MmuINT0154687 @ mm10
Intron Retention
Gene
ENSMUSG00000004626 | Stxbp2
Description
syntaxin binding protein 2 [Source:MGI Symbol;Acc:MGI:107370]
Coordinates
chr8:3641898-3643644:+
Coord C1 exon
chr8:3641898-3642055
Coord A exon
chr8:3642056-3642645
Coord C2 exon
chr8:3642646-3643644
Length
590 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
AACCTTCCCCTCCTGCCCAGGCT
3' ss Score
6.76
Exon sequences
Seq C1 exon
CGCTCGCTTTGGCCACTGGCACAAAAACAAAGCTGGAGTAGAGGCCCGGGCTGGGCCTAGGCTCATCGTGTACATTGTGGGTGGTGTCGCCATGTCGGAAATGAGGGCTGCCTATGAGGTGACCAGGGCCACTGAGGGCAAGTGGGAGGTGCTCATAG
Seq A exon
GTAAGTAGCCAGAACTGGGGTCCTTGGGAGTATGACTGTGGGGATTCCTGGGGACCAGGGCTGGACATGGGGTCCCTTAGAGTCTGCAGTTAGATTTGTTGTCCTCAAACGCCTAAGATGTGGGGACTTGGGCTTCTCTGGAGCCTGAGCCTAGATTCTGAGTCCTTAAAAGCCCAGGGCTAGAGTCTGGACTCTTTCTCTTGGGGGGGGGGGGGGGTGTCCTGTGCTGGACTCTGTAGTCTATTGAGATCTAAGGCTGAGCTCTGAGGTCCTTATAGGGCCTGCGACTGAGCTCTGGTCTTTGAGGGGCTGGGGCTGAACTCAAAGAATCCCTAAAGGGCTAGGATTAGATTATGAAAGTTCTGGGCTTGGGGGTGGGAATCTGGGGACTTTGAAAGGCTGGGGCTGGAGTCTTCAGTGGAGTAATCACCTGGGGCTGGATACCCCTGTTCCTAAGTTTCTGAACCCCTCAATCATTGAGAAGACAGGGCCCTGGTTTGCAGAAGGGCAGGAGTTTGTTCTCACCAGCCAGGACACGAGTCAGGAGGGAGGGACTCTACCTCCTCCTTTAACCTTCCCCTCCTGCCCAG
Seq C2 exon
GCTCTTCTCACATCCTTACTCCAACCCGCTTCCTCGATGACCTCAAGACACTGGATCAGAAGCTGGAGGGTGTGGCCCTGCCCTGACACAGCCCCTTGCCTCTGCCCTCTCCTATTCCAGAGAAATAAACGCTTCCCTTCTGTCTTCCCACCAGGGCTCACCTCATTTTCTTCCCAGAGGGAGCTGTATTGAGCCAGACCTCCCCCTGCGTTTTCACTGTCCTGCCCGAACCTTTCCCCGGCCCCCAGAAGCATCTGTAGCTTTCATTAACGCTGAGAACCTGGGCTGTAGGGTCAGTATTGGCTTGAAGTTTAGGAGGCACTGGCTCTCTTGCTGGGTCCTCCATCCAAACCCAGGCCTGATTTTGGCAGAGGAGATAGAGAGGTGCAGATTAGGGGTTGCCAGGGCTGCAACCCCACTGTCACTAGAGTTCTTTAGGCTGTAAGGTTAGAAATATAGGAAAAATTTTAACCTTTATCTTTATTTTGTGTGTTACACTTGTATGTATGTTTATGCATCATAAGTATCAGTGCCTGTAGAGGTCAGAATAGGGTGTGGGATCCCCTGGAACCAGAGTTATAAATGGTTGTGTGAAGCCATGAAGGTTCTTGAGTCTGCTGTGAGAACAGCTAGTCTCTTACCCACTGATGCATCTCCAGCACCAGAAATAGAAACGGAAATAGAGTAGACCTGAATCCTGACTCTTCCCCGGAACCTCCCAGGAGCTACTGCAAGTAGAACTTGAATCCCCAATTCCAGCAATCAGAGCTAGCATTTAAAATACAGCAAACTTGGGGCTGGTGAGATGGCTCAGCGGGTAAGAGCACTGACTGCTCTTCCAAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCGTAATGACATCTGACGTCCTCTTCTGGTGTGTCTGAAGACAGTTACAGTGTACTTACATATGATAAATAAATAAATCTTAAAAAAATAAATAAAATACAGCAAACTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004626:ENSMUST00000160708:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(9.6=100)
A:
NA
C2:
PF0099518=Sec1=PD(12.6=48.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGAGGGCTGCCTATGAGGT
R:
GCCCAGGTTCTCAGCGTTAAT
Band lengths:
345-935
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