MmuINT0141106 @ 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
chr3:88451345-88451786:-
Coord C1 exon
chr3:88451688-88451786
Coord A exon
chr3:88451451-88451687
Coord C2 exon
chr3:88451345-88451450
Length
237 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
CAGCCTCTTCCCCCCTCTAGGAA
3' ss Score
11.03
Exon sequences
Seq C1 exon
ACACAGTGTTTCAACTTCATTCGAGTCCTGGTCTCTTACAATGCTACTCACCTCTATGCCTGTGGGACCTTTGCCTTCAGCCCTGCCTGTACCTTCATT
Seq A exon
GTGAGTTGTCTGACCCCCACTACCCCCGCTTGCTCACAGCTCCCCCCCCCCCACCTCTCTTCACACCCATCCCAGCCTGTCCTCCGTAGCTTTGGGAATCTCTGGTCCCTGCGGACCCTCGTAAGATTCCCAGCCCCAGACCAATTTCCCTCTCTGTCCCTTTTACTTCCTCATGCTCCTCATCTCTCAGACGTGCGACCCTGGCATTCTGGGCTCCCAGCCTCTTCCCCCCTCTAG
Seq C2 exon
GAACTCCAAGATTCCCTCCTGTTGCCCATCTTGATAGACAAGGTCATGGACGGGAAGGGCCAAAGCCCCTTTGACCCTGTTCACAAGCACACAGCTGTCTTGGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064:ENSMUST00000029700:5
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=FE(18.8=100)
A:
NA
C2:
PF0140314=Sema=PD(12.4=76.5)
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:
ACACAGTGTTTCAACTTCATTCGA
R:
CGACCAAGACAGCTGTGTGC
Band lengths:
205-442
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