BtaINT0138354 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000054 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:HGNC:11137]
Coordinates
chr11:103897168-103897452:-
Coord C1 exon
chr11:103897346-103897452
Coord A exon
chr11:103897263-103897345
Coord C2 exon
chr11:103897168-103897262
Length
83 bp
Sequences
Splice sites
5' ss Seq
GCGGTGTGT
5' ss Score
5.95
3' ss Seq
CTGCTCCTGTCTCCCTGCAGAAG
3' ss Score
12.9
Exon sequences
Seq C1 exon
TTGTCTACTACATGGAGGGGCGGGACTCCATGCAGCTCATCTACCGCTGGACCAAGAGCCTGGACCCCAGCCTGAGGAAGGGGCTCTGGGCCCCAGAGGAGGACGCG
Seq A exon
GTGTGTCTGGGGCCTGGGGCCTGGAGTTCGGGCTGGACTGGGCTGGGCAGGTTGTGACCGGCTCTGCTCCTGTCTCCCTGCAG
Seq C2 exon
AAGTTGCTTCAAGCAGTTGCCAAGTATGGGGAGCAGGATTGGTTTAAAATCCGGGAAGAGGTGCCAGGTAGGAGCGATGCCCAGTGCCGAGATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000054:ENSBTAT00000000060:11
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:
PF139211=Myb_DNA-bind_6=PU(9.8=16.7)
A:
NA
C2:
PF139211=Myb_DNA-bind_6=FE(50.8=100)
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:
TGTCTACTACATGGAGGGGCG
R:
CTCCTACCTGGCACCTCTTCC
Band lengths:
180-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development