MmuINT0141135 @ mm10
Intron Retention
Gene
ENSMUSG00000026121 | Sema4c
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:MGI Symbol;Acc:MGI:109252]
Coordinates
chr1:36553926-36554400:-
Coord C1 exon
chr1:36554252-36554400
Coord A exon
chr1:36553989-36554251
Coord C2 exon
chr1:36553926-36553988
Length
263 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGA
5' ss Score
7.4
3' ss Seq
TGTGTCTGTCCAATCCTCAGATC
3' ss Score
9.11
Exon sequences
Seq C1 exon
AGCTGGTCACAGTAGTGAGGCGGTTCTCCCAGACAGGCATCCAGGACTTCCTGACACTGACCCTGACAGAACATTCTGGCCTTTTATATGTGGGGGCCCGAGAGGCGCTGTTTGCCTTCAGTGTAGAGGCTCTGGAGCTGCAAGGAGCG
Seq A exon
GTGAGAGGTGGGGCAGTGGGAGGCACTCAGAGGGGAGAGGGAAAGGACTCAGGGTGTAGCCTGTGCAGGCTGTCCCTCAGCCCAGCTCTCTTGGGGTGTCAAGATTAGCAATTGCTTTCTGCTCCTGGTTTCTGCTAGTTGGGGTGGTTTGGGGCTTCTGTCAGAATGGGGACCAGGCGTCATCAATGGTGTAGCTTAAGGGGTGTTTGCAGCACACTTAGCGCAGACCTGTGACATTGCTGATGTGTCTGTCCAATCCTCAG
Seq C2 exon
ATCTCTTGGGAGGCTCCAGCTGAGAAGAAAATTGAATGTACCCAGAAAGGGAAGAGCAACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026121:ENSMUST00000114991:3
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=PU(7.7=66.0)
A:
NA
C2:
PF0140314=Sema=FE(4.7=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:
ACAGTAGTGAGGCGGTTCTCC
R:
CTGGTTGCTCTTCCCTTTCTGG
Band lengths:
204-467
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