MmuINT0141271 @ mm9
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:94971546-94972022:+
Coord C1 exon
chr3:94971546-94971602
Coord A exon
chr3:94971603-94971920
Coord C2 exon
chr3:94971921-94972022
Length
318 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGG
5' ss Score
9.2
3' ss Seq
TAGAATTTTGGGTTCTCTAGGAC
3' ss Score
6.8
Exon sequences
Seq C1 exon
TTTCTGACATGGAGGAGTCAAGATATGGAGAACTGTGCAGTCCGGGGAAAGCTGACG
Seq A exon
GTGAGGAGTGGAGTGTAATTGGAGGGAAGGCGAGGACTGCCTTCAGGTAGTGCGCCGCCATGACTACTTCTTACTCCTTTTCTATCTATCCCAGCCCAAAGGGAAGAGAATTCATCCTTTTTAGTTCCCTTTATATATCCCAGGAAAAGAAAAGGGAGGTTCGGAGAGGCCAGAGAGCTTGCTGGAGGCTGAGGGCTAGTTAATAGCTTGAGACTTAGCCACATTGCTCTGACTGGCTCAAAAGTAGTAGTGTTACTTTCTGTGACCCCTAACTTCAGTTCCAGGCCTGTCACTGACCTAGAATTTTGGGTTCTCTAG
Seq C2 exon
GACGAATGCTACAACTACATCCGTGTTCTTGTTCCCTGGAACTCGCAGACACTTCTTGCCTGTGGAACAAATTCCTTCAGCCCTATGTGCCGCAGCTATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777-Sema6c:NM_011351:4
Average complexity
IR-S
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(14.2=100)
A:
NA
C2:
PF0140314=Sema=PU(1.5=83.3)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: