GgaINT1010146 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9075799-9076093:+
Coord C1 exon
chr12:9075799-9075834
Coord A exon
chr12:9075835-9076021
Coord C2 exon
chr12:9076022-9076093
Length
187 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
CACTTCTCCTCTCCCTGCAGGGG
3' ss Score
11.98
Exon sequences
Seq C1 exon
GGGGACCCAGGGAAGCAGGGGGACCCTGGCCGAGAT
Seq A exon
GTGAGTATCTCCTGGGAGTGTGAGTGTGTGTTCTTCTGCTGGGGACATGACACTCCTGCTTCGTGCCCCTTGGTCACTGTCCCCCATCCCATGCCATGCCACCATTCCTGGCTGTGCTCTCACCTCCCATAGCAGAGGCTGTGTGCTGCTGCTGCCCCGTGCCTCCCCACTTCTCCTCTCCCTGCAG
Seq C2 exon
GGGCTGCCCGGGCTGCGGGGGGAGCAGGGACCGCCTGGCACAATAGGACCGCTGGGACCACCTGGTATCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:60
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(15.1=100),PF0139113=Collagen=FE(10.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(8.2=25.0),PF0139113=Collagen=FE(22.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCCAGGGAAGCAGGGG
R:
GTCCCAGCGGTCCTATTGTG
Band lengths:
91-278
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]