DreINT0050249 @ danRer10
Intron Retention
Gene
ENSDARG00000079752 | col6a6
Description
collagen, type VI, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-041111-303]
Coordinates
chr16:36749425-36749603:+
Coord C1 exon
chr16:36749425-36749460
Coord A exon
chr16:36749461-36749540
Coord C2 exon
chr16:36749541-36749603
Length
80 bp
Sequences
Splice sites
5' ss Seq
CCGGTACAG
5' ss Score
5.65
3' ss Seq
CTTGGTTTGCTTGTTTTTAGGGT
3' ss Score
9.56
Exon sequences
Seq C1 exon
GGTCAATCTGGCAGAAGAGGGACGGCAGGTCTACCG
Seq A exon
GTACAGTACTGTAGAATGTTATAATTAAGCCACTGCAGAAGTGACATGGTTACTAAATGACTTGGTTTGCTTGTTTTTAG
Seq C2 exon
GGTCCCAGAGGGCCTCCAGGAGATCCAGGTTTACAAGGACTTCCAGGGGGCTCGGGTCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079752:ENSDART00000109703:20
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(15.9=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCAATCTGGCAGAAGAGGG
R:
GCCCCCTGGAAGTCCTTGTAA
Band lengths:
87-167
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]