MmuINT0141103 @ 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
chr3:88256893-88258768:-
Coord C1 exon
chr3:88258601-88258768
Coord A exon
chr3:88257054-88258600
Coord C2 exon
chr3:88256893-88257053
Length
1547 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TTGTCATTGCCTCCCAACAGGAG
3' ss Score
10.24
Exon sequences
Seq C1 exon
AACCATCTGGTGACCATCTCAGGCTGACCATGGCCCTACCATCCCTGGGCCAGGACTCATGGAGTCTCCTGCGTGTTTTTTTCTTCCAACTCTTCCTGCTGCCATCACTGCCACCTGCTTCTGGGACTGGTGGTCAGGGGCCCATGCCCAGAGTCAAATACCATGCTG
Seq A exon
GTAAGTGTCTAGTACCTGGGAGGTATGGATGGCACCATAGAGATGAAGGGGCTGAGGAAGGAGAAGGGTGTGCCAGAGGGGACGAAATGGCACGAAGAAACAGAGATGCCAGGGAGCCTGGGAGGGGCTGGGAGAAGAAGAGGCCACCTGAGGCACAAGTTGATCTGTAAGGGAAGGAAGGGTCACTGTGACCCTTTTCTGCCAACTCAGTGGTTTTTCTTTCCCTCAAATGTCAGTCACTAAGCAAGGAGCCTTAAACTCCTGACTGCTTTTTCAGTACCAGGAGCTGGAAAGCTAAAGCTCGCTCTAGATTGTCTGAGGAGCTGGAGGGCCCAAGCCAACTGCAGAGGTCACACCGGGCCAGATCCTGTCCAGGAGACTGGGCATCAGAAGGGATCCTAGCAGCTCACCCAGCCTCGGTGGTTTCTTGAGGAGGCTGTTCGGTTACTGACACCTTTAGTTCCAGGAAATGCCCCAGGGGAAGTGCCACATATACCACACACCCACCCACCCACACACACACACACACACACACACACACACAGAAGTAAGTTACTTCTGTTCACGGATGTAGTTTAGCATCCTTCTGAGGCAAAATGGTAAAGGAGATGTAGCAGTCGGTGGATAGAGCGGCATCTCTGGGTGGGATGGGAGTGCAGGCACAAACAAGCCTGCGTTTCAAGGGGAAGTACAATGAGCTCTCTTCAGAGTTCAGGAGAAGCCAATCTAGGCAGTATTGTTTCCATTTTGTCTTTGGATTCCTCTTGGTTTCCAGGCTTCCTGAGGCCAAAAGAGTAACAGCCAGATTGTCCTCTGACTAAAGCAAAAGTCCACATGTGCTCACTAGAGACTTATCTGAGGTGCTCTTTCCTCCTTGCTGATGTGCCAGTGTGTCAGGAACCCACACATTCACGTGTGTGTATGTGCACACATGCCACCACCAAGATATGTAGTGAACATGCACTACTAACCAACATATTCAGACTGTCCAGGTGGCTCCCAGGAATGCCCACACTGATGGGGCTCAGAAACCGAGAGGAAGCAGCCTTTTCTGCTGCAGTGGGCATTGCTGGTGGTGGGCAATTGCTATCGCAGAGTGAGGGGAGGAGACAGAGGAAACGGGGGTGGCAGGGATCTGTAACTACGACAAATCTTGAGGCGGACGACAGCTATCTCCGTTGCCTGTGGCTGAGAACCCCTTCCTGTGTCTACCTGTCAGCTCTCCCCCTCCCATCCTGCTTCACTGCATCCCCCCAGGCCTGAGACTGCATCTTCTAGCCTCACTTCATTTTCTGTCTGTGTCTTGAGCAGGCTCTCCCCCCAACACCACCAACAGTACCCAAGCTACCATTACCCTGTCTTTGGAACTTTTCACTTCTGGGGACTCAATCCACAAAGTTCCGATGCCCTGCTGTTGAAGGATGAAGGAAATGGAGGGGGGTGCCGCCAGTGAAGGGGGGCAGCTGCTGAGGCCTGCCACCCCTCCCCCACCTTTGCCTCAGTGGTCAGCTCCTTCTCATCCTCTCCTTGTCATTGCCTCCCAACAG
Seq C2 exon
GAGACGGGCACAGGGCCCTCAGCTTCTTCCAACAAAAAGGCCTCCGAGACTTTGACACGCTGCTCCTGAGTGACGATGGCAACACTCTCTATGTGGGGGCTCGAGAGGCCGTCCTGGCCTTGAATATCCAGAACCCAGGAATCCCAAGGCTAAAGAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064-Sema4a:NM_001163489:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.221 A=NA C2=0.002
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(72.0=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCTGGTGACCATCTCAGGC
R:
CATGTTCTTTAGCCTTGGGATTCC
Band lengths:
326-1873
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: