GgaINT0022916 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9080587-9080770:+
Coord C1 exon
chr12:9080587-9080649
Coord A exon
chr12:9080650-9080734
Coord C2 exon
chr12:9080735-9080770
Length
85 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
3' ss Seq
TGATCGTGTGTCCATCACAGGGC
3' ss Score
8.13
Exon sequences
Seq C1 exon
GGATTGCCTGGTCCCCAGGGCAGCATGGGGCTGCCTGGCCCCCCAGGACCCCCTGGTCTGGTG
Seq A exon
GTAGGTACCCCCAACCCACTCCTCAGGAGCAGCCCTTCTCACTGCCTCAGCTGTGGGTTGATTTCTGATCGTGTGTCCATCACAG
Seq C2 exon
GGCCCACCGGGTGCACCTGGGCTGCCAGGACAAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:82
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(31.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=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:
GTCCCCAGGGCAGCATGG
R:
ACTTGTCCTGGCAGCCCA
Band lengths:
88-173
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]