DreINT0153758 @ danRer10
Intron Retention
Gene
ENSDARG00000044433 | sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:ZFIN;Acc:ZDB-GENE-100913-1]
Coordinates
chr6:27506942-27507413:+
Coord C1 exon
chr6:27506942-27507054
Coord A exon
chr6:27507055-27507134
Coord C2 exon
chr6:27507135-27507413
Length
80 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TATATTCTGCTCACTATCAGGAC
3' ss Score
7.61
Exon sequences
Seq C1 exon
CACATTACTCCCAGGTCAGATGTACACAGTAGACGTAGTCACTCAGAGTGGTTTGCGCCCTGAAGACCTGCCATCAACCAGCAAATCTGCCGGGCCCCTACACTTCTGGACCA
Seq A exon
GTGAGTATCTTTCTAGGTTTGTGTTATGAACTCATGCACCACTGTTATAATAGCACATAATATATTCTGCTCACTATCAG
Seq C2 exon
GACCGCTTCCACCTCAAAATCTTTCAATCTCCCATATCACCACCACCTCTGCTCTGGTCACATGGGACCATCATCCTCAGAGTCTTCCAGATGGTTTTGTGGTCAATATTACTCGAGGTCTGAACACCCGCAGCCGATACCTACCTGGAGGAAGTTTAGGCACATACACCCTACGAGATCTCATTCCGGGACAACACTACCGACTTACCCTCACTGCTGTACGCAAAACAGGCCAGGACAGCATTCACAGCGTCCCTCAACACCTAGCCTTTGCTACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044433:ENSDART00000065255:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.231 A=NA C2=0.138
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(25.9=53.8)
A:
NA
C2:
PF0004116=fn3=WD(100=85.1)
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:
ACCTGCCATCAACCAGCAAAT
R:
CGGGTGTTCAGACCTCGAGTA
Band lengths:
178-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]