DreINT0153771 @ danRer10
Intron Retention
Gene
ENSDARG00000044433 | sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:ZFIN;Acc:ZDB-GENE-100913-1]
Coordinates
chr6:27471028-27471824:+
Coord C1 exon
chr6:27471028-27471141
Coord A exon
chr6:27471142-27471710
Coord C2 exon
chr6:27471711-27471824
Length
569 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TCTTGTGTTTTTGAATACAGACA
3' ss Score
5.54
Exon sequences
Seq C1 exon
ACATAGACGAGTGCCAGGAGACCCCATGTCTCAATGGAGCACAGTGCATACAGGGTGTCGGCAACTTCACCTGTAAATGCCAAGCAGGTTACACTGGGTTCCTATGCGAGTCAG
Seq A exon
GTGAGTACAGATCTTGGGAGTGTCACGGAAAGGCCATGGCTTTCCCCAGGGAACATTTTATTTTTTTCCACATTAGGCTTGCACTTATTCATTTGACAGATGGTGTTATCTAGACTGAAGACTGCAATAGCACAATACTTTTAAAAGGCAGCTAGTAAATGGAATTATTTTATCAGGTACTTTGATTTCTTTTGCTGTTTTCATTTTGGGTCAGGTTTTATGTTCCGAATATTGAAAGCGCTCTGAGCAGACCTTGATATGATTTTTTTAGGAAAAAGCACTGACATGATTCCCCTGGTTGACAAATTGGGCTTCCCACAATGGATTTTATTAATGAAATACAAACCCAGTTGTGAAGTTCTTTGAAAATGAATCTGCTTGGCTTTGTTTACCTTGAACCCTTGTTTCTACACGAGACCAGATTGATGTTCATACTAGACACCTGATTAATGAAACAATACACCTGCACAAATCCTAAAATATCAATACAGTCAAAACCAAGCTTTTCCAAGGTCTGACTTTTTCTAAGTCTGTACTCTAACCAATGAATCTTGTGTTTTTGAATACAG
Seq C2 exon
ACATCAACGAATGCATGTCAGTGCCATGTTTGAATGGAGGTGTGTGTGAAGACCTGGTAAATAACTACACCTGCACCTGTACAGCAAACTTCACTGGAAGCGCATGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044433:ENSDART00000065255:7
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=74.4),PF0000822=EGF=PU(8.1=7.7)
A:
NA
C2:
PF0000822=EGF=PD(89.2=84.6)
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:
ATAGACGAGTGCCAGGAGACC
R:
CTCACATGCGCTTCCAGTGAA
Band lengths:
222-791
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]