GgaINT0022891 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9074418-9074568:+
Coord C1 exon
chr12:9074418-9074453
Coord A exon
chr12:9074454-9074523
Coord C2 exon
chr12:9074524-9074568
Length
70 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
TCACTCCATCTATCCCTCAGGGT
3' ss Score
9.22
Exon sequences
Seq C1 exon
GGTGAGCGTGGAGAGAAGGGTGATGAAGGCACCCCG
Seq A exon
GTAAGTGGGAACCCTGTGGAGCGCTGTCCCCATGCTGCCCCCCAGCCCACTCACTCCATCTATCCCTCAG
Seq C2 exon
GGTGAAGCAGGCGTGCCTGGCAAACCTGGAGACAGGGGCCCACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:50
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(13.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(16.7=100),PF0139113=Collagen=PU(16.4=73.3)
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:
GGTGAGCGTGGAGAGAAGGG
R:
GTGGGCCCCTGTCTCCAG
Band lengths:
79-149
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]