DreINT0050371 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40219119-40219273:-
Coord C1 exon
chr6:40219238-40219273
Coord A exon
chr6:40219164-40219237
Coord C2 exon
chr6:40219119-40219163
Length
74 bp
Sequences
Splice sites
5' ss Seq
ACTGTATGT
5' ss Score
5.19
3' ss Seq
CCTTTGCTTCGATTTTTCAGGGT
3' ss Score
9.92
Exon sequences
Seq C1 exon
GGGAATCCAGGAGAACCAGGAATAAGAGGACCAACT
Seq A exon
GTATGTATATATGCACATTCATGTACAAAAGCAAATTAAATATAGTATTTCTAACCTTTGCTTCGATTTTTCAG
Seq C2 exon
GGTCCGATGGGTGGAAATGGACCCCCGGGGCCTCCTGGCGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:81
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(13.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.5=100),PF0139113=Collagen=PU(17.9=93.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGAATCCAGGAGAACCAGG
R:
CCCGGGGGTCCATTTCCA
Band lengths:
65-139
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]