MmuINT0141248 @ mm10
Intron Retention
Gene
ENSMUSG00000001227 | Sema6b
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:MGI Symbol;Acc:MGI:1202889]
Coordinates
chr17:56126217-56126632:-
Coord C1 exon
chr17:56126450-56126632
Coord A exon
chr17:56126367-56126449
Coord C2 exon
chr17:56126217-56126366
Length
83 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGA
5' ss Score
5.06
3' ss Seq
ACTTCACCCTGTGTGCCTAGGTG
3' ss Score
9.01
Exon sequences
Seq C1 exon
GCACCAGCTGACCCGAGTGGCTGTGGATGTGGGTGCGGGTCCATGGGGCAATCAGACAATAGTCTTCCTTGGCTCCGAGGCTGGCACAGTCCTCAAATTTCTTGTGAAGCCCAACGCCAGTGTCTCAGGGACCACAGGGCCCAGCATCTTTTTGGAGGAGTTTGAGACCTACCGGCCAGACAG
Seq A exon
GTCTGAGGATAAGCAGGGAGGTGGGAGTGGCTGGCTGAACAGCAGGCTGGGCGCACCAGCCTCACTTCACCCTGTGTGCCTAG
Seq C2 exon
GTGTGGACGACCCAGCAGTGCTGGTGAGTGGGGGCAGCGACTTCTCAGCCTGGAGCTGGATGCAGCCTCAGGGGGCCTGCTGGCAGCCTTCCCCCGCTGTGTGGTTCGTGTTCCTGTTGCCCGTTGCCAGCTGTACTCGGGGTGCATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001227:ENSMUST00000001256:13
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=FE(14.5=100)
A:
NA
C2:
PF0140314=Sema=PD(0.1=0.0),PF0143720=PSI=PU(16.1=17.6)
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:
ACAGGGCCCAGCATCTTTTTG
R:
ACAGGAACACGAACCACACAG
Band lengths:
167-250
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