DreINT0050553 @ danRer10
Intron Retention
Gene
ENSDARG00000037845 | col9a3
Description
collagen, type IX, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-030131-9799]
Coordinates
chr23:498513-498711:-
Coord C1 exon
chr23:498658-498711
Coord A exon
chr23:498567-498657
Coord C2 exon
chr23:498513-498566
Length
91 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TGTTTTTATCCACTCATTAGGGG
3' ss Score
5.28
Exon sequences
Seq C1 exon
GGTCATACAGGCCATAAAGGAAGTAAAGGAGAGTTGGGGAAAGATGGTGAGAAG
Seq A exon
GTGAGATGCTGTGATAGATTGAAGCACTATGCTCTTACTGAACCTGAAGCAGGGAATAACATGTTGTGTTGTGTTTTTATCCACTCATTAG
Seq C2 exon
GGGGATCAGGGCCCGCCGGGTCCACCAGGAGTCCCAGGAACTGTGGGATTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037845:ENSDART00000055139:12
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(28.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=100),PF0139113=Collagen=PU(10.3=38.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCATACAGGCCATAAAGGAAGT
R:
CTGTAATCCCACAGTTCCTGG
Band lengths:
108-199
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]