MmuINT0141000 @ mm9
Intron Retention
Gene
ENSMUSG00000057969 | Sema3b
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:MGI Symbol;Acc:MGI:107561]
Coordinates
chr9:107503159-107503833:-
Coord C1 exon
chr9:107503689-107503833
Coord A exon
chr9:107503379-107503688
Coord C2 exon
chr9:107503159-107503378
Length
310 bp
Sequences
Splice sites
5' ss Seq
ATGGTGCGT
5' ss Score
8.27
3' ss Seq
TGACGCACCTTGCCTTCTAGTGC
3' ss Score
6.98
Exon sequences
Seq C1 exon
TGGTGTCTTCCAGGGCTCTGCTGTGTGCGTGTACAGCATGAACGATGTGCGCCGAGCCTTCTTGGGACCTTTTGCTCACAAAGAGGGGCCTACACACCAGTGGGTGTCCTACCAGGGTCGTGTCCCCTACCCAAGACCTGGCATG
Seq A exon
GTGCGTTGCTAGGGACCGCTTGCAGTAATCCACTTCAAAGTCTCAAGGGTGGAGAATTTGACTCAGCCCGGCCCTGGGAGTTTTGCTGGGGGTGAGGGTGCAGTGTGATTCCGTCCTTTTGGAAGGGTGGGGAAATGTCACCATCATAAAAGATAGAGCTGTGCCCCTCAGAGCCTGAGGTTCGCCAAGGAAAGGCTCAGATAGATACTTAGGGTCCTTGTCACATCTTACCTTTCACGATCCCAGAGGCTTTGAACGGAGGGCTGACCACAAAACCCTGTATCTCTGCCTGACGCACCTTGCCTTCTAG
Seq C2 exon
TGCCCCAGCAAGACCTTTGGCACCTTCAGCTCCACCAAGGACTTCCCAGATGACGTTATCCAGTTTGCTCGGAACCACCCTCTCATGTACAACCCAGTCCTGCCCATGGGGGGGCGCCCTCTCTTCCTACAAGTGGGAGCTGGGTACACCTTCACCCAAATCGCCGCAGACCGAGTAGCAGCTGCCGATGGACACTACGATGTTCTCTTCATTGGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969-Sema3b:NM_009153:11
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(10.8=100)
A:
NA
C2:
PF0140314=Sema=FE(16.5=100)
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:
TGGTGTCTTCCAGGGCTCTG
R:
CATCGTAGTGTCCATCGGCAG
Band lengths:
347-657
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: