GgaINT1010130 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9064405-9064881:+
Coord C1 exon
chr12:9064405-9064477
Coord A exon
chr12:9064478-9064700
Coord C2 exon
chr12:9064701-9064881
Length
223 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
CAACCAGTGCTGTCCCATAGTGG
3' ss Score
4.09
Exon sequences
Seq C1 exon
ATGAGTGGGTGGCTCCTATTCCTCGCCCTGCTCCTGGCCCCCCAGGCTGCTGCCGCACAGAAGAGGAGCCAAG
Seq A exon
GTGGGTGCTGAGTACTGGGTACCGCTATAGGGCCTGCAGCGGGGTGAGAGGGGCTCTGCTGCTCCTCCCCGCTGCAGCACCCCAAACTTGAGCTTGGGCATGGGGAGCCCTATGGGAGTGGGCACCGATGTGACGTGAGCTCAAGGAGAAGGGACAGGTCTGGGAGTCCCATGCCACAGGGCACTGGGGGCCGATGTGGGTGCCAACCAGTGCTGTCCCATAG
Seq C2 exon
TGGTGTGCGAGAACGTGCTGGAGGCCGACATCGCCTTCCTGGTGGACGGCTCGTCCAGCATTGGCCGGAACAACTTCCGTGCCATCCGCACCTTCGTGGAGGACCTGGTGTCACCCTTTGTGCACGTGGTGGGCGAGAAGGCGGTGCGCTTCGCTGTGGTGCAGTACAGCGACGATCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(29.3=83.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGTGGGTGGCTCCTATTCCT
R:
CGTGGATCGTCGCTGTACTG
Band lengths:
252-475
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]