GgaINT0022857 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9067120-9067557:+
Coord C1 exon
chr12:9067120-9067248
Coord A exon
chr12:9067249-9067333
Coord C2 exon
chr12:9067334-9067557
Length
85 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
TGGCACCCTGCTCCCTACAGACG
3' ss Score
7.73
Exon sequences
Seq C1 exon
GTGTGGAGGTGCCAGTGGGTGCGGTGTCGGATCTCCGTCTCATCGAGGATTTGGGCAGGAGGGTGCGGCTGGGCTGGACCGGTGTCCCCGGTGCCACTGAGTACAAAGTGACGGTGCGCAACACCCAGG
Seq A exon
GTGAGTCGGGAGGATGGGGCCACGGTGCCATTTGCTTGGCATCCCCCGTGGCACTGAGGGCCCCGTGGCACCCTGCTCCCTACAG
Seq C2 exon
ACGGCACCGAGAGGACGAGGCGCGTCCCAGGCACGCAGACAGCGCTGGAGCTGGGTGACCTGCGGGAAGGTGTCACCTACCTGGTGCGTGTCTCAGCCCTCGTGGGCAGCCGGGAAGGCAGTGCCGCTGCACTCAGCATCCATGTCAGTAAGTGCACATGGTTAACCCCAGCCCTGGATTGTGGTGATCGCTCGGGGTGTCCCCATGCTGACGTCCCGGTGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.227 A=NA C2=0.347
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=84.1)
A:
NA
C2:
PF0004116=fn3=PD(51.9=54.7)
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:
TGAGTACAAAGTGACGGTGCG
R:
ACTGACATGGATGCTGAGTGC
Band lengths:
181-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]