MmuINT0141053 @ mm9
Intron Retention
Gene
ENSMUSG00000063531 | Sema3e
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E [Source:MGI Symbol;Acc:MGI:1340034]
Coordinates
chr5:14236042-14236433:+
Coord C1 exon
chr5:14236042-14236083
Coord A exon
chr5:14236084-14236266
Coord C2 exon
chr5:14236267-14236433
Length
183 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
GTTAATCTTGTTTCTTATAGCAA
3' ss Score
6.68
Exon sequences
Seq C1 exon
GATCCAGCCCCTATCATTTCTATGGAAATTTCTTCAAAGAGA
Seq A exon
GTAAGTTGCTTGGGTGTCTAAGTCTTTTCTGTTTGCTGCTTAAAACCAAAGTGTTTAAGAATGTCAAGACGTGATTTATGTAAGGAAAAAAGGTTGTTCACCATTTTCTATTATTATTGTACCACAGAGGGGCTATCTCAGGGAATTCTATAAATTCTGCTCTGTTAATCTTGTTTCTTATAG
Seq C2 exon
CAACAGCTTTACATTGGATCAGCCTCTGCTGTGGCACAAGTCAGATTCCATCACTGCGACATGTATGGCAGTGCTTGTGCTGACTGCTGCCTGGCTCGAGACCCGTACTGTGCCTGGGATGGCATATCCTGCTCCAGGTACTACCCAACAGGTGCACACGCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000063531-Sema3e:NM_011348:13
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(2.9=100)
A:
NA
C2:
PF0143720=PSI=PU(66.7=67.9)
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:
ATCCAGCCCCTATCATTTCTATGGA
R:
GCGTGTGCACCTGTTGGG
Band lengths:
202-385
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: