DreINT0131601 @ danRer10
Intron Retention
Gene
ENSDARG00000067859 | scospondin
Description
subcommissural organ spondin [Source:ZFIN;Acc:ZDB-GENE-051114-1]
Coordinates
chr24:40149013-40149657:+
Coord C1 exon
chr24:40149013-40149154
Coord A exon
chr24:40149155-40149533
Coord C2 exon
chr24:40149534-40149657
Length
379 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGA
5' ss Score
5.24
3' ss Seq
CCTGTGTGCTGTGTGTGCAGGAC
3' ss Score
9.39
Exon sequences
Seq C1 exon
TGTGTGTCGTGCCGGGCAGTGGGAGTGTTCTACAGAGAAGTGTGAAGCTCAGTGCTCTGTGTTAGGAGCCATGCACATCACCACCTTTGACCAGAAGAGATACGGCCTGCAGACTGCAGACTGCCGCTTTACTGCTGTAGAG
Seq A exon
GTCAGAAACTACACACTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGTTTGTGTGTGTGCATGTGTGTGCGTGTGTTTGTGTGTGTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTTTGTGACATATCAGGAAACAAATCTGTATAATGACATTGGTATGACACAGGTATTACAAAAAGGAGGTGAAATACGAGGACGTTCGTGACGTCTCAAAAAGCTTATAAATCACACAGGATGGGTGGGTTTAGTAGTAGGGTGGGGTGAGGGCAATAATCCGCGGGTCACCTGTGTGCTGTGTGTGCAG
Seq C2 exon
GACTTTGTGGATAAGAAGCTCAGCATCATCATCGGTGCAGGGCCGTGTGCTGGGGGAGAAGCTGGATGTCTGAGAGAGATGAGCATCACTGCGCTACACACCACACTCACTGTCACTGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067859:ENSDART00000136590:13
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:
PF0009313=VWC=PD(59.6=64.6),PF053758=Pacifastin_I=PD(59.4=39.6),PF0009420=VWD=PU(19.2=60.4)
A:
NA
C2:
PF0009420=VWD=FE(27.2=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:
CGGGCAGTGGGAGTGTTCTA
R:
CTGCATCAGTGACAGTGAGTGT
Band lengths:
254-633
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]