MmuINT0141231 @ mm10
Intron Retention
Gene
ENSMUSG00000019647 | Sema6a
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Source:MGI Symbol;Acc:MGI:1203727]
Coordinates
chr18:47281120-47281432:-
Coord C1 exon
chr18:47281292-47281432
Coord A exon
chr18:47281201-47281291
Coord C2 exon
chr18:47281120-47281200
Length
91 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
CGGTCATCCTTCTTCTACAGAAC
3' ss Score
9.45
Exon sequences
Seq C1 exon
GTGCAGCTATGATGGTGTAGAAGACAAAAGGATCATGGGCATGCAGCTCGACAGAGCGAGTGGCTCACTCTATGTTGCATTCTCTACTTGTGTGATCAAGGTGCCTCTTGGCCGCTGTGAGCGACATGGGAAGTGTAAAAA
Seq A exon
GTATGTATTCTTTTGCCTTACTGACATTTCGAAAATCCATTAGCAGATAGAAAGCAGTCCTGGTTAGCTGACGGTCATCCTTCTTCTACAG
Seq C2 exon
AACCTGCATCGCCTCCAGAGACCCGTATTGTGGGTGGGTAAGGGAAAGTGGTTCCTGTGCCCATCTGTCACCCCTTAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000019647:ENSMUST00000019791:14
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=PD(3.4=31.2),PF0143720=PSI=PU(13.8=18.8)
A:
NA
C2:
PF0143720=PSI=PU(41.4=92.3)
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:
AAAGGATCATGGGCATGCAGC
R:
ATGGGCACAGGAACCACTTTC
Band lengths:
179-270
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