GgaINT0022870 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9069957-9070255:+
Coord C1 exon
chr12:9069957-9070117
Coord A exon
chr12:9070118-9070213
Coord C2 exon
chr12:9070214-9070255
Length
96 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGA
5' ss Score
6.65
3' ss Seq
TCTTCCTCTTGTCTCACCAGCCA
3' ss Score
8.67
Exon sequences
Seq C1 exon
GGGTCCGAGTGCTGGCAGTGGGCTTGGAGGGGGCAGACCAGGAGCAGCTCCGGCGCATGGTCAGTGGTGAGGACCCACGCTTCGTCTTCCGCAACCGTGGGTCCCTGTCAGAGCTGGAGGGAGAGCTCACCGATGACCTCTGTACCATCATCTCCACCAGG
Seq A exon
GTGAGAGAATGGGGGCTGCCCAGGGCTGGGGAGCAGACCCCATGGAGCCAAGGTCTTCTTCTCCCACACTCACATCTCTTCCTCTTGTCTCACCAG
Seq C2 exon
CCAGAGCCAGAGCCAAAGCCCTGCACTGTGCAATGCCCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.722 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(26.1=85.2)
A:
NA
C2:
PF0139113=Collagen=PU(6.1=28.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCGAGTGCTGGCAGTG
R:
GCTTTGGCTCTGGCTCTGG
Band lengths:
178-274
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]