DreINT0050580 @ danRer10
Intron Retention
Gene
ENSDARG00000037845 | col9a3
Description
collagen, type IX, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-030131-9799]
Coordinates
chr23:499357-499539:-
Coord C1 exon
chr23:499486-499539
Coord A exon
chr23:499399-499485
Coord C2 exon
chr23:499357-499398
Length
87 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TGCTCCTCTTTTGGGTTTAGGGA
3' ss Score
9.17
Exon sequences
Seq C1 exon
GGTCCTGAGGGTCTGCCAGGACTCCCTGGTCTCCCAGGCACAGACGGACCTCCT
Seq A exon
GTAAGTACATGCAGCGCCCTCCAGAGGAGCAAATGTGCACAACACTTTACATATAATAATCATCATGTGCTCCTCTTTTGGGTTTAG
Seq C2 exon
GGACTTCCAGGAACTCTTCCTGAAGGCAGTGGAGATCTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037845:ENSDART00000055139:9
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(32.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(17.0=64.3)
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:
GTCCTGAGGGTCTGCCAGG
R:
CAGAAGATCTCCACTGCCTTCA
Band lengths:
95-182
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]