTGATGTGGGAGCGCCCGGTGAACCTGGCCAGCCG
Seq A exon
GTAAGTGCTGCTGCCTGGCAGCCCATCCCATTCCTGGCACGAGGAGTGGTGGCTGCGCCCAGCACTGTTCCTGCTGCTTTGTCCCCAG
Seq C2 exon
GCTCCCAGTGTGGCCACTGTCAGAGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:44
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=PD(7.6=45.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCGGTGAACCTGGCCAG
R:
TTCTCTCCTCTGACAGTGGCC
Band lengths:
53-141
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]