BtaINT0143043 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003525 | STXBP1
Description
Bos taurus syntaxin binding protein 1 (STXBP1), mRNA. [Source:RefSeq mRNA;Acc:NM_174619]
Coordinates
chr11:98378386-98379500:+
Coord C1 exon
chr11:98378386-98378524
Coord A exon
chr11:98378525-98379390
Coord C2 exon
chr11:98379391-98379500
Length
866 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGA
5' ss Score
6.66
3' ss Seq
TCAGGGTTTTGTTCTTGCAGGCA
3' ss Score
8.27
Exon sequences
Seq C1 exon
GACCTGGCCATGGGCACGGATGCTGAAGGGGAGAAGATCAAGGACCCCATGAGAGCCATCGTCCCCATTCTGCTGGATGCAAATGTCAGCACTTATGACAAAATCCGCATCATCCTTCTCTACATCTTTTTGAAGAATG
Seq A exon
GTAGGAACAGCCGGATATGACAGAGGAGACAGGCCCTTTCTTGGGGAAAATGAGGCAGCTGGGAGGGAGAGAACAAAGTGAAAAACAGCTCAAGAGACAAGGAAAAGGGAAGGAAAAGGAAGGTCTGAGGGGCTCTTTACAGCTGGAGAAATGTAGGCAGATCAGCTGCAGCTAGAGGCTGTGTATCCCCCAGTGATTCTAGAGTTAGTCGGAGGGACAGGATAATGAGAAGAGGGCTGGGTGAGGACAGCAGGGAGAGTCTATCAGCTGTATAGCCAGTTTATTAGAGCATTTCTGCCAGAGACTTTTAACTTACCCCACATTTGTAATCTGTGCCTTTATTTATTTGTTTTTATTTGGCTGCACTGGGTCTTGCTGTGGGATGCGGGATCTTTAGTTCACCAACCAGGGATCAAACCCAGGCCCCCTGCACTGGGAGCCTGGAGTCTTAGCCACTGGACCACCAGGGAAGCCCCCAATCTGTGCCCATAAATAAGGGATCTTTATGCACATATAGTTGCCATAAGTGTCCACTGTGCAAAAAGATGGACACAGAGACTCTCTTGTCCAAGCTGACTGTGACGTGGGCCCGGGATGGTGGGGACGGCTGAGAAGCAGGAGACGGATGGAAAGACAGGTCAGGAGGGGCAGTTGCTGGTGGTCATAGCCCAGGACAGAGTGGCTAGAGTTGAACAGGAGTCCTGGCCCTGCCTTGTCTTACAGTAAAGTCGATACATTGAGCGGATTAGTTCCCACTGATGCCAAGGAGGAGAGGGGGCACCATCCCCCACCCCAGGCACTTGGCTCTGCTTCTGAGTGTGCGATGCACAGTGGCTGGTATGGTGATCAGGGTTTTGTTCTTGCAG
Seq C2 exon
GCATCACTGAGGAAAACCTGAACAAACTGATCCAGCACGCTCAGATCCCGCCGGAGGACAGTGAGATCATCACGAACATGGCACACCTCGGGGTGCCCATCGTCACAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003525:ENSBTAT00000056141:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.135
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(8.3=100),PF140711=YlbD_coat=PD(1.0=2.1)
A:
NA
C2:
PF0099518=Sec1=FE(6.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGATGCTGAAGGGGAGAAGA
R:
GTCTGTGACGATGGGCAC
Band lengths:
233-1099
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development