GgaINT0022849 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9065402-9065813:+
Coord C1 exon
chr12:9065402-9065560
Coord A exon
chr12:9065561-9065649
Coord C2 exon
chr12:9065650-9065813
Length
89 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGA
5' ss Score
6.77
3' ss Seq
AGCCCCATGTCCCCCCACAGATG
3' ss Score
8.8
Exon sequences
Seq C1 exon
GAATCAAGAACGCCGACCGTCAGGAGCTGATCCGCGTGGCCTCACTGCCTACTGACTCCTTCTTCTTCTATGTGGGTGACTTCAAGCTACTGGGGACGTTGGTGCCGCTGATGACACGCAGGGTGTGCACAAGCTCAGGGGGCACTCTACGTACCCCTG
Seq A exon
GTAGGAGACCTTCAAAAGAGGACATGGGAGCTGCCTTAATGCCTTCTCCCCATGCACCCCGGAGCTGACAGCCCCATGTCCCCCCACAG
Seq C2 exon
ATGGACCAGGCCACTCTGGCCCCTCCAACCTGGAGGTCCTGGAGCACGGCCCCGATGTGCTGCGCGTCCGCTGGAGCCCGGCCAGCGGCCCCGTCACCGGCTATAGGGTGCAGCGTGTCCCACTGACGGGGCTGGGGCAGCCGCTGGCAGCCGAGCGGCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.185 A=NA C2=0.345
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.3=68.5)
A:
NA
C2:
PF0004116=fn3=PU(57.0=89.1)
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:
CCTCACTGCCTACTGACTCCT
R:
GTGCTCCAGGACCTCCAGG
Band lengths:
167-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]