MmuINT0141242 @ mm10
Intron Retention
Gene
ENSMUSG00000019647 | Sema6a
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Source:MGI Symbol;Acc:MGI:1203727]
Coordinates
chr18:47291096-47292007:-
Coord C1 exon
chr18:47291888-47292007
Coord A exon
chr18:47291185-47291887
Coord C2 exon
chr18:47291096-47291184
Length
703 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
AAGTGCCCGTTTGTCTGCAGAGC
3' ss Score
7.01
Exon sequences
Seq C1 exon
ATGGAAAACTCTACTCGGCTACAGTGACTGACTTTCTGGCCATTGATGCAGTCATTTACAGGAGCCTCGGAGACAGCCCTACCCTCAGGACTGTCAAGCATGATTCAAAGTGGTTGAAAG
Seq A exon
GTGAGCAGTTAAAGGAAGAAAGGAAGAAATCGGGGAGGGGATACATATCTCATAAGAGATGTAGAGTCTGGATGGACCAGACTGTAGATTCACTTTAGTAATGGATTCTGACAGTCAAAACCATGTAAATTGCATCTTTTGCCTCAACTGATTTATTTACCCCTCTTTCTCCCCTCCCATGGGCTTCTGGAACACTAACATAACTACCAGTGCTGCGACAATAGACTACACCACATTCATCTTTCCCTGCCTCAAATTCATTTCAGAGTCCCCAATGAAACGAGCTGAACAGAACATTCATGGAAAGGAAGGGGGGTGGGGGGGTGGGGGGATCGGAGATGGTGAGGAACAGGAAAGGGGCTATTCATAGCCCTGAGTGAGCCAGCGTGATGGAGCAATGTGCAAAAACTCCTCTAGGCAATATGGACATTCCATTGTGGAAAATAAAACTACAGAGATTTGCAAAATGTACTTATTCTTCACTGCCGGTTTGCAAAGCTTGTGAAAGATGTAATTTGTAGGCTCAAGTGCCTTCTGAAATCACTAGCGCTTGCACTTCTGAAGTCATTAGAAATGGTTAGTGTTAACCACATGTCTAATAGCCCTACACTTCCAATTAATAACACGTCTTTGGCTACACTTGATTAAAATTCCCTTAACACTATGTGACATATCTCCAATTAAAGTGCCCGTTTGTCTGCAG
Seq C2 exon
AGCCGTACTTTGTCCAAGCCGTGGATTATGGGGACTATATCTACTTCTTCTTCAGAGAAATTGCAGTAGAATACAACACTATGGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000019647:ENSMUST00000019791:8
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(10.3=100)
A:
NA
C2:
PF0140314=Sema=FE(6.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAAAACTCTACTCGGCTACA
R:
TCCCCATAGTGTTGTATTCTACTGC
Band lengths:
206-909
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