MmuINT0141113 @ mm9
Intron Retention
Gene
ENSMUSG00000028064 | Sema4a
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Source:MGI Symbol;Acc:MGI:107560]
Coordinates
chr3:88258601-88259683:-
Coord C1 exon
chr3:88259470-88259683
Coord A exon
chr3:88258769-88259469
Coord C2 exon
chr3:88258601-88258768
Length
701 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
GAAAGTGCCTGTTTCCTCAGAAC
3' ss Score
5.27
Exon sequences
Seq C1 exon
AAGCCAGCCAGGATCTGTCACAACTCGAGGTAGAAATTCTGGTTTCCCTGGCCTGAAACCCACACTGGCTCTGGCAGGATGGGTGCCTGGAGGGCCGCGCGCCCGTTCCAGCCAGGCTGAGCCTGCTTGCCTTGCCTGGACCCCCTTCTTTGCCTCGGATGGCACCCTGATTCAGGGTTTGAACACAGGACTTCTCAGTGTGGCTGGCTCAAGG
Seq A exon
GTATGTGAGATGAGGCGGGGGCGGGGGAGGGGTGTGAACCTGCATTCAGTGGCCATGGGGGAGGCTGATTGCGGAGCTCTGGGGAGGCAGACAGGGGGGCTGGAGAAGTTGAGAGTCTGCCAAGGACTCCTGCCCAGGCCACTCCCAGGAAATACAGAGGGCAGCCCCACCACAGTGGTAGATAAACTGGCACGCCCCTATCCCTAAGAAGAAGGCTAGATGGGCCCGATTAAGCAAGAGTCAGAGCCCCTGGGGGCTGAGGAGAGGGTAGGCTGTCTGCCTGGGTTGGGGTGAGTAGCGGGCATAAGGTGTCACAGCACAGGCCAGCCTGGGGAAATCTACCTTTTGCATACAGGAACTAGTTCCCTAGAAGACCTTTGCCCAGGGCCAGAGATGATCAGAGCTCTGGAGCACGGGGCCAGGAGATGCTGAGGGGGCAAAGTGGAAAGGAATTTTTCTGTGAGTCAGGTGAGAAATGGCAAGGTAGTTTTTTTAATGGTTAGGTGACCAGAGGCACAGCGTGGGCCACAGCAGCACCCTATGCAGAGGGCAGCAGGAGGCACCTTCAAGGCTGGGGATGGATGGAAGTGAGACTCTGAGGGCCCTTCCAGAGAGGAACTTCTGCCCCCTGGGGCTCTCCTATTGGCCCTCAGGAAGGGTGTGGTAAGCATGGCTAACCCAGAAAGTGCCTGTTTCCTCAG
Seq C2 exon
AACCATCTGGTGACCATCTCAGGCTGACCATGGCCCTACCATCCCTGGGCCAGGACTCATGGAGTCTCCTGCGTGTTTTTTTCTTCCAACTCTTCCTGCTGCCATCACTGCCACCTGCTTCTGGGACTGGTGGTCAGGGGCCCATGCCCAGAGTCAAATACCATGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064-Sema4a:NM_013658:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.221
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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:
GCCAGGATCTGTCACAACTCG
R:
CCTGACCACCAGTCCCAGAAG
Band lengths:
346-1047
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: