MmuINT0141143 @ mm9
Intron Retention
Gene
ENSMUSG00000021451 | Sema4d
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:MGI Symbol;Acc:MGI:109244]
Coordinates
chr13:51806569-51806993:-
Coord C1 exon
chr13:51806818-51806993
Coord A exon
chr13:51806726-51806817
Coord C2 exon
chr13:51806569-51806725
Length
92 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
TCACGGATTCCCCTCCACAGGAA
3' ss Score
9.55
Exon sequences
Seq C1 exon
GGCGACCAGGGCGGCCTGCGGACTTTGCAAAAAAAGTGGACCTCCTTCCTAAAGGCCAGGCTGATCTGCTCCAAGCCAGACAGTGGCCTGGTCTTCAACATACTTCAGGATGTGTTTGTGCTGAGGGCCCCGGGCCTCAAGGAGCCTGTGTTCTATGCGGTCTTCACCCCACAGCT
Seq A exon
GTGAGTTCACTTGTGAGTCCCTTGGCAGTTGGGGCCTGGTCACCCTGACGACCTCCTGCCCTCCTGACACTCTCACGGATTCCCCTCCACAG
Seq C2 exon
GAACAATGTGGGTCTGTCAGCGGTGTGCGCCTACACACTGGCCACGGTGGAGGCAGTCTTCTCCCGTGGAAAGTACATGCAGAGTGCCACAGTGGAGCAGTCTCACACCAAGTGGGTGCGCTACAATGGCCCAGTGCCCACTCCCCGACCTGGAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021451-Sema4d:NM_013660:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.094
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(13.4=100)
A:
NA
C2:
PF0140314=Sema=FE(12.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAGTGGCCTGGTCTTCAAC
R:
CTTTCCACGGGAGAAGACTGC
Band lengths:
171-263
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: