GgaINT0022859 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9067560-9067909:+
Coord C1 exon
chr12:9067560-9067695
Coord A exon
chr12:9067696-9067765
Coord C2 exon
chr12:9067766-9067909
Length
70 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
ATCTCGGCTGTCTCTCCCAGGTC
3' ss Score
9.36
Exon sequences
Seq C1 exon
GGGCATGCAGAGTTCCCGGCGGTGGGCAGTGTCTCGGAGCTGCGGGTGACGGAGGCCGGCCCCAGCCAGCTGCGGGTCACATGGAGGGGGCTGCCGGGCGCCGGGGGGTACCGGCTGACGTGGAGGGCCAGCGATG
Seq A exon
GTGAGTGCTGGGCTTGGAGGTGATGCGGTGGTGCCGTGGGAGCTCTCCCCATCTCGGCTGTCTCTCCCAG
Seq C2 exon
GTCAGGAGCAGTCTCGCTTCCTCCCTGCCAACCCTACTGCCTTCACCATCGAGGGGCTGCGAGCTGGCGCCATCTATGCCATTGGTGTCACAGCCATCATTGATGGCCGCGAGGGTCCCCCTGTCACCACCATGGGGAGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.109 A=NA C2=0.306
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(47.4=80.4)
A:
NA
C2:
PF0004116=fn3=PD(51.3=81.6)
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:
CAGCTGCGGGTCACATGG
R:
TGATGGCTGTGACACCAATGG
Band lengths:
169-239
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]