BtaINT0138452 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120775158-120775554:+
Coord C1 exon
chr3:120775158-120775283
Coord A exon
chr3:120775284-120775449
Coord C2 exon
chr3:120775450-120775554
Length
166 bp
Sequences
Splice sites
5' ss Seq
AAAGTGCGT
5' ss Score
5.93
3' ss Seq
CTCCGCTCCGTCTGTGGCAGGAA
3' ss Score
7.99
Exon sequences
Seq C1 exon
GACACCACCCAGTGTCCGACGCCTGCCTCTCGGGCCCTTGCCAGAATGGAGGCACCTGTGTGGATGCAGATCAGGGCTACGTGTGCGAATGCCCTGAAGGCTTCATGGGTCTCGACTGCAGGGAAA
Seq A exon
GTGCGTGTGGGCCAGGCCGCCGGGCTGGGGGCCCCATGGGGTGTGCATGTGGATACCTATGGAGAGGATCTGGGAGTGGGGAGAGGGGCTGCACAGCCGGTTTTATGGGACAGTGGTCAGGAGGGCGGCCCCATACTGAGGCCTGTCTCCGCTCCGTCTGTGGCAG
Seq C2 exon
GAACCCCCAGCAGCTGTGAGTGCCGCAATGGTGGCAGGTGCCTGGGGGCCAACAGCAGCCTCTGCCAGTGCCCACCGGGCTTCTTTGGGCTCCTCTGCGAATTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132:ENSBTAT00000064553:8
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=WD(100=72.1)
A:
NA
C2:
PF126612=hEGF=WD(100=36.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCACCCAGTGTCCGACG
R:
AATTCGCAGAGGAGCCCAAAG
Band lengths:
226-392
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]