BtaINT0138353 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000054 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:HGNC:11137]
Coordinates
chr11:103897346-103897759:-
Coord C1 exon
chr11:103897612-103897759
Coord A exon
chr11:103897453-103897611
Coord C2 exon
chr11:103897346-103897452
Length
159 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGT
5' ss Score
6.05
3' ss Seq
CCAGCCCCCTCTGTCCGCAGTTG
3' ss Score
10.18
Exon sequences
Seq C1 exon
ACGCACCGCAGCGCCTTCCAGTGCTTGCAGAGGTACCAGCAGCACAACCCGGCCCTGAAGCGCAGGGAGTGGACGGAGGAGGAGGACCGCATGCTCACGCGGCTCGTGCAGGCCATGCGAGTCGGCAGCCACATCCCCTACCGGAGGA
Seq A exon
GTGAGTCCCACACCTGCCGGGCAGGGCCCTGGTCCACTTGGGGGGGCGGGGGCGGTGCTGTGACGTCCGGGCCACCTGCGGTCAGTTCTCTGTGGTCAGCGTGGCTCCTCTCTGGGGGACCCAGGAAGCACGGCGCCAACCAGCCCCCTCTGTCCGCAG
Seq C2 exon
TTGTCTACTACATGGAGGGGCGGGACTCCATGCAGCTCATCTACCGCTGGACCAAGAGCCTGGACCCCAGCCTGAGGAAGGGGCTCTGGGCCCCAGAGGAGGACGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000054:ENSBTAT00000000060:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.080 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139211=Myb_DNA-bind_6=PD(50.8=62.0)
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PU(9.8=16.7)
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:
GCGCCTTCCAGTGCTTGC
R:
GTCCTCCTCTGGGGCCCA
Band lengths:
242-401
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development