MmuINT0141243 @ mm9
Intron Retention
Gene
ENSMUSG00000019647 | Sema6a
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Source:MGI Symbol;Acc:MGI:1203727]
Coordinates
chr18:47449630-47450838:-
Coord C1 exon
chr18:47450750-47450838
Coord A exon
chr18:47449848-47450749
Coord C2 exon
chr18:47449630-47449847
Length
902 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CTGTGTGCTTTTCCCTGTAGGTT
3' ss Score
13.14
Exon sequences
Seq C1 exon
AGCCGTACTTTGTCCAAGCCGTGGATTATGGGGACTATATCTACTTCTTCTTCAGAGAAATTGCAGTAGAATACAACACTATGGGGAAG
Seq A exon
GTAAGATGGGAGACTATCCCTGGCTCCATTGGTGACATTTTCAGAAACCTACTTTTGAACCAGCGTTGCTGTAAGTGATCTGGAAATGCAAATTGAACCCGATGACAACAGGGATGGCCAGAAGTGACAGACTAAGCTGTCTGGAAACCTGATCCACTTTTTCAGAGCAGTAACAAATTACAGGGAACCTCTTGAATAATCTCTACTGAAGATCTAACCAACAGATGTTTGGTTACTTTCCTACCGAATTCAAAGTGTTTTGAGATGTAGCTCCCAGGTATAATTTCTCCTCTTAATTGAGTTACTCCACAGAGACAATACATACCCAGTATCTCTAGGCAAACTGAGTCTTAGTTTTATTGCAGATGGTTTTATTGCAGAAAGAAACAGTTACAGGATGTTTATTTCTGTTACTTTATTTTATTTATTTTTTTTTACCAGACATCTGATCAAGGTCACTAAGTGAGAGGGCACAAATAAAATACCAGGGTGGCTTGCATGGTAGAGGGACTCACACTCCAAGTATGAGATTTCAGGCCCCAGAGGCAGCCAGTAGGGATGGCAGAGATGGTGCATACAAAGTGTGCTTTTGTCTGAGGAAATAAAAGCTAAGCAGTCTGTATGGAAATGAGTTTATGTGGCTGGGAGCTGATCCCCTGAAGGATTTATGGCTCTGTATTAAATGCCACTGCCTTATCTTTTAAAACATTCTGGTTCTCTGCTGAGTTTTTTTTTTTTTTTCCTTTTTCTTCTTCTTCTTCTGTTCCTGATTTTTAGAAACTCAATATTAAATTAAACACCTTGTTGTTCTGATTGCGTCATTAAGCAGAGGCAACTTCTTCTAAGGTCTTCCGCATTTCAGAAGGAAATGACTGCCTTTCCCTGTGTGCTTTTCCCTGTAG
Seq C2 exon
GTTGTTTTCCCTAGGGTGGCTCAGGTCTGTAAGAATGACATGGGAGGGTCTCAGAGAGTCCTGGAGAAGCAGTGGACATCTTTCCTGAAGGCTCGCCTGAACTGCTCGGTGCCTGGAGACTCTCATTTTTATTTCAATATACTCCAGGCAGTTACAGATGTGATTCGCATTAATGGCCGTGATGTTGTCTTGGCAACCTTTTCCACACCTTATAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000019647-Sema6a:NM_018744:9
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(6.7=100)
A:
NA
C2:
PF0140314=Sema=FE(16.5=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:
AGCCGTACTTTGTCCAAGCC
R:
ATAAGGTGTGGAAAAGGTTGCCA
Band lengths:
302-1204
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: