MmuINT0154673 @ mm9
Intron Retention
Gene
ENSMUSG00000026797 | Stxbp1
Description
syntaxin binding protein 1 [Source:MGI Symbol;Acc:MGI:107363]
Coordinates
chr2:32672806-32674025:-
Coord C1 exon
chr2:32673947-32674025
Coord A exon
chr2:32672910-32673946
Coord C2 exon
chr2:32672806-32672909
Length
1037 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
GTTTTTTCTCATTCTTGCAGCGT
3' ss Score
11.08
Exon sequences
Seq C1 exon
TCTGTCCACTCTCTGATCAGTGATTTTAAGGACCCGCCGACTGCTAAATATCGGGCTGCGCATGTGTTCTTCACAGACT
Seq A exon
GTAAGTACCCCATGGGCTGCTCCTGCTGGCCCAGGTTGGCATTTCTTCACAGTTCCATGGAGGCTGAGCTGGGGCAGGACAGCAGAAGAAATGAGCGGTACTACAGTTACTTAATCTTCTCTCTTCAGCAGATGAACACTGTAAGACACACACACACATGCACAAGTGTATACTCACACACATGCACAGGTATACAACATACATGTGAGTGTATACACACACATACGCACAAGCATATATTCACTCGTGCACAAGTGTACACACACACACATACACACACACGTTGAGTGTATACACACACATGCACAAATGTATAACACTATCAGAAAGAGAAGGAGAAGTAGTAGCAGTTGTTGTCTTTCTGATGAAAGCTAGCCCACCAGGCTCCTCTGGGAGCAGAGGGCTTCCTGCTGAGCACAGTTTCCGGGTGCTCCATTACAAGGCCATTCAGAATTCTCTGGAGCCCGTGGGCTGTTTCTGTGAGGTCTTTGGACCATAACTGTTCCAATGGGCTGGCCCAGAGTTGCCTTTTTGATTTTGTGCTGGGTTGTGTGTGGATAAGTTTTCCGAGTGGAGCAGCCACAGCGACAGAGTGGTAGCCTCGCCACTCTTCTCCCTCGGGGTAACACCCCAACCCCTGCTGAGACTGCAGAAAAGGAATGGAACCCCTCCTGGCACCTCAAGCTGTTTTTCCACCAGGAGCCTCCTGTGCTGGCTCTTGGTTCCATCATCAAATCTGTGTGCTTTCTTCCTCACCCTTTCTCAACGCCTGCTTGTGTGCTCTCCTTTGCCTGGAAGCAGCACCTAGTCTTTATTGGCTTGGGTAGCGCAGTCAGCTGCTGGCTGCTGTGTTGAGGGCCCTGCAGGTACTTTTCCATCTCTGGAACTCATGGACGGGATGCAGGTATTACTAGGTGCCTTTTTAGAATCTGAGTAAAAATAGGTGCAGTGACATCATGGCTGTTGACTGAGCTGGCAGATGAATGGACGGACAGACGGATGGACAGAAACCCCACTGTTTTTTCTCATTCTTGCAG
Seq C2 exon
CGTGTCCAGATGCCCTATTTAACGAGCTGGTAAAATCCCGAGCAGCCAAAGTCATCAAGACGCTGACGGAAATCAACATTGCGTTTCTCCCCTATGAGTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026797-Stxbp1:NM_009295:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(4.7=100)
A:
NA
C2:
PF0099518=Sec1=FE(6.1=100)
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:
TCTGTCCACTCTCTGATCAGTGA
R:
TGGGACTCATAGGGGAGAAACG
Band lengths:
182-1219
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: