DreINT0050381 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40212592-40212747:-
Coord C1 exon
chr6:40212703-40212747
Coord A exon
chr6:40212628-40212702
Coord C2 exon
chr6:40212592-40212627
Length
75 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
AAAGTGTTATTTACTCACAGGGT
3' ss Score
5.96
Exon sequences
Seq C1 exon
GGCCCAAAAGGAGACAAGGGGCCAGCAGGGATCAAAGGAGAAAGA
Seq A exon
GTGAGTGGTGATAATATAAGAAAGTGCCAATGCAGACTGTGAAGAAATGGAATTTAAAGTGTTATTTACTCACAG
Seq C2 exon
GGTGCTGCGGGAGATCCTGGAGATCCTGGGGAGAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:90
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.988 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(24.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(19.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCCAAAAGGAGACAAGGG
R:
TCTCCCCAGGATCTCCAGGAT
Band lengths:
79-154
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]