MmuINT0141257 @ mm10
Intron Retention
Gene
ENSMUSG00000001227 | Sema6b
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:MGI Symbol;Acc:MGI:1202889]
Coordinates
chr17:56129973-56130796:-
Coord C1 exon
chr17:56130706-56130796
Coord A exon
chr17:56130093-56130705
Coord C2 exon
chr17:56129973-56130092
Length
613 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCCTACCCCGCAATGTCCAGATG
3' ss Score
4.42
Exon sequences
Seq C1 exon
ATGGACACACTGCAGCTTCTTGGTGACAGCATCAGCGGTATGGCCCGCTGCCCCTATGACCCCAAACATGCCAATGTCGCCCTCTTCTCAG
Seq A exon
GTGAGTGGTCTCTGCTGTTGACATGTCCACTCCCAAGAGAGCTAGTTTCCATTTCTAAAATTCTGGTCACTCAGAGGCATCTGGGAAATGGGCAGAATCTAAGAGGACCTGGTCAGGGTCAGGGTCAGGATGGTGGCTAGTCTGAGCTGGAGGAAGAAATTTAGCCTGGGATCAAGGTTCAACTGGATTTAGTCTCATCCTGTATGAGGACTCAGCCTGGGATTCAGGCTCATTCAGTTGTAGGATCAGGATAGGATCCAGGCTCAGCTTCTCGACAGTCCTCACTAGGCTGAGGTTCTAATTTTTGCTCCTACCCCCTCTGGTCTTTCTATTATGATTGTTGTGGTTGTTGTTGTTGTTGTCGTCGTTGTCGTCTGGACCTTCTCTTATTGTTGCTGTTGTTATGATTTTCTGAGACAGGGTTTCTCTGTGTAGCCCTAACTGTCCAGGAACTCACTCTGTAGACCAGGCTAGCCTCAAACTCACAGAGATCCACCACCTTTGCCTCTTGAGTGCCGGGATTCGGGCTTGTGCTACGATGCCTGGCTTCTCTCTCGGCCTTCCCAGTCTAATCCCAATCTGCTTGCCTCACACCCTACCCCGCAATGTCCAG
Seq C2 exon
ATGGGATGCTCTTCACAGCCACGGTGACTGACTTCCTAGCCATCGACGCTGTTATCTACCGCAGCCTTGGGGACCGGCCCACACTGCGCACAGTAAAGCACGACTCCAAGTGGTTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001227:ENSMUST00000001256:7
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(7.1=100)
A:
NA
C2:
PF0140314=Sema=FE(9.5=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:
TGGACACACTGCAGCTTCTTG
R:
AAACCACTTGGAGTCGTGCTT
Band lengths:
206-819
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