MmuINT0141099 @ 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
chr3:88438443-88440878:-
Coord C1 exon
chr3:88440698-88440878
Coord A exon
chr3:88438562-88440697
Coord C2 exon
chr3:88438443-88438561
Length
2136 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
CCTTGTCTCTGTCTCTGCAGCCA
3' ss Score
10.77
Exon sequences
Seq C1 exon
TGCTCCATGGGCCCCTCCTCTGACAAAGCCTTGACCTTCATGAAGGACCATTTTCTGATGGATGAGCACGTGGTAGGAACACCCCTGCTGGTGAAGTCTGGTGTGGAGTACACACGGCTTGCTGTGGAGTCAGCTCGGGGCCTTGATGGGAGCAGCCATGTGGTCATGTATCTGGGTACCT
Seq A exon
GTAAGTATAGGCTTCCAGAATATACCTGGGATGGCACGAGCAGGGGCGCAAACCCAGGCTGAGGCAGGAAGCCTTTGAGTCCATCCCCGTGTTCAGCTCATAATTTAGCAGAGAATTAGTGTGTGAGCCCCCTGCTGGACTCAGGATGCGCAGTGCAATGGCAAGATAATCCGGTCTCTAGCCTTTCTGAGCTTTCAGTCGGCTGGGGAATATAGACCCCAGTCTATATTCCAGTCTTAGAAAGAGCTGTCCACCTTCTGGGAGGAGCCATATCAGAGGCAGGAGGAGAGGGTGGGAAGGAAAGCGGGACTGAAGGGGTCATCAAGGGTGACCTGGAGAAGGGTAGAAGCCACACCTCCCCAGCCCCCCACTTTCAAGCAGCCCATGCTGGATTCCAGCTTACTATGTAGTTAACACCGACCCTCAACTTCCTTCCGATCTACCTGCCTCTAACTCCCAAGAGTTTGGATAGAATAAGACCCTGTTCTGGAAAAGAGAAGAAAAGACGAGAAGAGAAAAGAAGAGGGGGGAAAAAAAGAACATGGCATGGTGGTGCATGCTTTTAGTTCCAGCACTTGGGAGGTAGAGGCAGGCAGATCTCTGTAAGTGCTGGGCCAGCCTAGTCTACTTAGTGAGTGTCGGGCCAGCCAAAGGCTACATAGTGAGACCAGACTCAAAAATAAAAGAATTTACAAGTTGGCAGCTAGCCTGAGTAGCAGAATGAGACCCTATTGTTAAGCAAGGCAGACCCGCCCTCTCTGCCTCCTGCCCCCACCCCCACCCCACCCCCTGCTCTGGGCATGATCCCCTCGATCTGCATCCCCACTCCCAGGATCCCCTGGATCTGCTCCACTTGACTTTCTAATTTACAGCTAATGCGCTGTGCAGTTTTCTCATTCACAACAGTTACGGTCTGCCTCCACCCACTCCACAAGCCTGGGAACTTTTGTCTCTGTCTTTCCTACTGTGTGCTCAGCACAGGCACAGCAGAGACAGGTCTCATAGCATGGCCTGGAAGAGTGACTGAGCCCAGTGTCTTCCTCCCATGGAAGTGCATGCCCTCAGTTGGCTGGCAATGGAGCACACTCCCCAGCCAACTGTTCCTCTTTCTGGAATGACTGTTAGACCCATCCCTCTCTCCTGAGCCCACCCTCATTCTTAGCTCATGACCCTGGTCCTCCAGCTTCCTACAGGACACATAGGTGTTTGGATAGGAGCTCCTGGCTCTCCCAGCCCAGCCTTACCCTTCTCAGCTTGATCTGCCAAGGGTCTCCTGTCTTGCCATCTTTGAACTGTATCTTTAGTCTTTCCTGTTTATTCAGAAGTAGTGGGGCTGAGGACACACCCTGGCAGCCAGAGTGCTTGTCTGCAGTTCCTAAAGCCCTGAGTTCAATCCCCAACACCTCATAAAACCAGGCTTGAGGCGTGGTGGCATATGCTCATCATTTTCCTACCTCAGATTTCTGTGTTCTAGGGAATTGAAACCATTAAAAGGGTGGTCAGGAGCAGGGTTTGGTGTTGCAGGATTGTAATTCTAATTACTTGGGAGGCTGAGCCAGGAAAAGTGCATGTTTGTCCAGCCTGGGCTTCTAAGACCCTGTCTCAAGTAAAAAGACGGCTGGGAATGTAGTTCAGGATCCTAGCTCATGAGAGGCCCTGCATTTAACCCTTCCTTTTCCCCTCATACTAGAAAAAAGACACAGATGACTCAGTTGTAGGGACGTGAATTTAGATGCTCAGAACACATGTAAAAGCTGGGTGCTGCCCTGGGTACCTGCAAATCCAGCAGTGGGGGTGGGGCAGTCAGGATTCCTGGTGCTTATTGACTACATAGCCAATCTAGGTCATGGGGAACTCCAAGTTCAGTGAGGGATCCTGTCTCAGCAATACAGTGGGGGGTGACTGAGTAAAACACATAGCCTGACTTATGTCCTCCACATGCATGTGTGCATCCATGCTTGTCACATATGTAACAATACACACAAGGAAAGGAAGATTGCCATGAGAACCCCCCCATCCCTGGACCATGGAGGGACTGAGTGGCCTGCGTGCCCTGTGACCATCTTGCTGAGGAGGAATGTGAGGGCAGTGAGAGGAAGAAGAGGAAGAAGTTCTACCTTGTCTCTGTCTCTGCAG
Seq C2 exon
CCACGGGGTCCCTGCACAAGGCTGTGGTGCCTCAGGACAGCAGTGCTTATCTCGTGGAGGAGATTCAGCTGAGCCCTGACTCTGAGCCTGTTCGAAACCTGCAGCTGGCCCCCGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064:ENSMUST00000029700:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.100
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.5=100)
A:
NA
C2:
PF0140314=Sema=FE(12.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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