DreINT0153765 @ danRer10
Intron Retention
Gene
ENSDARG00000044433 | sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:ZFIN;Acc:ZDB-GENE-100913-1]
Coordinates
chr6:27469561-27469990:+
Coord C1 exon
chr6:27469561-27469701
Coord A exon
chr6:27469702-27469827
Coord C2 exon
chr6:27469828-27469990
Length
126 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CACTTCCACTCTCTTCCTAGGCA
3' ss Score
9.6
Exon sequences
Seq C1 exon
GTCAATACATTTCAAGTAGTTCTCATCACAGATGGTGAACTCTCCTTCACCATCTTCCAGTACCACAATATTACCTGGACAACAGGAATGCATGCTACCAGTGGTGGAGATCTCGCTGGCTTAGGGGGCATAGCTGCGCAG
Seq A exon
GTAAGGTCTTTGCCATTACTTTTCAACTTTGGCACTTTGGATTCAAGTCTTGCCTTAAATGAACAAAATGCAATGTGAAAGAAACTACTCTGAGAGAACTGTCCTCCACTTCCACTCTCTTCCTAG
Seq C2 exon
GCAGGTTTTAATGCTGGTGATGGGAAGCGCTATTTCAACATTCCAGGCTCCCGAACAGATGATATTGTTGAAATTGAAACCACTACGAATGTGGGATATCCTGGTCGTTGGGTCTTTCGTATTGATGATTCTCATGTTCAAGTGGGTGGCTGCAACGACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044433:ENSDART00000065255:3
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:
PF061199=NIDO=PU(50.5=97.9)
A:
NA
C2:
PF061199=NIDO=PD(47.3=78.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTTCACCATCTTCCAGTACCA
R:
CAGCCACCCACTTGAACATGA
Band lengths:
251-377
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]