GgaINT0022874 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9070747-9071034:+
Coord C1 exon
chr12:9070747-9070839
Coord A exon
chr12:9070840-9070962
Coord C2 exon
chr12:9070963-9071034
Length
123 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GATGCTCCTCTCCCCTGCAGGGC
3' ss Score
11.42
Exon sequences
Seq C1 exon
GGCCGCCATGGACTGCCTGGCCCTCCAGGACCTGTGGGACCACGAGGGCCACCAGGAGAGAGCGTTGAGCAGCCGGGCAAGAAGGGGGACAGG
Seq A exon
GTGAGTGCCCCCTGTATCTGCACATCTTGGAGTCCCAGGCACAGGGACCTCCTCCCAGACATGGAGGGAGAGGGAGGACCTGGGAGGAGTATGGCCCTGCTGTGATGCTCCTCTCCCCTGCAG
Seq C2 exon
GGCTTCCCTGGTGCTGATGGGCGGCCGGGGCTTCCTGGCCCCCCCGGGAACCCTGGGTCTCCTGGCCAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:29
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=FE(45.5=100)
A:
NA
C2:
PF0139113=Collagen=PD(7.6=20.8)
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:
ATGGACTGCCTGGCCCTC
R:
CTGGCCAGGAGACCCAGG
Band lengths:
155-278
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]