MmuINT0154677 @ mm9
Intron Retention
Gene
ENSMUSG00000026797 | Stxbp1
Description
syntaxin binding protein 1 [Source:MGI Symbol;Acc:MGI:107363]
Coordinates
chr2:32664621-32666755:-
Coord C1 exon
chr2:32666625-32666755
Coord A exon
chr2:32664729-32666624
Coord C2 exon
chr2:32664621-32664728
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-Stxbp1:NM_009295:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(10.3=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
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: