MmuINT0141105 @ mm9
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
chr3:88255610-88256004:-
Coord C1 exon
chr3:88255942-88256004
Coord A exon
chr3:88255709-88255941
Coord C2 exon
chr3:88255610-88255708
Length
233 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAC
5' ss Score
7.2
3' ss Seq
ATTTCTTTGCTTCTCCATAGACA
3' ss Score
10.52
Exon sequences
Seq C1 exon
ATACCCTGGCCAGCCAGTGAGAGAAAAAAGACCGAATGTGCCTTTAAGAAGAAGAGCAATGAG
Seq A exon
GTAAACGCAGGTGGGGGCAGAGGGTGGGCGACAGAACCCTGGTGTCAGAGACCATCCCTGGTGACCACAGGGGTGGGGGCAGGAGGACCTGTTCCTGTGATTATCCAGTGGGTCATGTTCTGTCAAGTTTCTTGATCTCAACCCTCCTCTCCACTGGGGATGGGGGAGCATCCTCTAAGACCCCAGGAGGCGGGCAATCGGCCTGATAGCCTGATTTCTTTGCTTCTCCATAG
Seq C2 exon
ACACAGTGTTTCAACTTCATTCGAGTCCTGGTCTCTTACAATGCTACTCACCTCTATGCCTGTGGGACCTTTGCCTTCAGCCCTGCCTGTACCTTCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064-Sema4a:NM_001163489:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(11.7=100)
A:
NA
C2:
PF0140314=Sema=FE(18.7=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:
TGGCCAGCCAGTGAGAGAAAA
R:
AATGAAGGTACAGGCAGGGCT
Band lengths:
156-389
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: