MmuINT0154700 @ mm9
Intron Retention
Gene
ENSMUSG00000027882 | Stxbp3a
Description
syntaxin binding protein 3A [Source:MGI Symbol;Acc:MGI:107362]
Coordinates
chr3:108603653-108605109:-
Coord C1 exon
chr3:108605029-108605109
Coord A exon
chr3:108603792-108605028
Coord C2 exon
chr3:108603653-108603791
Length
1237 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
CTGCATTTTACTGTCCTTAGGAC
3' ss Score
8.47
Exon sequences
Seq C1 exon
CAAGTAGTCCATCTTAACTTAGCTGAAGACTGCATGAATAAGTTTAAGCTGAATATTGAGAAGCTCTGCAAAACTGAGCAG
Seq A exon
GTATGTACAGACCCAGAAACACCCACATCTGTAATAGATTCCCAGAGTGACTTTGTAAGCTATCACATAAAGGTTTTGCTCAATACAGCGGTTGAGTTCCACAGAATCATAGACTCTTAGAAGGGACTCGCCTAGGCAGTGTGTGGTGCCTGACGGCTCTGTGTTACTATAGCAAACCCTGAAATGATAGTCTACTGAGAAAAGGCTGATTTTGTCTCACAGGTTTGCTGGTTGGGTTTGGTGCTGGGCACACTTGGTTGAGAATACTTGAGACGTAGGGTCTTATAAACAATTGGCTTCACTGCTTTTAGGCATGTGGCACATCATAGCAGGGATGTCTGACAGAGCACAGGAGCTCACCGCATGGTAAGGACACCAGGAGGTAGACAGAGGCGAGGACAGTTGTCCCCTTCAAAGGCACAAAAAGACCTGAAGAGCTCCCTCTAGGTCCTGCTCTTAGATCCTTCACCTCTCAGGGACACCAGAGTCAGCCTTATCATGGGGCCCCGGGGTCACTCAGATCACACTGGAGCCCTCCAACACTGGCACGAGTCCCTCCCCTGTGATCTGCAGTTTGAGCTCTGGAGTGCTATGCTAGTGGAGCGTTGCAGGGCCTTCTCGGGGGCTGCGGTGCATGTGAGCTGTCCCACAGAACTCTGCACCCAACGTTTCTGTTTTGATTCTCTTGGTTTTTTTTTGTTTTGTTTTGTTTTGTTTTTTAAATATTCCTAACCTGTTCAGAATATGACACTAAGAGATATAGAATGCATGTTGCATGCAGTACTAACTATTCTGATAGCCACACTACAAAGTTAAAAAGAAGCGCAAGTGATTGCGGTGATAAATCTAACCTAACCCAATGTGTTCACACTATTGTTTGAACATGTGCTTAATATTAAAGGTGTTGATGAGGTATTTTCTGTTCTTTCACAAATCTTCAGAAGTCCATTGTTTTGCACCCAGAGCCCATCCTGACTCCGATGGAGCACATCAGAAGTGCGCAGACTCTCATTCTTAGTGGTGACCTTAGTGTCTAGCTCAGGTCCACATGACTTTCTCTCCCGCTGATTGCTTTATGACCTTTTATGTTTTGTGAAATGAATACTTTGCATCTAACGTTCCCATCTCCTGTGAAATACCATCTGTCCCACCAAAATCTGACAGTTTAATAGTAGATACTCCTATCGGGAAAGCAAGCATGGATTGTAGAGCACTGTCTGCATTTTACTGTCCTTAG
Seq C2 exon
GACCTGGCACTTGGAACAGATGCTGAAGGCCAGCGGGTGAAGGACTCCATGCTGGTGCTCCTCCCAGTGCTGCTCAACAAAAACCATGACAACTGCGACAAAATACGGGCAGTCCTGCTCTACATCTTCGGGATTAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027882-Stxbp3a:NM_011504:13
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=0.011
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(4.8=100)
A:
NA
C2:
PF0099518=Sec1=FE(25.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGTAGTCCATCTTAACTTAGCTGA
R:
TCCCGAAGATGTAGAGCAGGA
Band lengths:
214-1451
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: