GgaINT0022853 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9066094-9066583:+
Coord C1 exon
chr12:9066094-9066213
Coord A exon
chr12:9066214-9066433
Coord C2 exon
chr12:9066434-9066583
Length
220 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CCCCTCCATGTCCCCCCCAGGAA
3' ss Score
10.06
Exon sequences
Seq C1 exon
AGAGCCGTGGCGGCGTGCAGCATTTCCACGTGGCCGAAGCCGGGCCGACCTTCCTGAGGCTGTCCTGGCAGCCCGGGCCCGAGCCTCCCCAGGGCTACATCCTCAGCTACGCCGTGCCAG
Seq A exon
GTGAGGGGACATGCCGTGCCCCGCAGGCACCTCTTTGGGGTAGCTGCGCGTGCTGCAGCACCTGGCGGCCCCTCCCTGTCCCTGGGCGCTGCCCTGGCCCCCGTCCCAGCCTCACCCCGTGCTCCCCACCCCTGGCACCAGCTGGCATCCCCAGGGCAGGGAGCTGTGCACACCCCTTCCCCGCCACACACCTGCCCGCGCCCCTCCATGTCCCCCCCAG
Seq C2 exon
GAATGCCCCAGGGCGAGGAGAGGAGCCTGGGGGCTGGTGCACTGTCGGCCACTCTCAGCAACCTGCGCCCCAACACCGAGTACGTGGTGACACTGAAGGCACGCTATGCACAGCAGCCTGCAGCCACCGCCAGCCTCACCGCGCGGACGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.439 A=NA C2=0.412
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(47.4=90.2)
A:
NA
C2:
PF0004116=fn3=PD(51.3=78.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGCAGCATTTCCACGTG
R:
CTGCAGGCTGCTGTGCATAG
Band lengths:
230-450
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]