GgaINT1010149 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9076479-9076645:+
Coord C1 exon
chr12:9076479-9076514
Coord A exon
chr12:9076515-9076609
Coord C2 exon
chr12:9076610-9076645
Length
95 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TTTTCCCTCCTCCTGGTTAGGGA
3' ss Score
8.04
Exon sequences
Seq C1 exon
GGAGAAGACGGGACACCAGGAGAAGATGGGAGGAAG
Seq A exon
GTGAGGAGCAGAGCCCTGTATGGTCCCCATTGGTGTCACCTCTTGGACTGGGGACAGCATCATACTGAGTCTTTTTTTTCCCTCCTCCTGGTTAG
Seq C2 exon
GGAGACAAAGGTGATGCCGGAGCCCCTGGCAGAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:63
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(10.8=100),PF0139113=Collagen=PU(18.6=91.7)
A:
NA
C2:
PF0139113=Collagen=FE(10.8=100),PF0139113=Collagen=FE(18.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAAGACGGGACACCAGGAG
R:
CAGGGGCTCCGGCATCAC
Band lengths:
63-158
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]