DreINT0050568 @ danRer10
Intron Retention
Gene
ENSDARG00000037845 | col9a3
Description
collagen, type IX, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-030131-9799]
Coordinates
chr23:489717-489877:-
Coord C1 exon
chr23:489833-489877
Coord A exon
chr23:489750-489832
Coord C2 exon
chr23:489717-489749
Length
83 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
AAGGTTTTCTTTTATCTCAGGGT
3' ss Score
6.67
Exon sequences
Seq C1 exon
GGAGTTGCTGGAAGTGATGGTCTGCCGGGAGAGAACGGAGAGCCT
Seq A exon
GTAAGTAAACCAGTCGGACGTATAAGCACAGTCATGTTCAACTCAAACATGTTCAATATATTAAAGGTTTTCTTTTATCTCAG
Seq C2 exon
GGTCCGTATGGTCCTGTCGGACAGAAGGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037845:ENSDART00000055139:26
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(18.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(13.5=100),PF0139113=Collagen=PU(15.2=90.9)
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:
TTGCTGGAAGTGATGGTCTGC
R:
CTCTCCCTTCTGTCCGACAGG
Band lengths:
74-157
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]