GgaINT0022920 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9081204-9081360:+
Coord C1 exon
chr12:9081204-9081239
Coord A exon
chr12:9081240-9081318
Coord C2 exon
chr12:9081319-9081360
Length
79 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CTGACCCTGTGTTGCTGCAGGGT
3' ss Score
9.27
Exon sequences
Seq C1 exon
GGCATCGCTGGCCCTCCTGGTGCCAAGGGCGAGAAG
Seq A exon
GTAAGGAATGGGGTGTGCATTCGGGGGAGACCCTCCCCATAGCAGGCAAAGGTCTGTGCCTGACCCTGTGTTGCTGCAG
Seq C2 exon
GGTGAGCCGGCGCTGCTGGAGGGCGTGCTGCTGGGTGAACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:86
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(19.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(6.9=28.6),PF0139113=Collagen=PU(5.8=21.4)
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:
CATCGCTGGCCCTCCTGG
R:
GGTTCACCCAGCAGCACG
Band lengths:
75-154
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]