BtaINT0138352 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000054 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:HGNC:11137]
Coordinates
chr11:103904432-103905548:-
Coord C1 exon
chr11:103905419-103905548
Coord A exon
chr11:103904485-103905418
Coord C2 exon
chr11:103904432-103904484
Length
934 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
GTGTGCTTGCATTCCTGCAGATT
3' ss Score
10.21
Exon sequences
Seq C1 exon
ATGGATGTGGATGCTGAGAGAGAGAGGATCTCCAGGGAGATCCAGCAGCTGGAGAGGATCTTGGATCCTTGCTGCTCGAGCGTCAGCATGGACGTCTCAGAGTCCAGTCTCAACTCGGATTCGGATGCAG
Seq A exon
GTCAGCACCCACACTCCTTGGTCAGAGCGGCCGTGTCTGCCCTTGGACCACGGTCAGCCACAGTGCGTCACACCGCTGGGTCTTTAGTCCGCTGGCCAGCATCACCATGCTCTCATCAGCCCCTGGCCCTGCGGGCATGCATGAGCACCCTGCCTCTTGGGGCCGCAGGCTGTCCTGGGAGGGGGGCCCTGCTCTCCTTCTCAGGATCGGAAGGCTGCTGGCCTCAGCCCCCCGGCTTGAACAGTCTGCCACCGCTGAGACCCCTTGGATCTCTTCCTGGTGCTCAGGCAGCTGCCCTCTGTCGGAGGCCCCCGCTGCCAGGGCTCCCCTTCTGCCCACCCCATGTGCTCCCCTGGGCCCCGAGCACCCCTCCCGGCAGCTCTGGCCTGAGGTCTGCCTGCACAGACCGAGCCATCCAGGGCCCAGCCTCCCATCCCTCAGGCTCAGGGGCGGCCCTCAGGCTGAGCCTGTCACGGTTCCCAGCTACACGGGCCTTCTCTCACCTGATCCTGGGCCTCTGTGCGTGGCCCCCCTCCCCGCTCTGACCAGCTCCAGTTCCCCAAGGACAGAGCTGTCTCGCGTGAAGCCTGCCCTGGCTGTCCCTACAGTTCCTGTTTGCTCCATGCCTGGGGAAGCCCCACGTTAGGCTGACATCTTGTCTTTCTGGCTCATCCTACCCTCAGCCCAGTGCCCACTGCACACAGAAGGCTGTGCTCAGCCCCCCGGGCATAGGCGGGGAGTGGGGGAGGTCCACGCAGCGTGCATCCCACCCCAGGCCTCTTGTCCCCTGTGGACCTCCTCACTTCAGCTCCCCCCCCCCGCCGCCCCCCGGTCTGTGGCTGCACTGGCCGGTTGGTTTCAGCACCTGTGGGGTGCATCACCAGCTGCTGCGTCCAGCGCTGGGCACCGACACCGTGTGCTTGCATTCCTGCAG
Seq C2 exon
ATTTGCTGCCCGACGAGGACTTGGACTCGGACGCTGCTGGCCCACTGCTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000054:ENSBTAT00000000060:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.553 A=NA C2=0.815
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGATGTGGATGCTGAGAGAGA
R:
GAGAGCAGTGGGCCAGCAG
Band lengths:
182-1116
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development