BtaINT0138444 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120797106-120798729:+
Coord C1 exon
chr3:120797106-120797212
Coord A exon
chr3:120797213-120798638
Coord C2 exon
chr3:120798639-120798729
Length
1426 bp
Sequences
Splice sites
5' ss Seq
CAGCTGGGG
5' ss Score
-1.36
3' ss Seq
GCCCTCCTCCTCTGTGCCAGCAG
3' ss Score
5.79
Exon sequences
Seq C1 exon
GCCCTGCAGTCCTGGGCTTCTGACCCCTTTGGGTCCCTGCTGGGGACACTTTGGGCACTGGGGGTGGTCTCAAAGCCCAGGTTTTAGGGGCCTCGTCCATTGTCCAG
Seq A exon
CTGGGGACAGGAGGTCACCCGGGTCAGCCTGGCCACTCACGTGATCTCACAGTGACCCGCTTGCTGGGTGAGCCGCTGAACCTGGCCCTCACTCGTCCTCTGCCGTCCACGAGCTCTGAGAACCTGCGAGAGTCAGCACGGGTCAACAGGGGCTCTGGGCTGGGGTCTTGGGGGCAGCAGCTGAGGCAGGCACCTGGGGACCTGGGTCGGCATCGCGGGGGCACCGGGGTCGTTGAGCAGGCGCAGCTCGGGCAGGCGTGCGGGGGCCGGGCGGGTTCTCAGTGCCCTCTGGGGGAGGCCATCACGATGCCATCGTCCGTTGGTGCTGTCCCTCAGGGCTGCGGGCGGGCAGAAGAGGGGGTGGCCGTGTGGGCTGGTCTGGGGCTCCTCTGTGCCTGGCTGAAGAGGGGGTACCCCCCGTCTGCCCACGGAGGAGCTCTGGTTGCTGCCTGGGTTTTGTCCAGGCGCTGGTTCCAGCCCTCGCCCTGACCCAGGCTCTCCACCTGCAGGTGAGGCAAGGTCCTGGCAACCCGCCAGACTCACCTGGGCTGAGGCCCACAGCCCGCACACCCGGGAGAGGGGCAGCTCCTCTGTGGGTGGGTGCCGCCCGCCCCAACCCCGGGCTGGTGCCCTTCTCACCTGCATGCCCTTCCCTACCAGCTCACAGAGGGCCCCCCTCCCCTGTCCGCCTGGCAGGTGGGTCTGGGGCTGAGCTGGTCTCAGTGTCTCAGGGCAAGTGTGCTTCATGCCCCGAGGGCAGGCTGGTGGGTCGGGAGACGAGGGAGCCCAGCCTGCTGCCCACCTCCCTGCAGCACCTCACCGTCCTGACAGACTGTTTTGTGATCTGGAACAGGTAAGGGGGTTGTGCAGACCCCCGTGGGTGGGCAGGCCCGAGAGCAGACCCGCGTCCTCACTGTGGCCCTGGGCTTCTCCCCGGCTGCTCCTGCCTCCATCTGTCCATGTGCACTCCCTCCCTGCCTGTCCCAGCCCCCGCCCCGGCTGTCTTGCCCTCTTCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGGACGCGGCTGTGAGCTCCTGGCGAGCAGCGGCCCTCCTCCTCTGTGCCAG
Seq C2 exon
CAGCCTGCACGAAGGTGCCCCAGCCCTGCACGCGGCTGTTCTCAGAGACCAAGTCCATGCCGGTCTGGGAAGGAGGCGTCTGTCGCCATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132:ENSBTAT00000064553:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTGCAGTCCTGGGCTTC
R:
GACAGACGCCTCCTTCCCAG
Band lengths:
190-1616
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]