GgaINT0022939 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9084312-9084504:+
Coord C1 exon
chr12:9084312-9084365
Coord A exon
chr12:9084366-9084441
Coord C2 exon
chr12:9084442-9084504
Length
76 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGC
5' ss Score
8.8
3' ss Seq
ATGTCTGCTTCATCCCCCAGGGA
3' ss Score
10.68
Exon sequences
Seq C1 exon
GGAGAGCCGGGGCTGCCGGGGCGCTCGGGGCTGCCAGGAAGGAAGGGTGAGCCG
Seq A exon
GTAAGCACCGTGCTGGCACCGCGCTGCAAGGGGGGTGTGCATCCAGGGGCTCACGGATGTCTGCTTCATCCCCCAG
Seq C2 exon
GGAGAGCTGGGGTTGTCGGGAGCACCCGGCGTCCCCGGGAAGGAGGGGCTCATGGGACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:105
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(2.2=11.1),PF0139113=Collagen=FE(17.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.4=100),PF0139113=Collagen=PU(21.2=66.7)
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:
CTCGGGGCTGCCAGGAAG
R:
GTCCCATGAGCCCCTCCTTC
Band lengths:
89-165
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]