MmuINT0141006 @ mm10
Intron Retention
Gene
ENSMUSG00000057969 | Sema3b
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:MGI Symbol;Acc:MGI:107561]
Coordinates
chr9:107598217-107599716:-
Coord C1 exon
chr9:107599577-107599716
Coord A exon
chr9:107599176-107599576
Coord C2 exon
chr9:107598217-107599175
Length
401 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
GTCCCTTCCCTCACACACAGGTG
3' ss Score
9.89
Exon sequences
Seq C1 exon
ACTCTTCTCACTCTGTGCTGCTGGAGAAGAAGGTGTTGGGTGTGGAGAGCGGCAGCGCGTTTCTGGAGTGTGAGCCCCGCTCGCTCCAGGCGCATGTGCAGTGGACCTTCCAAGGTGCAGGGGAGGCAGCTCACACCCAG
Seq A exon
GTGTGCCTTGCTCCACCCTTCCTAACCAGGCCCATTTAAGAGAAGCTATGCCCTGCCTAAGGAGGCCTTTGGCCTGTACCTCATACCGTTCAGTGAGTCAGATTCCCTTATCATAGTTTGTCTCATCCTCTACTGTCCTTAGCTCCACAACCTAGTGATGCCCCAACTGTGCCCACCTAGACTCCTGACCCACCCTCTACCATCTGGAGAGAGAAAGCCCTCAACCCCCCACGCGCGCACTGAGGTTTCTAGTCTACCCAATCCCCCACTCACCTAGATGGACTCATCCTCCGAAGGCTAAGTTCACATACCCTTTAAAGTGAGTCAATGCCAGCACCCATTTTCCTTGTCCACCTTTGGCTTCCAATGATCCTTGTTTCTGTCCCTTCCCTCACACACAG
Seq C2 exon
GTGCTGGCTGAGGAGAGAGTAGAGCGCACTGCGCGGGGGCTGCTGTTGCGGGGGCTGCGGCGCCAGGACTCTGGCGTGTATCTTTGCGTCGCGGTTGAACAAGGCTTTTCACAACCACTGCGTCGCCTGGTGCTGCATGTGTTGAGTGCGGCGCAGGCTGAACGACTGGCACGGGCAGAGGAAGCAGCCGCTCCTGCACCTCCTGGCCCTAAACTCTGGTACCGGGACTTTCTGCAGTTGGTGGAGCCAGGCGGTGGCGGAGGTGCAAACTCCCTGCGAATGTGCCGCCCGCAGCCCGGGCACCACTCTGTGGCAGCAGATTCACGTCGTAAGGGTCGCAACAGACGGATGCATGTCTCTGAGCTCCGTGCTGAGCGTGGACCACGTAGTGCAGCTCACTGGTGACTCGGCTGTCCCCACAATGGGACGAGGCTGAATATGACACTCCAAAGAGGGGCAGACAGATGCCAGGAAGACAAATGAGTTATGGCTGGGCCACACTGAGGTCCTTGGGCCAACAGAGACACCTAACCCTTACATAGGCCCTGGCCAAAGGGTAGCTTATTTATTAACAAGATAACCCGTGGATGTAGCCTCAAAGAGTGGCCTAAGCTCAATTCAGGATCTAACCAGGAGGGAGGGGACAGAGACGTGGGGTTCCAGAGTGGACCAGGACCAGAGAGTTGTCTTGGGTGGCAGCCCTGGGGAAAGAATTCTCTTTCTTGGGCAGCAAGCAGCAAGCTGTGAACAGATTAGACCGTTGGGTATGGGGTGAGGCAGGCCAACTGTACTAAAGTAACGCAATAAACACATTATCAGCTGACATTGGAATGGCCCCAGCAGACAACAGGTAGTCCTAGACCTTGCTGGGGGCTCTTGGGTATCGCCCTAGGGGTCTCAAGACCTGCATTTTCCTCATCCAAGAATGCTAAAGTGAAGATTAAACGTGTTAGTAGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969:ENSMUST00000102532:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.418
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(14.1=19.1),PF0768612=V-set=PU(48.9=97.9)
A:
NA
C2:
PF0768612=V-set=PD(48.9=34.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTGCTGCTGGAGAAGAAGG
R:
AGAGTTTAGGGCCAGGAGGTG
Band lengths:
345-746
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