DreINT0050215 @ danRer10
Intron Retention
Gene
ENSDARG00000077139 | col6a3
Description
collagen, type VI, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-070501-8]
Coordinates
chr9:24115637-24115811:-
Coord C1 exon
chr9:24115761-24115811
Coord A exon
chr9:24115673-24115760
Coord C2 exon
chr9:24115637-24115672
Length
88 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TATTTTTACTTTTATTGTAGGGT
3' ss Score
8.14
Exon sequences
Seq C1 exon
GGTGAAGATGGAAGGGATGGGTTTGGTTTTCCTGGTCCCAAGGGAAGAAAG
Seq A exon
GTGAGCATATATATGTATTTCAAGTATGTAGTTAGTATGTCTTTCTCAAATTGTATTTTACTCTAAATTATTTTTACTTTTATTGTAG
Seq C2 exon
GGTGATGAAGGTTTTCCTGGTTTTCCTGGTCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077139:ENSDART00000138754:30
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(12.9=61.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAAGATGGAAGGGATGGG
R:
CTTTGGACCAGGAAAACCAGGA
Band lengths:
87-175
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]