BtaINT0138438 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014132 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr3:120790908-120792066:+
Coord C1 exon
chr3:120790908-120791020
Coord A exon
chr3:120791021-120791784
Coord C2 exon
chr3:120791785-120792066
Length
764 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
CCTGCTCCATGCTCATGCAGGGC
3' ss Score
8.77
Exon sequences
Seq C1 exon
GGCCTTGCTGCCAGGAAGGAGATACGCCATCTGGGTGACGGCCCTCAGCGGGCTCGGGGGGCAGGAGCGCCCCACGGAGAGCCTGGCCTCGGCCCCGGTGCATGTGTGGACCC
Seq A exon
GTGAGTAGAGGGGTGAGGGCTCAGCTCCCTTCCGGAAGCACTCCTAGCCCTGCCCTCAGTCTCTGAGTGGCCGCAGCCCCGGAAAGCTGCCCTGGGCATGTGCCCAGAGGTGCCTGGGAAGGTGACTGCAGGGGGCTGGGCAGGGCCCCTGCCGGGATGACCTCCCTAGGCCGCCCTCACTGTGGGTGCTCCTGGGCCCTCGCCAGAGCAGGGTCACCGAACAAGGGCAGGAGGAGAAGACAGCGAGGATGGGCAGGCTGTCCACCCGGGCGAGGACACCCAGCCCTCACCGCCCCCCCGCCCCCCCCGCACACGGGCTGTCCAGGCACAGGAGGGGCAGTGAGCAGGGGTGGGGAGGGCAGAGCCTCGCCTGGTGGGACAGGCAGACAGCAAGGCTCAAGTCCTCACTCTGACCCTGGGTGTGGGGTCCCTGGCCCACCCTCTGCCCATCTAGCCCACTTCCCTACCTACATCCCAGGAGAAGGTATGCATGGCCAAGCTCAGGGGATGGAAAATGCCATGCGGGAGGGCAACCTGATGGACTGAGCTTGGAGGGGGGAGCCTCACGGGGTGGCTACTGTTGCCGGCCCTGAGCAGCTGCCAACTTCCCTCCACCGGTCCTCATGGACACAGTGAGGTCTGTGACAACGCGGTCTGGCTTCCAGCAAGGCTTCAGCACTCTGAGTCAGATCTTTAGAGTGTGTCCTGGGCAGAAGACCCCACCAGCTCCCTTCACTCCCCTCCCCTGCTCCATGCTCATGCAG
Seq C2 exon
GGCCTCTGCCGCCAGCCAACCTGACCGCCGCCCGAGTCACGGCCACCTCTGCCCACGTGGTCTGGGATGCCCCTGCTCCGGGCGCCTCTCTGGAGGCCTACGTCATCAACGTGACCACCAGCCAGAGCACGAAGAGCCGCTACGTCCCCAACGGGAGGCTGGTGTCCTACACGGTGCGGGACCTGGCGCCCGGGCGGCGGTACCAGCTCTCAGTGACAGCTGTGCAGAGCACCGGGGGCGGCCAGCTGCACAGCGAGCCCGCCCACCTGTACATCATCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014132:ENSBTAT00000064553:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.197 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(29.1=64.1)
A:
NA
C2:
PF0004116=fn3=WD(100=86.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGCCAGGAAGGAGATACG
R:
CTGCACAGCTGTCACTGAGAG
Band lengths:
335-1099
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]