GgaINT0022933 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9083232-9083502:+
Coord C1 exon
chr12:9083232-9083288
Coord A exon
chr12:9083289-9083430
Coord C2 exon
chr12:9083431-9083502
Length
142 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
TTCTGTTCTCCCCTTTGCAGGGA
3' ss Score
12.31
Exon sequences
Seq C1 exon
GGTGATACCGTTGTGGTGGAGGGGCCTGCTGGGGCGAGAGGCAGCAAGGGGGAGCCG
Seq A exon
GTAAGAGCTGGGGGTCTGCTGGGGGACCCTGCCTCAGGGGGCACGTCCACCCCATACACCCCCATGTCCCTGCACGGGTAGGAGCTCTCTCCTCCCCACCCCAACAACCCCTGATCCCATCCTTCTGTTCTCCCCTTTGCAG
Seq C2 exon
GGAGACCGTGGCCTAAAGGGCACTGAAGGGGACAAAGGAGAGAAGGGGGAGCAGGGAATGCCCGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:99
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=PD(5.1=15.8),PF0139113=Collagen=PU(21.7=68.4)
A:
NA
C2:
PF0139113=Collagen=FE(38.3=100),PF0139113=Collagen=PU(5.6=20.8)
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:
TTGTGGTGGAGGGGCCTG
R:
CTTCTCTCCGGGCATTCC
Band lengths:
119-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]