MmuINT0154677 @ mm10
Intron Retention
Gene
ENSMUSG00000026797 | Stxbp1
Description
syntaxin binding protein 1 [Source:MGI Symbol;Acc:MGI:107363]
Coordinates
chr2:32809101-32811235:-
Coord C1 exon
chr2:32811105-32811235
Coord A exon
chr2:32809209-32811104
Coord C2 exon
chr2:32809101-32809208
Length
1896 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGG
5' ss Score
7.66
3' ss Seq
CCAAGTCCTGTCTCCTCTAGGTA
3' ss Score
9.39
Exon sequences
Seq C1 exon
GGTCCCGACAAGGCACGGTCCCAGCTCCTGATCCTGGATCGTGGCTTTGACCCCAGCTCCCCTGTGCTCCATGAACTGACATTCCAGGCTATGAGTTATGACCTGCTGCCTATCGAAAATGATGTTTACAA
Seq A exon
GTAAGGATTAAGTGACAGGGGTCACAGGACTAGCTCTGTGGACAACGGAGTTCCTCTGATTAAGAAAAAAGGATGTTTTGTGGTTTTTTAAAAATGTTTTCTCATTTTGTATGTATATATAGCATGCATGGATGTCATGTGTGAAATGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGTGCGTGAGCACAAGAGTAGACCCATAATTGATATTGGCTGTCATTTTTTAAATCACTTTCTGCCTTATTGAGGCAAAGTCTTTAACCGCATGTAGAGTTTGCCAGTTTCCCCCAGGCACCTTGTCTCTGCATCCCTAGTTCTAGATTCCAGATGGCTGCCATCCCTGCCCCACATTTATGTGGGCTCTGGGCATCTAAGCTCCTGTCTTCATCAAACTTCCGAGGCAAGTGCTTCATCCACTGAGCCTTTTCTCCAGTCCCCCACAAGCATGGTTTTAATATAAGGAAAAATACGAGCACTGATAGATTCCATTTCTTAGATAAGCCCATGAGGTCTCTGTGGGCTTTCCCTATCCATGTATCATTCCTACATGCCTGCCAACAGGACAGAACACTAAGTCTTTCTTTCATAGCTCACATCACTTCAATTCATTGCTTCTTAGATGTGTTGACAGGTTGGTTTTCTGTGTGTCTTATTCACACGTTCTTAATTACAGACCACAAAAAATGACTGCTGTAAAATATTTCAACAGAGTTCCTGAACGTTCTGTGCAGTGGAGCTGCTTTCTTCTTTATAAAAAGATTACCCACCTGTAACCTTGGCATTCAGGAGCCTAAGACAGGAGGGTCATGAGTTTGAAGCCAGGATGGACAACTTAGTGTGAGACCCTGTCTCACAACAAAGAATGGCTTTATGTGAAGGTTCTGGGGCTGGAGAGATGGCTCAGTGGTTAAGCAAGGCCCTGACTTTGATTTCCAGCACACACATGGTAACAAACAACTACTTTAAACTCTAGATGCAGGGGATCTGATGCCCTCTTCTGGCCTCCACAGACACCAGGCATACACGGGGTGCATGGACACAAATAAAGCCTCGTACACATCAAATAAAATAAATGCAACTTTGTAAAAATGAAGGTTCCACTGGTTATGGGATTGCACTTCTTTAATGCCAGCACTCAGGTGGCAGCGGTAGGAGCATCTCCAACGGTTCAAGGCCAGCCTGACCTACAACAGCAAGTTCCTACTTGGTTATGTATAGCCAGGACTACATACAGGCACCCACTCTCAATTAATTTACTAATTAATTGATACTAAAAATGAAGATTCTGAAAATATTTGTGGTTGTCAGCCCCTGTCTCTTGGTTCTGGGGTTCTGGCCTCCTCTGAGCACTCACAATTCCATGTGTAATAATAAGCTGTGAACACAAATGGCTGGAAAGCTTTTAGGCACCTTACATTTGCAGATGGAGGGGCAACTATGTAACTATGTAACTGTAGACTCACATAGAACTGCCACTGGGCCTGGACTCCCTCTCCCATCCCCCAACAGACCCAGGCTCTGAAGGGTGAAAGCACAGCTACAAGTTGCTGGCTTTGAGCTTTCTCCTTGCCCAGGGAACTGGTCATTTTGTGCTGTTCCAGATAAACTGGGCAGCCTGACAGGTGGCTGGTGTTATGAGCCACGCCTGGGATCACCTGGCAGTCGAGAGAACAGGTGTTATCCTTAGGAACCAGAGGAGACAGACATCTGGGTGTGGAAGTGCACACCTGTAATCCCAGCATTCAAGGGGTGGAGGCAGGAGGGTCAAGAGTTCAAGACCGTCGTAGCTATTTATGGAGTCTGAAGCTAGCCTGAGATACTTGAAATCCTGTCTTATGGGGGCAAAGGTCATGCCATGAGGACGCCGGGCCTATCCAAGTCCTGTCTCCTCTAG
Seq C2 exon
GTATGAGACCAGCGGCATTGGAGAGGCGCGGGTGAAGGAGGTGCTACTGGATGAGGACGATGACCTGTGGATTGCGCTGCGACACAAGCACATCGCAGAGGTGTCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026797:ENSMUST00000050000:9
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(12.4=100)
A:
NA
C2:
PF0099518=Sec1=FE(10.4=100),PF140711=YlbD_coat=PU(28.0=75.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCCGACAAGGCACGGT
R:
TGGGACACCTCTGCGATGT
Band lengths:
238-2134
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types