DreINT0050557 @ danRer10
Intron Retention
Gene
ENSDARG00000037845 | col9a3
Description
collagen, type IX, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-030131-9799]
Coordinates
chr23:494690-494896:-
Coord C1 exon
chr23:494843-494896
Coord A exon
chr23:494744-494842
Coord C2 exon
chr23:494690-494743
Length
99 bp
Sequences
Splice sites
5' ss Seq
ATAGTAAGC
5' ss Score
5.26
3' ss Seq
CAACATCATCCTCTAAACAGGGG
3' ss Score
7.55
Exon sequences
Seq C1 exon
GGGGATGTTGGAGAAAAAGGACCTCAAGGTTTTAAAGGGCCCAAAGGAGAGATA
Seq A exon
GTAAGCACTTTTTATCATCAGATCCTTGTTCACACTGCAGACCTTTCCATTTCTGTAGTATAAGGTTGACTAACGTTATCAACATCATCCTCTAAACAG
Seq C2 exon
GGGAAAATAGGCCCCAAGGGCGTGCCTGGAGGTGCAGGACCTAAAGGAGAACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037845:ENSDART00000055139:16
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(21.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.2=100)
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:
GGGGATGTTGGAGAAAAAGGACC
R:
AGGTTCTCCTTTAGGTCCTGCA
Band lengths:
108-207
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]