DreINT0050279 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40203577-40203808:-
Coord C1 exon
chr6:40203773-40203808
Coord A exon
chr6:40203658-40203772
Coord C2 exon
chr6:40203577-40203657
Length
115 bp
Sequences
Splice sites
5' ss Seq
GCAGTGCGT
5' ss Score
4.08
3' ss Seq
TTTTTATCTGTCCTCTACAGGGA
3' ss Score
11.35
Exon sequences
Seq C1 exon
GGGGAAGCAGGGCAGCCAGGTGTCCCAGGAGAAGCA
Seq A exon
GTGCGTATTCATATTTAGCAGCCTATAACGTCAGCGCATGACTGGCACATGCAGTCCCCAGACTCAGCCGTTTCCCCATGACTGAATCTTATTTTTTTTTATCTGTCCTCTACAG
Seq C2 exon
GGAACACCTGGTAAAGATGGCCTGCCTGGCATGAGAGGAGAGAAGGGAGAAGTTGGGCTCATAGGATTGCGAGGCCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:103
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(15.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(36.1=100),PF0139113=Collagen=PU(10.3=29.6)
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:
GAAGCAGGGCAGCCAGGT
R:
CTTGAGGCCTCGCAATCCTAT
Band lengths:
114-229
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]