GgaINT0022936 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9083854-9084050:+
Coord C1 exon
chr12:9083854-9083889
Coord A exon
chr12:9083890-9083969
Coord C2 exon
chr12:9083970-9084050
Length
80 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
ATGCTGTGTGCTTCCTTCAGGGC
3' ss Score
9.96
Exon sequences
Seq C1 exon
GGAGAAGTTGGTGTGCCAGGGGAGCCTGGTGAGCCG
Seq A exon
GTGAGGAGCAGTGTCTCAGTACCAGTGCCACCCTATTGCGGTGCAGGAGTGGTCCTCATCATGCTGTGTGCTTCCTTCAG
Seq C2 exon
GGCTTGCCTGGCCGGGATGGCATTGCTGGAGCACGAGGAGAGAAGGGGGACATAGGGCCGCTGGGCTTGCGTGGCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:102
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(12.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(28.9=100),PF0139113=Collagen=PU(15.3=55.6)
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:
GGAGAAGTTGGTGTGCCAGG
R:
GGCCCTATGTCCCCCTTCTC
Band lengths:
95-175
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]