BtaINT0138436 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120787087-120788989:+
Coord C1 exon
chr3:120787087-120787383
Coord A exon
chr3:120787384-120788805
Coord C2 exon
chr3:120788806-120788989
Length
1422 bp
Sequences
Splice sites
5' ss Seq
CGCGTGAGT
5' ss Score
8.4
3' ss Seq
TGCTCACCCACTGTCCCCAGGAC
3' ss Score
9.04
Exon sequences
Seq C1 exon
AGCTCTTCCCACCAACGGCCCTCAAGGTGGAGCAAGTGGAAGAGAGTGGGGTCTCCATCTCCTGGCGCCCCCCCGAAGGCCCAGCGGCCAGGCAGCTGCTGGATGGCTATGCCGTCACCTACGTGTCCTCGGACGGCTCCTACCGCCGCACAGACTTCGTGGACCGGGGCCGCTCCGCGCACCAGCTCCGGGCCCTGGCACCCGGCAGGGCCTACAACGTCTCTGTCTTCTCGGTCAAGCGCAACGCCAACAACAAGAACGACATCAGCAGGCCCGTGGTGCTGCTTGCCCGCACGC
Seq A exon
GTGAGTGGCTCGGGCTGCCCGCCCCCCGAGGGCCCCGCCCTGGTGTGCCCCCAGCAGGGTGCCCAACCCAGCCGAGAGGGCCCCTCCTCTGGAGGAGAGGGACAGTGATGGGGGATGGAGGGGGCTGGGGACTGCAGGGGGGGCCCCTGAGAAGGGGCTGGGACTGCCGTGGGGTGAGGACGGAGCCTCCCCGCAGGCTGGAGCAGAGGCAGCTGTGGGGCAGCAGGGAGGCCGTTTGGGTATGCTGCCCTGAAGGGAGTTGTGCGGAGCAGCTGGGCTCGGCTGGCTTGTGTGCTCCTGGGGCTGTGTGCGAGGGGGAACCCCGGAATACTTCCATGATGTGGGTTGGTGGGGGCTGGCCCTGGGAGTCAAGAGATGGGGAGGGCAGGCTGGAGGATGGAATGAGAGCTGGGCAGTGGCATGACCGCTGGGCATGTTGGGAGCCCCTTGAGGGTGGCTAGCAGGGCGGGGCAGGTGGGCACAAGTGGGAACAGGCTGGTGCGTACACAGGTGGGCACATATGGACAAGTCAGCATGGGCGGGCAGGTGAGCACAGGTGGGCAGGTGGGCACGGCCAGTCACGGGAGCAGGGCAAGCGAGGCAGGCATGGCCTGCCGGCCAGGTGAGCAGGAAGACGAGGGTCCTGGAGGAAGAGGGGAGCCCCTTCTCGGGTCCCTCGGAAGGAATGCGGCAGGCATCCTCCGCGGATGCCGACAGCCAGGACGCTGATGGCCAAGTGTGAGGAGGGACGAGGCCTCAGGGCGGGGTGTCCTGGGGAGGGACAGCACACGGGGCCAGGAGGGTGGCTGCAGCATGTGACAGAAGAGCCTCGGGGGCTGGGGACGGGCAGGGCCATCCTGAGCCCGGCTTTAGCAAGAAGCACTTTTGAGGCTGCTCGAGGTGGGCTCTGGAAGGAAGACAGCCTCCCCCGTGCCATCGGGGTAGGGGTGAGGCACCACTTCCTGCAGACCAGGGCTTGGCACTCTGGGAGCTGGGGCACCCCCTCAACTCCCTCAGCCAGGGGTTCGGACCCTTCCCTGGCGTCAGTGAGGCCTCTCCTGGCTTCTCCCTGGCAGGCCCCAGGAGCCCCCAGATGGTGCAGAGAGTCACTGTCAGAGCCACCAGCCAGCCAGGGAGCCAGGAAGGTCCCACCCTGCCCCCTGGCAGGCCCAGACCACGCAGGGCAGAGCCTGCAGCAGCCCCTCTGCAACGCCCCTGCCCTGAGGCAGTGGCCAGGGCATGTCCACCTGCCCCTGGTCCCTGCTAGACTGAGGGGCGCCTGCAGCAAGCCCAGGCTGGACGGGCATCTCGAGGCCAGTCTGTACAGGTCCCCAGGGCCCTTCCTGAGCCCCGTCTCCAGCCCTGGCCCCACCCTCCAGGGGTGAGGAGGGGCCACACAGGCTGCTCACCCACTGTCCCCAG
Seq C2 exon
GACCCCGCCCCATCGAGGGCCTTGAGGTTGCCAACGTGACAGCCAGCGCCATTTCGGTGCGGTGGGCTCTGCACAGGATCCGCCACGCCACCGTCAGCAGCGTCCGCCTGTCCATCCGCCACCCTGAGGCCCAGGAGGAGCAGTCCACTGACGTGGACAGGAGTGTGGACAGGTTCACGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132:ENSBTAT00000064553:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.070 A=NA C2=0.242
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=83.0)
A:
NA
C2:
PF0004116=fn3=PU(69.8=96.8)
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:
TCACCTACGTGTCCTCGGAC
R:
AACCTGTCCACACTCCTGTCC
Band lengths:
358-1780
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]