DreINT0050367 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40222584-40222779:-
Coord C1 exon
chr6:40222708-40222779
Coord A exon
chr6:40222629-40222707
Coord C2 exon
chr6:40222584-40222628
Length
79 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CTGTTGTTTTCTAATCTTAGGGA
3' ss Score
8.71
Exon sequences
Seq C1 exon
GGCTACACAGGTGCTCGTGGGGAGAAAGGAGACAAAGGAGCAAGCGGAGAAAGAGGAAAAGATGGCTCCCCA
Seq A exon
GTGAGTATACCCTTAACTGACAAAAGAACTTAGTCTCTGTTATTTAATTTGCAATCACACTGTTGTTTTCTAATCTTAG
Seq C2 exon
GGAAGTCAAGGAGAGTCAGGAAAACCAGGACAAGATGGGAAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:78
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(36.5=100),PF0139113=Collagen=PU(21.2=70.8)
A:
NA
C2:
PF0139113=Collagen=FE(19.2=100),PF0139113=Collagen=PU(22.2=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:
GCTACACAGGTGCTCGTGG
R:
GCTTCCCATCTTGTCCTGGTT
Band lengths:
114-193
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]