MmuINT1030846 @ 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
chr9:107605447-107607092:-
Coord C1 exon
chr9:107607034-107607092
Coord A exon
chr9:107605588-107607033
Coord C2 exon
chr9:107605447-107605587
Length
1446 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CTCCACCCACTCTCCTGCAGCAA
3' ss Score
7.86
Exon sequences
Seq C1 exon
CTCCTGGGACCTGAGCTTGCTGTGGAGTGTACAGTCATCCCTTAGCTGTGGAGGGACAG
Seq A exon
GTAAGGACCTGGGGTGCCTGGCCCACCATTCCTGCTGCCTGCTGCACAGAACTGTCAGGGATGGTCTCGGCTGATTCTTCCTGCTTTGCCTTATCTTAGTGACAGGTTTCTGGAACTATATCCTTGGGGCACCCTTCACCTTGAAACCCAGAAGGAGAGGGCCATCTTTACCTGCCCAACCCTTGCTCTCATTCCACTCCTGCGGGGCCACCGGTCTCCAGCCAGTCCCAGCTGCCTGTGCCGGTCACCCGATCCACCCTGTAGCCCTGCAAACTTTATGGTATTCGGGGCGGTGGCTGGCCTGGTGGAGGCGGGGGCTTTTACTTAAAGGAACCGTCAGAGGGTGCCCTGTGGGCCCTAGCCTTCTTCCCTTCCCCAGGACAAGAGGGGTCAAGGTGGGAGACCCCTGTCAGAGTTCTTGGTGGAGTGTGGGAAGGCAGCCTTGTCAGCCTCACAGACTTCTAGTACCTGAGAAAAGGTGCAGGCAAGTGTGACCAGATGAAAGGAAAGGGGGGCAGGGGAGAATCGGGTCCTGGCCTGGGAGGGGTCCAGGAACTGGTGTGTGTGTTGGGAGGGGGGGGTAGAAAGTGAATTGAGGGGAGAGCTTCAACCCAGCCAGCAGCTAATTTCCTTCTTTAATCACACTGGGACCTTGGCTCGAGTGCCCCACTGTCCTGTGTACTTCTGTAAGGGAGAGCTGTAGGAGCCAGAGCCTGGATCTACCTGAGTGTGCCAGGCAAGGCGTCTGGTTCAGTGGAGGGGCTCAACAATGACAGGGAAACTTAAGACCCTGAAATGGCAGGGACTTTGAGGGCAAATAATTGTTCCACCTGGAGCTTTAATTTAAGTGAGCCAGAACCGTCCATGGGCCTCAGTCCTCGCTTGGGTCTCTGTGTGCCCGGCTCCTTCTAACCCTCAGGCTACAGAGAGGAATCGGTCACAAAAACTGGGTCTGCTGGATTTGGCCTGAGTCTGGATCAGGGCCCTGAGAAGAATAGATGGCACTTGTCAACGGAAGCGATCGATGCGGCTTTTGTGTTCACTTGCATGTCCGCTGTGCCTGCACACACACCTGCCCATGTGCACATATGTGATTCATGTGCTGAACAGGCAGATTTAATGCTGGCACACACTTGACTAGATGTATACACACGGCACCGCGTGTTAAGTATACAGATTTGTACGTCAGCTTATATCTACATAGGTGTGACACCTGCTTGCTCATAGACATGTATGCATATGGACACGCACACACGCTCATGTATACATACATGTGTTCGGGTATGTGTGTTCACAAAGGGACCCTCAGAAATATATTCATATCCGTAGTCACCCACAACCTTGGATCCAGTCCCCAAAGTGCCCCTGCATTTCCCTGCCTGCCGGTCTGTGGGTACACGGCCACCTCCTGAGGCCTCGCCCCCCCCTCCACCCACTCTCCTGCAG
Seq C2 exon
CAACTGCTTTGCTCTTTGCACTTGGTGCCCTCTGGAATGACCACAGGATCTGACTCTCATCTGTCGGCTCTTCGCCCTTTACTGCCTGGGGACCTTGTCCGCATCATCAGTATCCTTGTCTCTGCCCCAGGCTGGCATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057969:ENSMUST00000102532:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCTGGGACCTGAGCTTGC
R:
CCTGGGGCAGAGACAAGGATA
Band lengths:
190-1636
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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