MmuINT0141280 @ mm9
Intron Retention
Gene
ENSMUSG00000027200 | Sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:MGI Symbol;Acc:MGI:2387661]
Coordinates
chr2:124483707-124484301:+
Coord C1 exon
chr2:124483707-124483838
Coord A exon
chr2:124483839-124484145
Coord C2 exon
chr2:124484146-124484301
Length
307 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
AGTTGCTGTTTTCGTTTCAGGCC
3' ss Score
10.02
Exon sequences
Seq C1 exon
CATTCCTGGTTCTGCAGTCTGTGCCTTTAGCATGGACGACATTGAGAAAGTGTTCAAAGGGCGGTTCAAAGAGCAGAAAACCCCAGACTCTGTTTGGACAGCAGTTCCCGAAGACAAAGTACCAAAACCAAG
Seq A exon
GTAAAGAAAAGAGGCAAAGGTTTGTTTTATTGAACAGCCTTCCTCCCCCCTGAACATCAGGACCATCTTAATATCTGTCATTCAACCTCCCACCCCAGCAGGGCATCCCTCCGAGGCCAATACATGTTATCCTGTTATACCCTGTGCATTTGGCTCTGCAAATGCCCATAAAATTCTGGGAAATGACATTACTGCTCTAGTTTTTCTGTCCCTCCTTCCTTTCTTGACCTCTTCTCTACAGAATGTGTGCTTACCCCTTAAATCCAGCATGCGAGAAAATGATCAAAAGTTGCTGTTTTCGTTTCAG
Seq C2 exon
GCCTGGCTGTTGTGCCAAACACGGCCTCGCAGAAGCTTACAAGACCTCCATCGACTTTCCAGATGACACCCTGGCTTTCATCAAGTCCCACCCGCTGATGGACTCTGCCGTCCCACCCATTGCCGATGAGCCCTGGTTCACAAAGACACGGGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027200-Sema6d:NM_199239:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.4=100)
A:
NA
C2:
PF0140314=Sema=FE(12.2=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:
ATTCCTGGTTCTGCAGTCTGTG
R:
TGACCCGTGTCTTTGTGAACC
Band lengths:
286-593
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: