GgaINT1010134 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9064701-9065125:+
Coord C1 exon
chr12:9064701-9064881
Coord A exon
chr12:9064882-9064965
Coord C2 exon
chr12:9064966-9065125
Length
84 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
ATGTGTCCTGATGTCCCCAGGGT
3' ss Score
9.47
Exon sequences
Seq C1 exon
TGGTGTGCGAGAACGTGCTGGAGGCCGACATCGCCTTCCTGGTGGACGGCTCGTCCAGCATTGGCCGGAACAACTTCCGTGCCATCCGCACCTTCGTGGAGGACCTGGTGTCACCCTTTGTGCACGTGGTGGGCGAGAAGGCGGTGCGCTTCGCTGTGGTGCAGTACAGCGACGATCCACG
Seq A exon
GTGAGCCCTGGGGATGGGGCATGCGGGGCTGCGGGACCGTGGGGCTGGGAAATTACGTGTCCCCATGTGTCCTGATGTCCCCAG
Seq C2 exon
GGTGGAGTTTGGCTTCTCCCAGCACATCAATGGCACGGGCATCCAGAAGGCCATCCAGCAGCTGAGCTACAAAGGTGGTAACACACGGACTGGCGCTGGGCTGCGCTACATCTCTGACAACTTCTTTGGTCCCACGCAACTCCGGCCCGGGGTCCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(29.3=83.6)
A:
NA
C2:
PF0009223=VWA=FE(30.5=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:
CTTCGCTGTGGTGCAGTACAG
R:
GAGTTGCGTGGGACCAAAGAA
Band lengths:
175-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]