MmuINT0141100 @ mm10
Intron Retention
Gene
ENSMUSG00000028064 | Sema4a
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Source:MGI Symbol;Acc:MGI:107560]
Coordinates
chr3:88438183-88438561:-
Coord C1 exon
chr3:88438443-88438561
Coord A exon
chr3:88438341-88438442
Coord C2 exon
chr3:88438183-88438340
Length
102 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCCTCCATCTCTTTGCCCAGGGT
3' ss Score
7.9
Exon sequences
Seq C1 exon
CCACGGGGTCCCTGCACAAGGCTGTGGTGCCTCAGGACAGCAGTGCTTATCTCGTGGAGGAGATTCAGCTGAGCCCTGACTCTGAGCCTGTTCGAAACCTGCAGCTGGCCCCCGCCCAG
Seq A exon
GTGAGAAGGGACCTGAACAGAACACAGTCCTCCTGTGGAGAACAGCTGGGGAGCCCGGGCCAGGGTGCTAGGGCTCCTGACACCCTCCATCTCTTTGCCCAG
Seq C2 exon
GGTGCAGTGTTTGCAGGCTTCTCTGGAGGCATCTGGAGAGTTCCCAGGGCCAATTGCAGTGTCTACGAGAGCTGTGTGGACTGTGTGCTTGCCAGGGACCCTCACTGTGCCTGGGACCCTGAATCAAGACTCTGCAGCCTTCTGTCTGGCTCTACCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064:ENSMUST00000029700:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.100 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.0=100)
A:
NA
C2:
PF0143720=PSI=PU(61.4=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTGCCTCAGGACAGCAG
R:
AGACAGAAGGCTGCAGAGTCT
Band lengths:
242-344
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