GgaINT0022935 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9083696-9083889:+
Coord C1 exon
chr12:9083696-9083767
Coord A exon
chr12:9083768-9083853
Coord C2 exon
chr12:9083854-9083889
Length
86 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TTTGCTGTTGCCTTTACCAGGGA
3' ss Score
8.82
Exon sequences
Seq C1 exon
GGTGCAAGGGGTGAACCAGGTGAGAGGGGCTCCGCAGGCTTCCCTGGGGCACGCGGCCCTGGTGGGCAGAAG
Seq A exon
GTAAGGAGATGGGCACCCTGTACCACTGTGGGGTCCCCTCACTGCCCAGAAGCCCTGACCCACATCTTTGCTGTTGCCTTTACCAG
Seq C2 exon
GGAGAAGTTGGTGTGCCAGGGGAGCCTGGTGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:101
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(35.0=87.5),PF0139113=Collagen=FE(25.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(12.2=100)
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:
GCAAGGGGTGAACCAGGTG
R:
TGGCACACCAACTTCTCC
Band lengths:
87-173
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]