GgaINT0022934 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9083431-9083767:+
Coord C1 exon
chr12:9083431-9083502
Coord A exon
chr12:9083503-9083695
Coord C2 exon
chr12:9083696-9083767
Length
193 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGG
5' ss Score
10.26
3' ss Seq
ACCTGGGGCTGTGCTTGCAGGGT
3' ss Score
6.92
Exon sequences
Seq C1 exon
GGAGACCGTGGCCTAAAGGGCACTGAAGGGGACAAAGGAGAGAAGGGGGAGCAGGGAATGCCCGGAGAGAAG
Seq A exon
GTACGGGGCGGGACAGCAGGGCTGGGGAATGGGGGGCTCATGGTTGGCAGCAGCTAGAGGGACCCAAGAGCATTCTTGTGCCCCATGTGCATCCATGCCTCTGGCACAGTGCTGGGTGTCCTGGCAGTGTGTGGCCCTGCACTGGCCAAAGCTCTCCCTCCTTCCCAGTGCTGACCTGGGGCTGTGCTTGCAG
Seq C2 exon
GGTGCAAGGGGTGAACCAGGTGAGAGGGGCTCCGCAGGCTTCCCTGGGGCACGCGGCCCTGGTGGGCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:100
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=FE(38.3=100),PF0139113=Collagen=PU(5.6=20.8)
A:
NA
C2:
PF0139113=Collagen=PD(35.0=87.5),PF0139113=Collagen=FE(25.6=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:
GGAGACCGTGGCCTAAAGGG
R:
GTGCCCCAGGGAAGCCTG
Band lengths:
124-317
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]