BtaINT0138435 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120764601-120765552:+
Coord C1 exon
chr3:120764601-120764741
Coord A exon
chr3:120764742-120765389
Coord C2 exon
chr3:120765390-120765552
Length
648 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
CTTCTCCAAACCGCCCCCAGGCC
3' ss Score
8.09
Exon sequences
Seq C1 exon
GTCAACACGTTCCAGACGGTGCTCATCACAGACGGCACGCTCTCCTTCACCATCTTCAACTACGAGTCCATCACGTGGACCACGGGCACACACGCCAGCAGCGGGGGCAATGCCAGCGGCCTGGGGGGCATAGCGGCCCAG
Seq A exon
GTAGGGGCCCTGCTCCCCACCGCCAGGGCTATCACGAGCTGGAGAGGCAGGCAGCTGCCCCTCCCCCCACACACACCCAGGGCAGGGCCTCTCATGGCCAGAACCGGAAATATTCCCGGCCGGAGGCACTTGTCCTGGCCCACACAGCCAGCCTGACAGCGCTAGCTGCCCCCAGGACAGAGTTCTGTGTGCCCCGCGGCTCCAGGGTGGCCTGGCCAACGGCCCTGGTCTGAGGGTCAGTGGCCAGCAGAAAATCCCAGGCATGCAGGGCGGTCAAGTGCAACCCGCCCAGGGTCTGAGAGCGCCCTCTCCTCCCGGCTCTCTAGTTTCTTCTAAGATCACACCGGCCCCCGGCCCCAGGGGAGGCCCAGAAGCCCAGGAGAGAGCAGGAAGGGGCGGGGCAGGGGTGGGGTGGGGCGGGGAGCGGGCTGCCAGGACACCACAAGGTCAGCACGGGAGGAACCACAGGTTAGGGTGGGCCCAGCTGGGAGGCAGGGTGGGCCCGGCTGGGAGGCAGGGTGGCACGGACACGCCTGACCCTTTAACGCTCCCAGCTCGAGGCAACCACGCGGGAGGCGGGCCTTGGGAGCTTTGGGGAGACCTGCAGACCCAACCCGCCCCCGCCCTCCTTCTCCAAACCGCCCCCAG
Seq C2 exon
GCCGGCTTCAACGCGGGAGACGGGCAGCGCTACTTCAGCATCCCCGGCTCGCGCACAGCGGACATGGCGGAGGTGGAGACCACCACCAACGTGGGCGTGCCCGGGCGCTGGGCGTTCAGAATCGATGATGCCCAGGTGCGCGTGGGGGGCTGCGGCCATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132:ENSBTAT00000064553:2
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=0.073
Domain overlap (PFAM):
C1:
PF061199=NIDO=PU(50.5=97.9)
A:
NA
C2:
PF061199=NIDO=PD(47.3=78.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCCAGACGGTGCTCATCAC
R:
GCACCTGGGCATCATCGATTC
Band lengths:
272-920
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]