BtaINT0143047 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003525 | STXBP1
Description
Bos taurus syntaxin binding protein 1 (STXBP1), mRNA. [Source:RefSeq mRNA;Acc:NM_174619]
Coordinates
chr11:98385181-98386957:+
Coord C1 exon
chr11:98385181-98385335
Coord A exon
chr11:98385336-98386831
Coord C2 exon
chr11:98386832-98386957
Length
1496 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
CGGCCTCTGTTCTCCCGCAGGTT
3' ss Score
12.68
Exon sequences
Seq C1 exon
CGCCCGCTATGGGCACTGGCATAAGAACAAGGCCCCCGGGGAGTACCGCAGTGGTCCACGCCTTATTATCTTCATTCTGGGGGGCGTGAGCCTGAACGAGATGCGCTGTGCTTACGAGGTGACCCAAGCCAACGGCAAGTGGGAAGTGCTCATAG
Seq A exon
GTGAGTGGGCCGTGTTTTCTAGAGGGAAGGGCTGCTTCATGCACTGTGACTCCATTCCACGCTTTGGTGTTTCATCCTATCTCCAGTTCTCCGCTGCCCCTGCAACACTTTGCCTCTAGACACGTCTGTGGACAGCAGCCACGGAGGGGTGAAGGGGCCCTTCCTCAGGTCTGCTCTGCTTCTTGACAAGCGGCAGCCCCACATGGTGGGAAGTGCCTGGTCCCAGGCCCCAAAAGACTCAATGTTCCTGCTCTGTCACTGCCACTCGGGCCCCCTCAAAAGTGCTGCCCTCTCCAGGCTGTGATTTCCTCACCCACCAAAATTGGGTTAAGGGCACCCACTTACAGCCTAAACTGGGCCTGGGGTGGAGGGGCATGTCAGTTTCTTGGCCTCGAGCCTCACGTCCGGAAGATGCTCAGTGAACAGGTCAATGAGCCCTGGCCCCGGTACCTGTCAGTTAGAGATACATAGTCCAGGCGTGCAAGCAGATACTGCTCAAAACGTATCCGTCTGGCTTCTCGGCTCTGCTGAGGGCTGCCCCAGCCAGCTCCTACCACTTCAGGGTCTATCATATCCCTGCTGGTTTTCCAGAAGAAAGGAAGCAGCTCCTAAGAGCTGACTTAAGGCAGCAGGAGAAGATTTTCCCCTTTTTCATGTCTACAGGAGCCTCCCCAGTTTCTCCGCCCGGAAGAGGAAACATTGAGAAAAATCTTTGCTTTCTCCAAATGCCTTCTTTCTTGTGCCCTTAACAAACTGGAGTTGCCTCTGCCCAGGGTGCCTCTTGGCATTAACTGACCAGAGATGACTAGCACCTCCTCTCCTGGCCGGGCCCTGCCCTTGCCCCTTAGCTCAGTAAGAGGTGTCACTTTTATACCTCCACTTTGCGGGGAACCAGTCCACGTGGCCCTTCCTGGGTGCATCAAGATGGACCTGGCACTGTCTTCACAACTCTGAGCTTCCAGATCCCACCATTCAGGGGGGAGATTGCACATCCCCACCCCTACCCCCGCCCCTCCCTACTCCCAGAAGCCTCTCTGGCCACCATTTCTCCCTGGGTTTTCTCCTTTTTTGGTTACATAGGCCCCCCGTGGCGGAGCTCTCTGTGTTTTTGGCTTCCATACGTGTTGCATGAGCGTGTTGGCTAGTTCTGCTCAAACACAGCTCTCCTGGGCCGACGCGTCCCAGCCAGGCTTCGTTGTAACCCCCTCTTCCACGCTGGCCTGACCTGAGGGTCCCTGTCGGGAGGTGGAGACCCGGGGAGACACGGTCACCCGTGCAGATGGGTGGAGAGGCCTGGTGCAGACCGCCTACGCCCGCTATGCGGCCCCGCCCGCTATGTGCTTGCATGCCCGCCCGCCCGCCGCGTGTGCACCTCGCGTGTGCGCATGCGGCTCGCTCTCTCGCACCTCATTGGCTGCATAAACGTAGGCCTAAGTTGGCATGCTCCTGTAACGTACCTGTGTTCAAGCAGTCAGCCGGCCTCTGTTCTCCCGCAG
Seq C2 exon
GTTCTACTCATATTCTCACTCCCACCAAATTTCTCATGGACCTGAGACACCCCGACTTCCGGGAGTCCTCTAGGGTATCTTTTGAGGATCAGGCTCCAACAATGGAGTGAGAGCCAAAGAAACAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003525:ENSBTAT00000056141:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.250
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(9.4=100)
A:
NA
C2:
PF0099518=Sec1=PD(2.5=37.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGCTATGGGCACTGGCATAA
R:
TTTGTTTCTTTGGCTCTCACTCCA
Band lengths:
278-1774
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development