BtaINT0143056 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003525 | STXBP1
Description
Bos taurus syntaxin binding protein 1 (STXBP1), mRNA. [Source:RefSeq mRNA;Acc:NM_174619]
Coordinates
chr11:98370967-98372715:+
Coord C1 exon
chr11:98370967-98371097
Coord A exon
chr11:98371098-98372607
Coord C2 exon
chr11:98372608-98372715
Length
1510 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
GTGGGACGTCTCCTGTCCAGGTA
3' ss Score
5.76
Exon sequences
Seq C1 exon
GGCCCGGACAAGGCACGCTCCCAGCTCCTGATCCTGGACCGTGGTTTCGACCCCAGCTCCCCCGTCCTGCATGAGCTGACTTTTCAGGCTATGAGTTACGACCTGCTGCCTATTGAAAATGACGTATACAA
Seq A exon
GTAAGTACACGTGACTGCAGCTTTGCAAATGAACCAGACACACCTCTAATTTAAGGACACAGATGTCGTTAATCCTAGGAAAAGCAGGTACATTCATACAGTCTTTTTTTTTAATTTGGTTTTGGCTGCATTGGGTCTTAGTTGTGGCCGGCAGGCTTTCACTAGTTGTGGTGAATGGGCTTTCAGGCCTGGTTGCCCTGGGGCGTGTGAAATGTTAGTACCCTGACCAGAGATCTGACCCACATCTCCTGCACTGGAAGGCAGACCCTTAACCACTAGACCACCAGGGAAGTCCCCATACAGTCTCACTAATAAGCCTGCATGCTTTTTTCGAGTCCCAAAGTGCAACTGCACCATCAGCTAGAAACCTCTGCCTGTTTTGGGGAACAAGAACTTGAAATGTTTAGTTCACAGCTCATGTCACTTCACTTCACAGCCGGTTTGGATGTGTTAATATTGTTGACTTGTGTAAGAGCGTACCTTACTCAGAGTTAAAACTTCTTAACTACAGACCATGAAATATGATGATAAAATATGCCAGTAGGAGTTTCTTACCAAATTTTTTAAAATTAATTTATTAATTTATTTATTTTTGGCCACACCATGTGGCATGTGGGATCTTAGTTCCCCAACCAATAATTGAACCCACATCCCTGGCTTTGGAAGCACAGCGTCTTAACCATTGTACTGCCAGGGAAGTCCCGTATTACTGAGTTTTATTTGCACTTTACTTCATTGTAAACAGTTTTCTTGGTAGCAGTCATCAGAAACTCAGTCTCTAAAAACATAGTTTTCTTTTTATGGGAACAGACTACATTGTTCTCGTGTCATTGATTTTATAACCTCAACCATAAAGATAGTGGTTTCAAAATGAAGATTCTAAAGATATGACTGAATCTCAGCTTTCCCCCTTTGGTATCTGTAATTCTCGATTTCCCTTAGATGTTCACGGTTGTACTTGTGACAGTTTGCTGAGGGCCTGTTGCAGGCAGCTGCCAAAGGCTATTTCAGTCCCACACATTAAGGATGGTGTCCCAGGCCATCCCAGGAACAAGTGTGATCCCCGCCTCTCCTTTCCAAGTGCCTCCAAAACCACCTATAACCTGACTGCACACCTGAGCCAGGTGGCTCCAGTGGAGCACTTACCAACTGACCCTGAGGGTTTTAAAACAGAACTTCAAGTCAGTTGACTTTGATCAGACCTTTAGGTCTCTTCCTGCCCTAGAAATTGGTAGCCTTGGGAATTCCCTGGTGGTCCAGTGGTTAGGAGTCCATGCCTCTGATGAGGGCCTGGGTTCAACCCTGGTCAGGGAACTAAGATCCCACAAGATGTGTGGTGTGGCAAAAAAAAAAAAAAAAGGAAACCACCAGCCTCATTAGATGCCACAGACCTGACGCAGACAGCGGCACCTCAGATGATCGGAGGGCTTGCTGTGCAGTCGTTCGTGTGAGCGTCGGTCTGTTATAAACCAGGGGATTGGGTGAACTGTGTGGGACGTCTCCTGTCCAG
Seq C2 exon
GTACGAGACGAGCGGCATCGGGGAGGCGCGGGTGAAGGAGGTGCTCCTGGACGAGGACGACGACCTCTGGATAGCGCTGCGCCACAAGCACATCGCGGAGGTGTCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003525:ENSBTAT00000056141:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.045 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(7.7=100)
A:
NA
C2:
PF0099518=Sec1=FE(6.5=100),PF140711=YlbD_coat=PU(28.0=75.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAAGGCACGCTCCCAG
R:
GACACCTCCGCGATGTGC
Band lengths:
230-1740
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development