DreINT0050210 @ danRer10
Intron Retention
Gene
ENSDARG00000077139 | col6a3
Description
collagen, type VI, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-070501-8]
Coordinates
chr9:24116863-24117065:-
Coord C1 exon
chr9:24117030-24117065
Coord A exon
chr9:24116926-24117029
Coord C2 exon
chr9:24116863-24116925
Length
104 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
TGGCCCTGTTGCATCCTTAGGGT
3' ss Score
9.13
Exon sequences
Seq C1 exon
GGCTCTGATGGTAGACGAGGGCCTCCTGGTCAAGCT
Seq A exon
GTGAGTACATAAAACACATTAGCTCACGCTCTTTAGCTCATGCTATTATTGAAAATTAATTTTTGATTTTGTTGACTTTGTTGATGGCCCTGTTGCATCCTTAG
Seq C2 exon
GGTGCTGCTGGAAGACCTGGAAGTGATGGTTTAGCAGGAGAACCAGGAATTGGAGGATCTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077139:ENSDART00000138754:25
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=PD(4.2=25.0),PF0139113=Collagen=FE(18.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(17.0=68.2),PF0139113=Collagen=FE(29.6=100),PF0139113=Collagen=PU(25.4=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCTGATGGTAGACGAGGG
R:
CCGAGATCCTCCAATTCCTGGT
Band lengths:
99-203
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]