MmuINT1030847 @ mm10
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
chr3:88454679-88455739:-
Coord C1 exon
chr3:88455548-88455739
Coord A exon
chr3:88454847-88455547
Coord C2 exon
chr3:88454679-88454846
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
ACTCGAGGTAGAAATTCTGGTTTCCCTGGCCTGAAACCCACACTGGCTCTGGCAGGATGGGTGCCTGGAGGGCCGCGCGCCCGTTCCAGCCAGGCTGAGCCTGCTTGCCTTGCCTGGACCCCCTTCTTTGCCTCGGATGGCACCCTGATTCAGGGTTTGAACACAGGACTTCTCAGTGTGGCTGGCTCAAGG
Seq A exon
GTATGTGAGATGAGGCGGGGGCGGGGGAGGGGTGTGAACCTGCATTCAGTGGCCATGGGGGAGGCTGATTGCGGAGCTCTGGGGAGGCAGACAGGGGGGCTGGAGAAGTTGAGAGTCTGCCAAGGACTCCTGCCCAGGCCACTCCCAGGAAATACAGAGGGCAGCCCCACCACAGTGGTAGATAAACTGGCACGCCCCTATCCCTAAGAAGAAGGCTAGATGGGCCCGATTAAGCAAGAGTCAGAGCCCCTGGGGGCTGAGGAGAGGGTAGGCTGTCTGCCTGGGTTGGGGTGAGTAGCGGGCATAAGGTGTCACAGCACAGGCCAGCCTGGGGAAATCTACCTTTTGCATACAGGAACTAGTTCCCTAGAAGACCTTTGCCCAGGGCCAGAGATGATCAGAGCTCTGGAGCACGGGGCCAGGAGATGCTGAGGGGGCAAAGTGGAAAGGAATTTTTCTGTGAGTCAGGTGAGAAATGGCAAGGTAGTTTTTTTAATGGTTAGGTGACCAGAGGCACAGCGTGGGCCACAGCAGCACCCTATGCAGAGGGCAGCAGGAGGCACCTTCAAGGCTGGGGATGGATGGAAGTGAGACTCTGAGGGCCCTTCCAGAGAGGAACTTCTGCCCCCTGGGGCTCTCCTATTGGCCCTCAGGAAGGGTGTGGTAAGCATGGCTAACCCAGAAAGTGCCTGTTTCCTCAG
Seq C2 exon
AACCATCTGGTGACCATCTCAGGCTGACCATGGCCCTACCATCCCTGGGCCAGGACTCATGGAGTCTCCTGCGTGTTTTTTTCTTCCAACTCTTCCTGCTGCCATCACTGCCACCTGCTTCTGGGACTGGTGGTCAGGGGCCCATGCCCAGAGTCAAATACCATGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064:ENSMUST00000029700:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.220
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
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:
ATTCTGGTTTCCCTGGCCTGA
R:
GCATGGTATTTGACTCTGGGCA
Band lengths:
345-1046
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