DreINT0131599 @ danRer10
Intron Retention
Gene
ENSDARG00000067859 | scospondin
Description
subcommissural organ spondin [Source:ZFIN;Acc:ZDB-GENE-051114-1]
Coordinates
chr24:40146360-40148755:+
Coord C1 exon
chr24:40146360-40146516
Coord A exon
chr24:40146517-40148514
Coord C2 exon
chr24:40148515-40148755
Length
1998 bp
Sequences
Splice sites
5' ss Seq
GTGGTACTG
5' ss Score
2.53
3' ss Seq
TGCCTGTGTTGCATTCCCAGAGC
3' ss Score
8.1
Exon sequences
Seq C1 exon
GTGGATCCCGGGCCGTATATTGACACCTGCCTGTATCTGTTCTGCAGTTTGGAGGTAAAAGACAGAGATACTGCTGTGTGTGACACACTAGCGAGCTACGTGCGCGAGTGTGCTCAACAACACATCATTATCAGCTGGAGGAGAAGAGGATTTTGTG
Seq A exon
GTACTGTTGACTTTTTCTTAAACTAACAGTAGCATGCTTTTGACTTGTTTTTATGATTATGTATCCATGCAATGTAAGAAATTAGTGCTTTAATCACGATTAATCACATCCAAAATAAAAGTTTGCTTTGACTTAATTTAAACATGTGTGTATCTTTATTATGTGTATGAATACACACATGCATGCATATATTTGAGAATGTTTATTTATATTTAGATATAAAATACATGTGCATATGATACAAATTATGTATTGATTTAAATATCTGTCACAAAATTGTTTTCTATAGTTTTTTATCTATGTATGTTTTGTTTGTGTATCATTCATTTTTCTTTGTATCACATTTACATAATACATATATTTATCAACACACACTCACATATAATTACATATATTACAAAACACACTTTTATTTTGGATGTGAATAATCGAGATTAATCTTTGCCCGGCACAAAAAATAAACATATCTGTGTCTTTTTTTAAATTTTTTATAATAAAGTTATAAAGTCAAATATATATTTTTTCATTATGGGATATATTTACAATATTTTTTATGTGATATATTATTTGAAACAGTGTAAGTTATACATTGGCAGACATTTAATGAGTTGCATGTGGCTACATGCACTGTTGTATTATATTTTATCATATTTTTGTAGGCTTTTGTAGGCCATGTTTATGTTAATATGATTACAATGCACTATAAATTTGCTCCAATGTTGTGTGAAAATGCATTTTTTTAAATATGAGTTAAAGGCACTGCATTATAAGATATGATACATTATTATTATTATTATTATTATTGTTGTTTTTATTATTGTTTGCTAAATTATTTGAAATGTTTTTGATATTTGAAATATTTGAAATATTAAAAAGATAAAATCACTAAATAAAAAATCTAAAATTATATATATATATATGAGAGAATGAGAGATTTTAGACATTTACTTTCACATTTTTTATGTGTGTGCTGTTTAGTTTTATTTAGTTTATTTCTATATTTGTTATTTTATTATTTGAAATGGGTTAAATATACAGTAAAAGTTTGATAAAATCATATAATAAAAAATATGAAACCAATTTAGTTTAATTTAGCTGTTTTATTTTAATAAAAAACACCCTAAAACAATTTTTGTTTAATACAAAATATTCATACTGGGGGCATTGCTGGACATAAAGCTCTACTAGGGCACAGCACCCCCTCCAAAAAAACATACAAAAACAAACAAACAAATAAATAAACAAATAAATAAAAATAAATAAATAAATAAAAAATATTGCATACATAAATAGCTTTCGTTAGCGTTGGTTTGGTTACACATACTGAATAACGTCCTAATTCTGGGATAACCTCTCTTAATAAATACACTTGCATATTAAGTGAATTTCAAAGCGTTTTCTGGTAAATGGGGTCTAACAATGCCCCTGATTCATACATATATATATGTATATATATATATATATATATATATATATATATATATATATATATTTAATTTATTACATGTCGATAAATTATTTTGGACATTCACTTTTAAGTGCACTTTTTTCTATTTTTTGTTTCTTGTCTTTCTGTGTGTGCTGCTTTGTTTTATTTTGCTTATTTCTATGTTTGTTGTTTAGTTATTTTAAATAAGGGAAATATAAATAAAGATAAATAACAATTAAACCAATTTAATTCAGCTGTTTTTAAATAAAAAACAACATAATATAGCGAATGTTTTGTATAATAACTTAATTATGCAAAATATTATTTTATTGTAATATTATTTATTAATGTTTAGAATAATTCTGTTTAATTTTTAGGTTTTATAAAACAAAATATATGATTAAATTGACTACATTTAAATGTAATTATTACAATTATTGTTATATTTTAGACATTCACTTTTTGAACTCCATTTTTTGTTTCTTGTCTTTCTCTGTTTGCTGCTTATTTTTATTTTCTTGTTGTGTGTTATGCACCTGTAGTCATATCTGCCTGTGTTGCATTCCCAG
Seq C2 exon
AGCGTGTGTGTCCTCGAGGTCAGGTGTTTTCTGACTGCGTGTCCTCCTGTCCGGCCACATGTGCGTCTCCTCGACCTCCAGCAGCGGGTCAGTGTCGGGACGAGTGTGTGGGGGGATGTGAGTGTCCTCAGGGTGTGTATCTACACGCGGGACAGTGTGTGAGGCGGGATGACTGCCCCTGCTTCCACAGACGACACTCCTACAGCGCAGGACAAACCATCAGACAGAGATGCAACACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067859:ENSDART00000136590:11
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=FE(69.3=100)
A:
NA
C2:
PF087426=C8=PD(0.1=0.0),PF0182612=TIL=WD(100=69.1),PF0009313=VWC=PU(38.5=24.7),PF053758=Pacifastin_I=PU(37.5=14.8)
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:
ATCCCGGGCCGTATATTGACA
R:
GAGTGTCGTCTGTGGAAGCAG
Band lengths:
352-2350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]