GgaINT0022869 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9069703-9070117:+
Coord C1 exon
chr12:9069703-9069846
Coord A exon
chr12:9069847-9069956
Coord C2 exon
chr12:9069957-9070117
Length
110 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGG
5' ss Score
8.48
3' ss Seq
TGAAGGTGCTGTTGGCGCAGGGG
3' ss Score
2.22
Exon sequences
Seq C1 exon
GGGCAGCCATCACCTTTGCTAGGACCTACCTGCTGAGCCCTGGTGCGGGACGGCGGCCCAGCGTGCCGGCGGTGCTGGTAGTGCTGGCCGACGGCCCCTCCGGGGATGATGCCATCACTGCTGCCAGGGATGCCAAGGCAGCGG
Seq A exon
GTGAGGTTGGATAGGGACCCTATGGGATGGGGTCCTCATGGGATGAAGTTCCCATGGGATGAGGTCCCCTTGGGCGATCCAGCCAGGTGCTGAAGGTGCTGTTGGCGCAG
Seq C2 exon
GGGTCCGAGTGCTGGCAGTGGGCTTGGAGGGGGCAGACCAGGAGCAGCTCCGGCGCATGGTCAGTGGTGAGGACCCACGCTTCGTCTTCCGCAACCGTGGGTCCCTGTCAGAGCTGGAGGGAGAGCTCACCGATGACCTCTGTACCATCATCTCCACCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.184 A=NA C2=0.722
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(27.3=100)
A:
NA
C2:
PF0009223=VWA=PD(26.1=85.2)
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:
GACCTACCTGCTGAGCCCTG
R:
CTCTCCCTCCAGCTCTGACAG
Band lengths:
247-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]