GgaINT0022847 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9064966-9065299:+
Coord C1 exon
chr12:9064966-9065125
Coord A exon
chr12:9065126-9065205
Coord C2 exon
chr12:9065206-9065299
Length
80 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCG
5' ss Score
8.7
3' ss Seq
TGAGGCTCACGGCTCTGCAGATC
3' ss Score
5.73
Exon sequences
Seq C1 exon
GGTGGAGTTTGGCTTCTCCCAGCACATCAATGGCACGGGCATCCAGAAGGCCATCCAGCAGCTGAGCTACAAAGGTGGTAACACACGGACTGGCGCTGGGCTGCGCTACATCTCTGACAACTTCTTTGGTCCCACGCAACTCCGGCCCGGGGTCCCAAAG
Seq A exon
GTATCGGGGTGGGGAGTGGCATTTGGGACATCCCAGAGGGAAGCGGAGGGTCCATGGGGCTGAGGCTCACGGCTCTGCAG
Seq C2 exon
ATCTGCATCCTCATTACGGATGGCAAGTCCCAGGATGATGCTGAACAGCCGGCGCTGAGACTGAAGAGCCTGGGCATCAAGGTCTTTGCTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:3
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=FE(30.5=100)
A:
NA
C2:
PF0009223=VWA=FE(17.8=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:
TTCTCCCAGCACATCAATGGC
R:
TGGGACTTGCCATCCGTAATG
Band lengths:
179-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]