MmuINT1030857 @ mm10
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:95163432-95164513:+
Coord C1 exon
chr3:95163432-95163521
Coord A exon
chr3:95163522-95164338
Coord C2 exon
chr3:95164339-95164513
Length
817 bp
Sequences
Splice sites
5' ss Seq
GGGGTGGGT
5' ss Score
3.34
3' ss Seq
TTTCTGTCTCCTTACTCCAGGGC
3' ss Score
10.53
Exon sequences
Seq C1 exon
AGGCAGCCTGATGAGGGAAGAAGGGGAGAGCGGGGCACGTTCAGCCATTTCTTCTCACCCGTCCTTTCTATCCTTCGTTCAGCATAGGGG
Seq A exon
GTGGGTCTGCTCTTCTCCCCACGATGAGAGCATGCATTGGTTCTTAGGAGCCAGGGAGGCAACAGGGGGCTCCGGGCTGGGAGGGGGCCCAGTGGTCGAGGAGACAGCTGCAGCCAGAGCTAAATTTAGCCTCTGATCTGGCTTTGATGCAGATTCATTTTTGGCTAAGACAGCCCCTCCATGCACACCCCATCCCTCCCTGCCCAGCTTCTTCCTCAGCCATGGGAACGGCCCCTGAAGTATGAGCTTCGGCTGGGTCAGTGACCCCCAGGCTGTCTGTCCCTCTCCTTCTGTTCTTTCTCAGCCTTAGACAGGACCATGGCTGCCGCACAGCTGCCTTTGCCTGGGCGCAGTGCCTACAGCACTCCCAGGGTGCTGTGGGGGTCTGTGAGGGGAGGGGAAACAGACTTGGTGCCCTCTTCCTTCTCCAAGTGCCAAGGAGTCACTATTTATAATTTTAAGGCTTAAGTGTCTAATTATAGCTGAGAAGGGGTTAGCACAAGGGGGGCCAGGAGGTGTCACCTACTGAGTGTCCCAGACCTAGGCAGGAGAGAGGAAGAAAGGCTGGGAGGGGCAGAGGATTTGTGCTGTCCTTACCTGGGGTCACACCAGCAGGCAGCACACCAACCAGTTTGGGCCAGTTGGAGAGGGAAGGGCCTTGAGTGACAGACAGTGACAGCTGGCTGGGAGTGAGGCAGAGATGGCTCTTTGCCCCACCCCATAGGGTCTTCTGGGGATAGACCTGGGGAGGAGTCTGCCTGCAACAAGGGTAGAGAGAACTTAGTCCCTTCCCCCCCTTTCTGTCTCCTTACTCCAG
Seq C2 exon
GGCCGGCACATGGGTGAGGGGGTACCCCCTGGGGCGTGAGCTGCCCCGCACAGGATGCCCCGTGCCCCCCACTCCATGCCCCTGCTGCTCCTGCTGCTGTTGCTGTCATCGCTCCCCCAAGCCCAGGCTGCCTTTCCCCAGGACCCCACCCCTCTGTTGACCTCTGACCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777:ENSMUST00000090823:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.105
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGCCTGATGAGGGAAGAAG
R:
TTGAAGGTCAGAGGTCAACAGA
Band lengths:
262-1079
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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