MmuINT0141144 @ 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
chr13:51805281-51806725:-
Coord C1 exon
chr13:51806569-51806725
Coord A exon
chr13:51805504-51806568
Coord C2 exon
chr13:51805281-51805503
Length
1065 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGC
5' ss Score
8.99
3' ss Seq
GCGGTGCTTTTACCCCACAGTGT
3' ss Score
8.47
Exon sequences
Seq C1 exon
GAACAATGTGGGTCTGTCAGCGGTGTGCGCCTACACACTGGCCACGGTGGAGGCAGTCTTCTCCCGTGGAAAGTACATGCAGAGTGCCACAGTGGAGCAGTCTCACACCAAGTGGGTGCGCTACAATGGCCCAGTGCCCACTCCCCGACCTGGAGCG
Seq A exon
GTAAGCAGGGTCTCGAGCTCTGGGGAGGGCTCATCTTCTCTGGATCTCAAGGCCCCCCAAGCATGAGACCACACAGATCCTAGTGCATCCCGGCAGAGGGTTGCATGGCAACAGGAATCTGGGTGCTGGGCTGAGTAGCTGCCGGGCCTGGGGTGAACAGTGAAGCTGTTCCTTTCTGATCTCCTCTGTGTTGGGTAGCAGGCCTCACTGCATGCTGCCCGGACGAGAGAGTCTACCGCCGGGCTCCTTTGAGAAGTGGACATTGCACAATGGCAGGCTTGCTTCATTTCCCATTTCCTGCAGACAAAAAAAACCTGTTTGTCAGCCTGGGCTGTCTCCTGAGGCAGCCTGTCCACTAGATAACAGGAATCATATTCTTTCCTCCTAGATACAGTAAATTAGTAAAGAAAATTCTAGGGTTGCCTGCATATTGTTGCCACGTGGTGGATGGGTGTGGGTATGGAGGGGCTTGGCTCTTGAAGCTCTCCCAGGATGGACTGTTCTGTGAGTGTCTGGCCTCGACACCTGGTTATTCTCATAACTCATAATTCAGGTGTTCAGTAAAACATGGCTAGGGAGCTGGGACCAAAAAAAAAAAACTCTTTACAACTTTTTTTTCTTTTGTGCTACCCAGAATCTGGCTTTCTCTCCTCTCTCTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTCTGTGTGTGTGTGTCTGTATAACAATATTTAACAAGCTTCCTTTGGCATACTTTCTTCTCATAGAAAAGCTGTGAAATGAGTGCTTTTTAATCTGGAAGTTTGCTAAGTTTTTTCATTGGCTACTAATTCCTCTACTGATCCTGAGACAATTATGTCCCGTGGCTTTAAAAGCACAGCTCTTTGTCTCTGGGGAGGTCACCTTAGCCCCTGTTACTCTTTGGAGAAGTGTGACCATGGCCCTCCAGGGCTTCTCTTCTGTGTGCTCAGTTGAAGCTAAGTGGGCATGTGACCGCGGTGCTTTTACCCCACAG
Seq C2 exon
TGTATCGACAGTGAGGCCCGGGCAGCCAACTACACCAGCTCCTTGAATCTCCCAGACAAAACACTGCAGTTTGTAAAAGACCACCCTTTGATGGATGACTCAGTGACCCCGATAGACAACAGACCCAAGCTGATCAAAAAAGATGTAAACTACACCCAGATAGTGGTAGACAGGACCCAGGCCCTGGATGGGACTTTCTACGACGTCATGTTCATCAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021451-Sema4d:NM_013660:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.094 A=NA C2=0.013
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.0=100)
A:
NA
C2:
PF0140314=Sema=FE(17.1=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:
CAATGTGGGTCTGTCAGCGG
R:
GTCGTAGAAAGTCCCATCCAGG
Band lengths:
358-1423
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: