GgaINT0022890 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9074219-9074453:+
Coord C1 exon
chr12:9074219-9074299
Coord A exon
chr12:9074300-9074417
Coord C2 exon
chr12:9074418-9074453
Length
118 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGCG
5' ss Score
5.65
3' ss Seq
TCCCCTGACCTGTGCTATAGGGT
3' ss Score
8.64
Exon sequences
Seq C1 exon
GGTGACGCAGGGGAGCCGGGTGAGAAGGGTGAGCCAGGCAGAGTGGGTGCACCAGGACAACCAGGGCAGCGTGGCAAGGAG
Seq A exon
GTAGCGTGGGGCCGGGGGCAGTGGAAGATGCTATGGGGATGCTGAGGCCCCAAGGAATGGGGAGCAGCACAGAGGGATACTGGTGACTTGTTCTCTTGTCCCCTGACCTGTGCTATAG
Seq C2 exon
GGTGAGCGTGGAGAGAAGGGTGATGAAGGCACCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:49
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(31.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(13.1=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:
AGGGGAGCCGGGTGAGAA
R:
GGTGCCTTCATCACCCTTCTC
Band lengths:
106-224
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]