BtaINT0138355 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000054 | SNAPC4
Description
small nuclear RNA activating complex, polypeptide 4, 190kDa [Source:HGNC Symbol;Acc:HGNC:11137]
Coordinates
chr11:103895182-103897262:-
Coord C1 exon
chr11:103897168-103897262
Coord A exon
chr11:103895330-103897167
Coord C2 exon
chr11:103895182-103895329
Length
1838 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TGTTTTTATGTCGCCTTCAGATA
3' ss Score
10.05
Exon sequences
Seq C1 exon
AAGTTGCTTCAAGCAGTTGCCAAGTATGGGGAGCAGGATTGGTTTAAAATCCGGGAAGAGGTGCCAGGTAGGAGCGATGCCCAGTGCCGAGATCG
Seq A exon
GTGAGTGGGACAGCTCTGGGCAGAGGAAGGCTTGCTGGGGTTGCTTCCAGGTGGGCCACCAGGTGGGTAGGGAGACTGGCCCAGGGTGGCCTGCTGGTGTGGGAAGAGGGTGTGGCCTTGGGGGCAGGGAGGATGCAGATGGACCCGCTCAGGAAGCAGGGTCGCTTCTTTTTGAAGCCAGACGTGTGCACGGGCTCCACTGGACATCCTTTGAGATCCCCTGGTGGCAGTTTCCCTGAGTTTTTTTTTAAGCAGTATTATTCATAATTCACGTAGAAACCATTCATTTAAAGTAGGTAGTTCTGTAGGTTTGGGTGTATTTCTTGAGCTGTGTAGCCATCATCACAATTCTAGAACATTTTGATCACCCCACAAAAGAAACACTATTCCCTACAGAAAAAAAAAAAAATTCAAGAATGGACCAAAGAGACTTCCCGGGTGGTCCGGTGGGTGAGACTGTGCTCCCAGTGCCGAGGGCCCGGGTCCCTTCCCTGGCCAGGGAGCTTGATCCTACGGACCACAACTGAGACCCAGCGCAGCCAAATAAAGAAATAAATATTAGGGGAAAACAAGGCACAATGGGCTTGAACGCACGTTTCTCCAAAAGACGCATAAATGGCCTTGAGCACGTGAAGAGCGCCGGCGTGGTCATTACGGAAATACAGGTCAGCGCCACCAGGTCAGCGCCACCGCAGGGTGCCGCTTCACGCACTTCAAGATGGCGCATGTTTTATAAAAATGGGAAATAAGTGTCGGAGGGGATGCAGAGAAATCAGAACCCTTGTACACTCTTGGTGGGATTGAAACAGGGCAGCCGCTGTGGAAAAGAGTTCAGGGATTCCTAAAAAGATAAACAGAGAATTACTGTATTATCTTGGAGAAGGAACTGGCAACCCACTCCAGTATTCTTGCCTGGAGAATCCCACGGACAGAGGAGCCTGACGGGCTGCAGTCCATGGGGTCACGCAGAGTCAGGCACGACTGAAGCAACTTAGCACAGCATGTTGTCTAGCAATTCCACCCTGTACCCAAAAAATGGAAATCAGGGACTCAGACATTGTCCACCCCTGTTCATAGCAGCGCTGGACACAGCAACCAAAAGGTGGAAACGAGCCACGTGTCCATCAGCAGATGAGCAGATAAACAGGCGCGATGCTGACGCTGCATGGACACTGAGCGGGGCTCTCGCGCGTGCCGCGCCGGGACTGAACCTCGGAGGCCGCGTGGCTGTGCGTGCTCGCTCTTCTCAGCGGTGCCTACGAGTGAAGTCACGGGGTCATGTGGGGATTCGGTTTAACCTTCCGAGGAGTGACCATTTTCCAGAGTGGCTGCACCACCTTCAGGGCATCCCCACCAGCAGAGTAGGAGGGTCTCCGCGTCCTCACCGGCTCACACTTCATTTTTGATTCAAGCCACCCTAGCGGTGTGAGGCGGGATCTCTGCAGTTCCGGTCTGCTTTTCCCAAAGGGTGTTGATGTCGAGCGCCTTTCTCGTGTGTTATTTGGCCATTTCTGTGTCTTCTCTGGAGAAATAGCTATTTCTGTCCTTTGCCCATTTTTAAACTTGAGTTATGAGGGTGCTTGGTATATTCCAGGAACAAGTCTCAGCAGACACATGATCTGCGGACCCCCTCTTCTAATCTCTGGGTTGTCTTTCACTTTCTTGAAAGTGACCTTTGAAACACAGAAGTTTGTAACTTCGTGCAAGTCCAGTGTGCCTGTGTTTTCCTTCTGGTGCCTGTGCTCTGGGTGTCGTGGCTTAGAAATGGCTGCAGGCGCCAGGACAGCGGCAGGAGCGCGTTAGCTTCTAAAGTCCCTTTGTTTTTATGTCGCCTTCAG
Seq C2 exon
ATATCTCAGAAGGTTACATTTCAGCTTGAAAAAGGGACGATGGAATTCCAAAGAAGTGAAGAAGTTAATTGAATTGATAGAAAAATACGGCGTTGGTAAGCCCGGACTCCCGTGTTTGCGTACCGTTCACTCACGTGGTGGTGGTAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000054:ENSBTAT00000000060:12
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=FE(50.8=100)
A:
NA
C2:
PF139211=Myb_DNA-bind_6=PD(36.1=44.0)
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:
GCTTCAAGCAGTTGCCAAGTA
R:
GTTACCACCACCACGTGAG
Band lengths:
238-2076
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development