BtaINT0138434 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120786789-120787383:+
Coord C1 exon
chr3:120786789-120786902
Coord A exon
chr3:120786903-120787086
Coord C2 exon
chr3:120787087-120787383
Length
184 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TCTTGACCGAAACCCTGAAGAGC
3' ss Score
-1.74
Exon sequences
Seq C1 exon
TGAGTGACCCCTGCTTCTCCAGCCCCTGTGGAGGCCGCGGCTACTGCCTGGCCAGCAACGGGTCCCACAGCTGCACCTGTAAAGTGGGCTACACCGGCAGGGACTGTGACAAAG
Seq A exon
GTGAGGCAGCGAGGGCGCCAGCGTGGGGGCTCCGGTCTCGCCTGAGGGCTGCAGACACCCCGCGGGGCAGGACAGGGAGCCGAGCGTCCCCAGGCCCAAGGGCCAGACACCCGCCTGGGGGCCGGGACTTGCCCGGCCGACAGCTGACACCCCCCTTCCCTTGTTCTTGACCGAAACCCTGAAG
Seq C2 exon
AGCTCTTCCCACCAACGGCCCTCAAGGTGGAGCAAGTGGAAGAGAGTGGGGTCTCCATCTCCTGGCGCCCCCCCGAAGGCCCAGCGGCCAGGCAGCTGCTGGATGGCTATGCCGTCACCTACGTGTCCTCGGACGGCTCCTACCGCCGCACAGACTTCGTGGACCGGGGCCGCTCCGCGCACCAGCTCCGGGCCCTGGCACCCGGCAGGGCCTACAACGTCTCTGTCTTCTCGGTCAAGCGCAACGCCAACAACAAGAACGACATCAGCAGGCCCGTGGTGCTGCTTGCCCGCACGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132:ENSBTAT00000064553:19
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=0.070
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0004116=fn3=WD(100=83.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGTGACCCCTGCTTCTCCAG
R:
CGTCCGAGGACACGTAGGT
Band lengths:
248-432
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]