BtaINT0138374 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000054 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:HGNC:11137]
Coordinates
chr11:103900797-103901249:-
Coord C1 exon
chr11:103901177-103901249
Coord A exon
chr11:103900962-103901176
Coord C2 exon
chr11:103900797-103900961
Length
215 bp
Sequences
Splice sites
5' ss Seq
AACGTGAGT
5' ss Score
9.54
3' ss Seq
GTCTGTTTGTCTGTCTGCAGTTT
3' ss Score
9.31
Exon sequences
Seq C1 exon
TCAGCTCCCGGAGGAGGCCTTGCTGGGCGACAGGCTGGACAGCCACGACTGGGACAAGATCTCCAACGTCAAC
Seq A exon
GTGAGTCCCAGTGGCCAGGGCGGGTTCAGCACCGGTCATTGAGGCCACGACCTGCGTGGCCACTAGGCCTGCTGGGACTCCCTTTGGTCACACGCAGGTCCAGCAGCATGGATCGCTTTGGGGGCTTCCCCGCCGGCACTTCCTGGCAGCCTGGACAGAGACCGCACTCCCCGCGGCCCACTCCCACACAGACAGGTCTGTTTGTCTGTCTGCAG
Seq C2 exon
TTTGAGGGAGGCCGCAGCACGGAGGAGATCCGCAAGTTCTGGCAGAACCACGAGCACCCGAGCATCAACAAGCAGGAGTGGAGCGAACAGGAGGTGGCCCAGCTGAAGGCCGTCGCAGCCAAGCACGGCCACCTGGACTGGCAGAGTATCGCCGAGGAGCTGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000054:ENSBTAT00000000060:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.120 A=NA C2=0.200
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PU(45.9=50.9)
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:
CGGAGGAGGCCTTGCTGG
R:
CCAGCTCCTCGGCGATACTC
Band lengths:
228-443
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development