DreINT0131602 @ danRer10
Intron Retention
Gene
ENSDARG00000067859 | scospondin
Description
subcommissural organ spondin [Source:ZFIN;Acc:ZDB-GENE-051114-1]
Coordinates
chr24:40149534-40151318:+
Coord C1 exon
chr24:40149534-40149657
Coord A exon
chr24:40149658-40151145
Coord C2 exon
chr24:40151146-40151318
Length
1488 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAAA
5' ss Score
2.44
3' ss Seq
ATGACTGTGTTGTGTCCCAGGCT
3' ss Score
7.93
Exon sequences
Seq C1 exon
GACTTTGTGGATAAGAAGCTCAGCATCATCATCGGTGCAGGGCCGTGTGCTGGGGGAGAAGCTGGATGTCTGAGAGAGATGAGCATCACTGCGCTACACACCACACTCACTGTCACTGATGCAG
Seq A exon
GTCAAACATCATTCAGTGTTCATTCATTCATCCATCCATCCATGGATGTACTACTTTACATCCATCTATCCATCAAGTCATTCATCAATCTGTCCATACACCCGTGCATCTAGCTGTCCATCCTTGACCGATTCTTCTGCCAACCATTATTTCATCCATCTGTCTATCCACCCATCCGTCTATCCATTTATTCATCTATCTATCATCCATCCATCTAGCTGTCTATCACTGATTATTTATCCACCATTCCATCCATCCATCCATCCTTTCATACATCCAATTATTCAACACCTATTCTTTTGCCCATCTGTCATCCATCCATCCACCCCATTCATCCATCTTACCATCTATCCCTCCATCCATCCATAATTCCATTTTCATTCATTCATTCATTCATTCATTCATTCATTCATTCAGTTATTCAATCTTTATTTTTGTCCATCCATCCATCCATCCATCCATCCATCGCTGATTCATTTATTATTTAATTGATGATTTATATTTATTATTTATATATGCGTATTCTTCTGCTATCCACTCATCATCCATTCATCCATTAATCTGTCAATCCATCCATCAATCCATTCATCACTATCCACCCATTCAAACATTCATTCATCACTGATTATTCTGCCTAGCCATCATTAATCCATCCATCCATCCATCCATCCATCCATTCATTCATTCATTCAAGATTCATTCATCCATCTGTCTGTCCATCTACCAAGCCATCACCCATCCATTCATCTGTCAATCCATCAATCGATTCATACATACATCCATCCATCACTGATTCATTCATCCATCAATCCACTTATTCGTCACTGATTCTTTTGCCCATCCATTCATTCATCCATCTATCCATCCATTCATCCATCATTTATTCATCCAGCTATCGATTAGTCAATCCATTCATTTATCTATCATCGATCCATCTAGCTGTCTGTTCATCACTGATTATTCTGAAAACCATCCATTCATCCAACTATCCATCCATCCATTCATCATTTTCATGTTCATTCATCCACCATCATCCACCATCCATCGCTGATTAATTTATCCATCCATTCATTCAGTGCTGATTCTTCTGCCGTATACTTATTTGTCCATCTATCCACCCATCCATCCATCCATCTATTCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATTAATTAATTCATTCATTTATTCAATATTCATCCATCCATCCATCTGTCCTTCTATCAATCCATCATTCACCCATCTGTCAATCCATCCATCAATCCACTTATCCATCCATTCATCCATGCATCACTGATTCATTTGTCCATCAATCCACCCATTCGTCACTGATTCTTCTGCCCATCCATTCATCCACCCATTCATCAACTTTCATTGACTCATTAATCTATCAATCCATCCATCATTCATTATTCGTCTATCCATCACTCCACCCATCCACTTTACTCTATGTCCATGACTGTGTTGTGTCCCAG
Seq C2 exon
GCTCAGTGCTGGTGAACGGGCACAGGAATCCTCTGCCGGTGGTCACAGGAGATCTGCTGGTCAGGCGAGCGTCCTCTAGTGTCCTGCTGATTCAGGCGTTCGGTGCTCAGCTGATGTGGCATCTGGACGGGCCTTTATTATTCATCACCCTGCAGCCTGGCTTCGCTCATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067859:ENSDART00000136590:14
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:
PF0009420=VWD=FE(27.2=100)
A:
NA
C2:
PF0009420=VWD=FE(37.7=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:
ACTTTGTGGATAAGAAGCTCAGCA
R:
GAAGCCAGGCTGCAGGGT
Band lengths:
287-1775
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]