BtaINT0143054 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003525 | STXBP1
Description
Bos taurus syntaxin binding protein 1 (STXBP1), mRNA. [Source:RefSeq mRNA;Acc:NM_174619]
Coordinates
chr11:98368214-98370185:+
Coord C1 exon
chr11:98368214-98368362
Coord A exon
chr11:98368363-98370100
Coord C2 exon
chr11:98370101-98370185
Length
1738 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
CGTCCCTCCTCCCTTGTCAGGGA
3' ss Score
9.97
Exon sequences
Seq C1 exon
GTGTATTCCTTGGACTCTGCTGACTCTTTCCAAAGCTTCTACAGTCCCCACAAGGCTCAGATGAAGAATCCGATCCTGGAGCGCCTGGCGGAGCAGATCGCAACTCTGTGCGCCACCCTGAAGGAGTACCCAGCCGTGCGGTACCGGGG
Seq A exon
GTAAGGCTGCACCCCAGGCTGCCTTCGGTGACCCCCCCAAGTGAGGAACTTCCTCTGGCCTTCCCATTTTCTGGCAGTTGTCTCCAGAGGGTCAAGATCTGAGCATCTCACATTGACTATTTTCCAATGTTTTTGTTATTTTCTAAATTTTTAATGTGAACTATACTAATATATGCAGAAAAGGGCATGGAATACATATATTCAGTTATATAACCAAGCACAAACCCCCATGTAACTGTAAGCCAGATTTCCTTCAGTTTTTTATCTCTTTCTAACCTTAAAAAGGGTCTTCCCTGGTGACTCAGATGGTAAAGAATCTGCCTTAAAACAAATACACTCTTTGAAAAAGACATTTCAGGGTAAGATAAAATACAAGGAAAATAATTCTCCAAAGGACACAGTCCTCAGATTTGATCGAGTCATTCACTCGTCATTTACCTGCTGTGTGCTAAGTGCTAGGTTGGGGGCTTAACCTGAAGACACAGCCTCTGCCCTTGGAAGCCCCTGACCCAGGCGGGCAGGTAGGATGTGTACTGGCATAATGTACATCCGAGCTGTGCACACCTGCAGCTTAGGCCTGCGGGACCAGTGCCTTGGGGCAGCGCAGGCCACGGGCCTGGGCGTCCAGAAAGGAGCAAGCCCGGCTTCAGAGCAGAGGCGGCATCTGAGCCAAGGACAGGTCGGGATTTCCGTAGACCGATGAGGAGCTGGGGGCATTTTGTGTGGACAGTTGGGATGAGTGGAAGCATGACCCTGGAAAAGAAAGGGGAAGTTTGAGAAGGGCTGGCAGTCTCACCCTGCATACGTGCAGGCAGCAGGGCACGGGAAAACCATTTCTGGAGGCCTTGGGTGCCAGGTTTGGGGTCATGCCCTTCAGTGGTTGTCATTGGGCAGCCTCTGAGGGAGTGAACACAGAGGCGTGGGAGTGCAGGGGTCACAGTCATGCAAGGAGAAGCAACCAGAAGGCGGGATGCTGCCAGAGCAGTGGAGGGCCTGATCGGGAAGTGCCAAGGCGCCTCATCACCTCTTGTCCCTGGGGATGGGCACCCGTAGGACAACCCTCCCCCCACCAGGGTCCTCACCGACAGACGCCTGGCAGAAGTTAAAAAACGAGGGCTGGGAGCTCACTTGTTGGGAGGATGGGACTGGGGGTGGAGCTGCTTCTGCACTAAGAGCGGCCAGGTGGTGGGCAGCAGCCACATGATGAACATCACCCAGAGGAACTTAGGAGGCGCTGGAGGCTCAGCCAAGAGGGAAGGTCCAGAGGTTCTCAACTTGCATCTTATAGCTCTGCCAGCGGAAATGTCACTTCCAACAAAACAAAACAGGGTCCAAGGGAATTTGAACTGAGGGAAGTGAAGATCAAGTAGGTCAGGCTGAGATAGCCTGACGTTGGGGAAAGGACACGTGGCTGTGTCCACACTCTGCTGAAGTGTGGCTGTTTTAACTGGAGCTGCTTGGGAAGACCCCCTCTGTTTCCACTTGGATGGTTTTGTTTTTGTTTTTTTTTTTAAGAAACTAGAAAATCATTTACATTCCAGGCACTGAGCTAAGTATTTTGTTTTTTCCTTTTTAACCGTACATGTAATCTGAGTTATATTTTCTTGTAAAAGAATAATACAGATGAAGCTCATCTCTCCCTTGACCCTCCCGCACTGTCCTGCCTTCCTCCCTGAGGGCAGACAGTGCCATCCGTTGGGACAGGGTGGCTCACCCTCCGTCCCTCCTCCCTTGTCAG
Seq C2 exon
GGAATACAAGGACAACGCTTTGCTGGCTCAGCTAATCCAGGACAAGCTCGACGCCTACAAAGCCGATGACCCGACGATGGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003525:ENSBTAT00000056141:7
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=0.241
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(8.8=100)
A:
NA
C2:
PF0099518=Sec1=FE(5.0=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:
ATTCCTTGGACTCTGCTGACTCT
R:
CTCCCCCATCGTCGGGTC
Band lengths:
230-1968
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development