BtaINT0138426 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120776298-120777833:+
Coord C1 exon
chr3:120776298-120776414
Coord A exon
chr3:120776415-120777716
Coord C2 exon
chr3:120777717-120777833
Length
1302 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGC
5' ss Score
7.93
3' ss Seq
TGTCTGTCTGTCCCTGGCAGCCC
3' ss Score
9.57
Exon sequences
Seq C1 exon
CGCTGCCGTCGCCGTGTGACTCCGACCCCTGCTTCAATGGAGGTTCCTGTGACGCGCACGAAGACTCCTACACGTGCGAGTGCCCGCGGGGCTTCCACGGCCGCCACTGCGAGAAAG
Seq A exon
GTGGGCACGGCAGGGGCGCCTCCCGCCTCCCGCCGCCACAGCGCTCTCCGCACAGTTACGGGGGGCGGGGCGGGGCGCCTGCCGCCAGTCGCAGCGCTCTCGGCACAGTGCACTCCCCTCCTGCTCACTGTGTTTCCAGTGGGATTTAGAATCACCGATTTATAAAAAAACTCAGTGTTGTCCACTCGCTAGTTCTGTCCAACTCTCTGTGACCCCATGGCCGGCAGCACGCCAGGCTTCCGTCCTTCACCATCTCCTGGAGTTGGTCAGATTCACGTCCACTGAGTCGACTTTATAAACGTAATGCAGCTGGAGAATGTCGACGTTTTACAACACTTGGCCACGTAGGAACGTAAGCGCTCCTACGCAGATACGCTGCGGGCGTCACTGCGCGCGCCCTGCCTGCCCAGCAGTCCCTCCAGCAGGAGAAGCAGCACTCAGGACTGTTTTCAGTGACCCAGGCATCCTCTGGTCAGGGCCCAGGGTGCTGGCTGCCTGGCCCCTGTGCCCACGTCTGTCCTCCCGGGCTTGGCACCTGGGCCCCGTCCAGCCCTCTTGCTGCCTCACGTGTCCAGAGAGCTGAAACCTGAACCCCTGCCTCTGCCACTCCCACGGGGCCCTGAGACTGGGCCCCCGGGGGTCTGACCACAGAGCCCACGGCCTCCACACCCCTGCGGAGGAGGGCTTTCCAGAGAGCAGGCTGATTCTGTGCAGAGCCACCGAGGTCCTGCACACTTGGCCAAGGCGTCCCCAAGAGGGGGCAGAGGGACATGGCGGGGCGGGGGTGGTGGCCGGAACCTGGACAAGCGTTCTGTGAGGCCCCACAGGGCATGGGAGGGAGGCCCCTCCTGCCTCACATCCCCCCCAAGATCGTCAAGCAGGCCGAGGGTCTACACTGCTGGCTGAGCTGTGAAGGTGCGACATCCACCCCGCAGGCCAGGGAAGGCCCTCAGTGCAGGCACAGGAACACGCAGATCTGAGTGGGAGTGCCACGGCTCCCCACTCAGCAGGAAGGCGGCAGTGGGCAGCTCTCCAGCGCTTCCCCAACAGAGCCCGGTCAGGGCAGGGGGGTGGAGGGTGGCAGGTGCAGGGGTGGGACTCAGGCGCAGGGGGCCGGGGCAGTGGGTGCAGGGGTGGGGCGGCGGGCACAGGGCCCCCAAGCCAAGTGGGGAGCACCTGGTGAGCTCGGCCCTGGGCAGCAGCCTCAGGGGCTGTGCTGACCAGCAGCCCTGGCCTGCGGGCACTCTGGGCCAGGAGGCTGGACCCAGCTAACCAGCCTCTCTGTCTGTCTGTCCCTGGCAG
Seq C2 exon
CCCGGCCGCGCCTGTGCAGCTCTGGGCCTTGCAGGAACGGAGGCACGTGTAAGGAGGCGGGCGGCGAGTACCACTGCGACTGCCCCTACCGCTTCACTGGCAGGCACTGCGAGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132:ENSBTAT00000064553:11
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=77.5)
A:
NA
C2:
PF0000822=EGF=WD(100=77.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGTGACTCCGACCCCT
R:
CAGTGCCTGCCAGTGAAGC
Band lengths:
214-1516
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]