DreINT0153769 @ danRer10
Intron Retention
Gene
ENSDARG00000044433 | sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:ZFIN;Acc:ZDB-GENE-100913-1]
Coordinates
chr6:27470080-27470636:+
Coord C1 exon
chr6:27470080-27470205
Coord A exon
chr6:27470206-27470522
Coord C2 exon
chr6:27470523-27470636
Length
317 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAC
5' ss Score
5.88
3' ss Seq
GTTATTTTGTGTTTTGATAGAAG
3' ss Score
4.75
Exon sequences
Seq C1 exon
CTTCAGTCTGTGCCAATTTAAGGCCCTGTCGAAATGGTGGACGTTGCATTGATGACTGCATCACTGGAAATCCCTCTTTCACTTGTTCGTGTTTGGCTGGATTTACTGGACGCAGATGCCAGATAG
Seq A exon
GTAAACCAATGATGAAATCCTTCCATCCCCCATGACCTGTATCATCCTTTGTGTTCTTCCTTGCCAGGAAAGAGAAAGTCAGCTTGTAAAAGCAGAATTCCACCCTGTAAGCCAGTGGGACAACCCAAGGGAGAGAATTTCCCCTGGTCACATCTGTATGCAATACGCATACAGTTGAGTCTGTCCGATGTTTTGCAGTGGTCAAATCATTACCTTTTCCTCCACCCCTATGCACTTTAGGATTCCCTCTTGTTTTCATTCCTGTGCGCAAGTCTAATAAGTCACGTCATATTTGTTGTTATTTTGTGTTTTGATAG
Seq C2 exon
AAGTTGATGAGTGCTCCTCATACCCCTGTCAAAACGGAGGCACATGTGTGGACAAGATCAACCACTTCATCTGCCTGTGCCCAGTGGGATTCATAGGGGCAACATGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044433:ENSDART00000065255:5
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:
PF0000822=EGF=WD(100=83.7)
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
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:
CTTCAGTCTGTGCCAATTTAAGG
R:
CTGTCTCACATGTTGCCCCTA
Band lengths:
240-557
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]