DreINT0050382 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40212395-40212627:-
Coord C1 exon
chr6:40212592-40212627
Coord A exon
chr6:40212491-40212591
Coord C2 exon
chr6:40212395-40212490
Length
101 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
AAAGACTCTTTATTGTTCAGGGA
3' ss Score
5.7
Exon sequences
Seq C1 exon
GGTGCTGCGGGAGATCCTGGAGATCCTGGGGAGAAT
Seq A exon
GTGAGTACCTGCATTGACTTCAGAGGCAGAACTGCCAGCACCACAATCACTTTCATCTCCTCTATAATACATGCATCATTAAAAGACTCTTTATTGTTCAG
Seq C2 exon
GGAGTGAGAGGACCCCCGGGACCCAAAGGGGTCAAAGGAGAGGCTGGAGTGGGGATGACTGGTCCTCCAGGACAGCCGGGACCCATTGGCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:91
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(19.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(27.6=50.0),PF0139113=Collagen=PU(28.1=50.0)
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:
TGCTGCGGGAGATCCTGG
R:
CTTCAAGCCAATGGGTCCCG
Band lengths:
130-231
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]