MmuINT0141121 @ mm10
Intron Retention
Gene
ENSMUSG00000030539 | Sema4b
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B [Source:MGI Symbol;Acc:MGI:107559]
Coordinates
chr7:80212796-80213325:+
Coord C1 exon
chr7:80212796-80212959
Coord A exon
chr7:80212960-80213262
Coord C2 exon
chr7:80213263-80213325
Length
303 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TTTCCCTCCTCCTTCCACAGCTG
3' ss Score
12.5
Exon sequences
Seq C1 exon
GCTCTGAAGAAAGGCTGATTAGAAAATTTGAAGCTGAAAACATCTCCAACTACACGGCCCTTCTGCTGAGCCAGGATGGCAAGACGCTGTATGTGGGGGCCCGAGAGGCCCTCTTTGCACTTAACAGCAACCTCAGCTTCTTGCCAGGCGGGGAGTACCAAGAG
Seq A exon
GTGAGAGACATCTGAGGATGGCTAGGGGTGTGTGTTTGTGTGTGTGTGTGTCTGTGTGTGTGTCTGTGGTGTGTGTGGTGTGTATGTCAGGGAGAGGTGTGTGTGTGTGTGTGTGTGTGTTAGTGTGTGTCAAGGAGAGGTATGTGTGAGTCTGTGTATGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTTTGGGAAGCTGGCCTGCTGGTCAGGATGCTCTGGACGGGACAGGACAGGAGTGTGGCTCTGTACACCCTCTGTGCCCTTGCACACCTATTTCCCTCCTCCTTCCACAG
Seq C2 exon
CTGCTGTGGAGTGCAGATGCTGACAGGAAGCAGCAGTGCAGCTTCAAGGGCAAGGACCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030539:ENSMUST00000032754:3
Average complexity
IR
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=PU(35.2=67.3)
A:
NA
C2:
PF0140314=Sema=FE(19.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCTGAAGAAAGGCTGATTAGA
R:
GGTCCTTGCCCTTGAAGCTG
Band lengths:
222-525
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