DreINT0153772 @ danRer10
Intron Retention
Gene
ENSDARG00000044433 | sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:ZFIN;Acc:ZDB-GENE-100913-1]
Coordinates
chr6:27471711-27472343:+
Coord C1 exon
chr6:27471711-27471824
Coord A exon
chr6:27471825-27472310
Coord C2 exon
chr6:27472311-27472343
Length
486 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
GTATTTTCCCCATAAAACAGAGT
3' ss Score
4.09
Exon sequences
Seq C1 exon
ACATCAACGAATGCATGTCAGTGCCATGTTTGAATGGAGGTGTGTGTGAAGACCTGGTAAATAACTACACCTGCACCTGTACAGCAAACTTCACTGGAAGCGCATGTGAGACAG
Seq A exon
GTGTGCTCTTACTCTTGAGTTCAGCCAATCATCTTACTTTATAAATGCCAGGCGCAACACATTATCCGGTCTTTGTTTTTGTTTCCATTTGTGAGGCGAAAAATGTTTAATGATAGAATGTGTTTACACAGCCAGCCACCTACTTTCCCCTTTACATTTGGCTTGCTGTAACATTTTCCAAGAAGCTGAAAAAGTGAAATGGATAAGGAGAGTGAAACACTATAGGATAACTATGGCTTTTGACCACGTGTCTGAGTACTTCAACTAAATCCTTTGTTAATAACATCAAGTTATCAGTTTCATTTTGGCCCTTTAGGTCAACAAAGTGGCTTAAAATTTAAATGGGGTTTCGATTTGGTTTAGTTATTTATGGATTTACCTTTATTTTACACATATCACTTAATTAAACATCAGTAAATGGTTTGATTGTGTTACTCTAGTAATACCTCCACAACATACTAATTAAGTATTTTCCCCATAAAACAG
Seq C2 exon
AGTTGGTTGTTGCTGATGCTGCAAATCAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044433:ENSDART00000065255:8
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=PD(89.2=84.6)
A:
NA
C2:
NO
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]