MmuINT0141155 @ 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
chr13:51808048-51809174:-
Coord C1 exon
chr13:51809061-51809174
Coord A exon
chr13:51808200-51809060
Coord C2 exon
chr13:51808048-51808199
Length
861 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGT
5' ss Score
11.81
3' ss Seq
CCTGTGATGCCACCCCACAGAGC
3' ss Score
7.2
Exon sequences
Seq C1 exon
GGGGCGAGCTCTACTCTGGGACGTCCTATAATTTCTTGGGCAGTGAACCCATCATCTCTCGAAACTCTTCCCACAGTCCCTTGAGGACGGAGTATGCCATCCCGTGGCTGAACG
Seq A exon
GTAAGTGTGTGCTGCCAGCCTTGTGGGTCTACCATTTTATTCTTCCTCTAGCTGTCCCCAGGTCACAGGAGCCGGGGGAGGCGGGGGTGGGGTGGGGGTGGGGTGGCGGCTGCTCATGTCAGATCCTAGGCAGTGCTCTTTGGAACTGCTCAAGGCCCGCACCAGAGTAGCTGTCTTGCTCACTGCTAATAGCATTGTTTAAATCTGATTCTCTGACATACCCCACCCAGCCCCACTTCCACCCCGTCCCCCAAATGCAGTTTGGGAGACTTTAATAAAATGAAGCTCTAATGGGAAGTTGAGAATGTAGACACTGAGTTTGGGTGTCATCTTAGATGTGGAGACTCTTGGGTCTGGCCGGGTGGTGTTGAAATGTGTCTTTACTCCCAGACAAGCATATCAGGGTGTGGATGATGGGGGCCCTTTGTGGGTGTCTTTTTTGTGGGGATGCTGACCAGTGATGCAGGGCTTTTTCGAAGCCCCTTGATCTGGAGTCAGACCCTGGAGTCTGAGATCTGAGACAGCCAATTTCTCCTTGGGCCTCCCCAGGAGTCTGGAAATCCTTCGGGTGGCTGATTTGGCCCTTGTTTAAATTGGCAGATACTCTAGCATGCCAGACCAACCACCAGCAGAGAGGCCTCACCCGGCTTCCTCTGTGGCTATCTTGGTGAAGCTGAGGAGGGTGGCGGGCGTCCTCTGGGCCTGGAGTTCACAGTGTGGCATACATACTGTAGACGTCCTAGAAGGGAAGCTTCCAGGCTCTAAGGCTGCCCTTGCCAGCCTGCAGCACCCCAGGGAGCAGGTAGAGAGGTGGCTTGGTAGCTCCGTGTACAGAAACCATCCTGTGATGCCACCCCACAG
Seq C2 exon
AGCCTAGCTTCGTCTTTGCTGACGTGATCCAGAAAAGCCCAGATGGTCCGGAGGGTGAAGATGACAAGGTCTACTTCTTTTTTACGGAGGTATCCGTGGAGTACGAATTCGTCTTCAAGTTGATGATCCCGCGAGTTGCCAGGGTGTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021451-Sema4d:NM_013660:8
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(8.8=100)
A:
NA
C2:
PF0140314=Sema=FE(11.5=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:
CGAGCTCTACTCTGGGACGTC
R:
CTTGCACACCCTGGCAACTC
Band lengths:
262-1123
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: