DreINT0131598 @ danRer10
Intron Retention
Gene
ENSDARG00000067859 | scospondin
Description
subcommissural organ spondin [Source:ZFIN;Acc:ZDB-GENE-051114-1]
Coordinates
chr24:40146160-40146516:+
Coord C1 exon
chr24:40146160-40146285
Coord A exon
chr24:40146286-40146359
Coord C2 exon
chr24:40146360-40146516
Length
74 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TTTAATCTTGTGTTCTCCAGGTG
3' ss Score
11.16
Exon sequences
Seq C1 exon
GTGTGCAGTGATGCTGCTGAATTGGGCCACAGCTGTGATCTGTCCAATGATGTTTCTCTACGGAGAGATGCAGAATCAGCCTGTCATCTTCTGAAAGAGACTCCGTTCTCTCACTGCCATCATCAG
Seq A exon
GTGAGAGAAAAATACACTTTAAATAAACGAAACTTTATTCCTCCTGACTAACTCTTTAATCTTGTGTTCTCCAG
Seq C2 exon
GTGGATCCCGGGCCGTATATTGACACCTGCCTGTATCTGTTCTGCAGTTTGGAGGTAAAAGACAGAGATACTGCTGTGTGTGACACACTAGCGAGCTACGTGCGCGAGTGTGCTCAACAACACATCATTATCAGCTGGAGGAGAAGAGGATTTTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067859:ENSDART00000136590:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF087426=C8=PU(28.0=50.0)
A:
NA
C2:
PF087426=C8=FE(69.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAGAGATGCAGAATCAGCC
R:
CACGTAGCTCGCTAGTGTGTC
Band lengths:
168-242
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]