GgaINT0022868 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9069499-9069846:+
Coord C1 exon
chr12:9069499-9069625
Coord A exon
chr12:9069626-9069702
Coord C2 exon
chr12:9069703-9069846
Length
77 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGG
5' ss Score
6.9
3' ss Seq
TCCTTTTATCCTCCCTCCAGGGG
3' ss Score
11.85
Exon sequences
Seq C1 exon
GTGGGCCTGGCCACGTACAGCTACCGCAGCCTGCCCTGGCTGCTCCTCAACCGCTCCAGCGAGCTGCCCGCCGTGCTGGAGCAAATCCGCACCATGCGCTACGAGGAGCCCAGCGGCAATGCCATTG
Seq A exon
GTGAGGAGATGTGCTAGGGCTGGGCCAGTAGCCAGTGGGACCTTGCTGACCCTCCCATCCTTTTATCCTCCCTCCAG
Seq C2 exon
GGGCAGCCATCACCTTTGCTAGGACCTACCTGCTGAGCCCTGGTGCGGGACGGCGGCCCAGCGTGCCGGCGGTGCTGGTAGTGCTGGCCGACGGCCCCTCCGGGGATGATGCCATCACTGCTGCCAGGGATGCCAAGGCAGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.184
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(23.9=100)
A:
NA
C2:
PF0009223=VWA=FE(27.3=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:
GGAGCAAATCCGCACCATGC
R:
CAGCAGTGATGGCATCATCCC
Band lengths:
173-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]