DreINT0050281 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40202722-40202912:-
Coord C1 exon
chr6:40202859-40202912
Coord A exon
chr6:40202776-40202858
Coord C2 exon
chr6:40202722-40202775
Length
83 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CGAAATGCGTCTGTTCACAGGGG
3' ss Score
6.47
Exon sequences
Seq C1 exon
GGGGAACGAGGCTCCAAGGGGGTTTGTGGACCAAGCGGACAAAAGGGAGACAAG
Seq A exon
GTGAGTAACATGGAGAGCTTGAGGAAAGTTTGTGTTGTGTCTGCTTGTTTTTGCTGGGAGTGACGAAATGCGTCTGTTCACAG
Seq C2 exon
GGGGATTCTGGGATTAATGGAAGACCGGGATTGCCTGGGAGGAAAGGAGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:105
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(12.5=50.0),PF0139113=Collagen=FE(21.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.8=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:
GGGAACGAGGCTCCAAGGG
R:
TCTCCTTTCCTCCCAGGCAAT
Band lengths:
103-186
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]