MmuINT0141110 @ 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
chr3:88447991-88449852:-
Coord C1 exon
chr3:88449680-88449852
Coord A exon
chr3:88448142-88449679
Coord C2 exon
chr3:88447991-88448141
Length
1538 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGC
5' ss Score
6.64
3' ss Seq
TCTTCTCTGGCTGTCTTCAGGCA
3' ss Score
9.62
Exon sequences
Seq C1 exon
AACGACGTGGGCGGTGAAAAGCTGCTGCAGAAGAAGTGGACCACCTTCCTCAAAGCCCAGTTGCTCTGCGCTCAGCCAGGGCAGCTGCCATTCAACATCATCCGCCACGCGGTCCTGCTGCCCGCCGATTCTCCCTCTGTTTCCCGCATCTACGCAGTCTTTACCTCCCAGTG
Seq A exon
GTGAGCAGCAAGGCAGGGAAAAGGAGGGCTGCGACCCAGGGAGGCGGGAGCGGATAGAGCCTACTTTACATTCCGTGCTTTGCATAGGAAGGCATCTGAGCATCACCAGACCCCCGGAACCGGACTGTCTCTCATGTGTAGGGAAGAAACAAAGCTCAGAGACTAGCTTCATTCTGCCTAGAAGGAAGCTTACAGGAGGCAGACACTAGAAATCAGCAAAATACCTAGCATCATGCTGCATGCCGTGTTCTCAGCACTTGGGAGGTGGAGGCAAGAGGCTAAGGAACTGGAGGCCAGTCTGAGCTACACAGAGAGAGCTTGTTGTCTCAAACAAAATAAAACATTGATAAAACAAAGACATGGTGGTGAGGAAGGAAGATCAGGAGTTCAAGGACTAATGCCTCAAAAATAAACAAGGGCTGGGGATGTAGCTCAGTTGGTAGAGCATTTGCCTAGCATGCACAGAGCCCTGAGTTGGATCCCAGCACCACCTAAGTCAGGGATGGTGGTAGATGGGAAGAAGAGACAGGAGGCCATCCTCTGCTCCATACTAATGATAGCCTCAGCTACTGGAGACTGTGTTAAGACAAACAAACAAAACCAATTCACTAGGCTAGGAAATGGAAGTAAAAGAAAATACCAGAAAGGCAGGACAAGGGTCTGTAGCGCTCAAATGCTATTGTAAAACTAAACACAGGCTGATGAGATGGCTCAGCTGTTCAGAGCACTGACAGCTCTTCCAGAGGTCCTGAGTTCAATTCAATACCCACATGGTGGCTGACAACCACCTGTAATGGAATCTGATGTCCTCTTCTGATGTGTTTGAGGACAGCTACATATACTGTACTGTCCAGTGTACTCATATACATAAAATAAATAATTTAAAACAAAAGAAAAAGAAAAAAAGTAAAACTAGACACAAACTTAGCACTAGCTTCCTAATGGCCATAGGTTATCGTTATGAGTGAGAAAACAGGAAGGACTTGCTCAGAGACCAAGAAAGGTCCAAAGGTCCCACAGCCACAGTCTGGCATCACAGTGTTTAGACACCTGCCAACCATGTATCAGGAAGCGAAGGTTTCTGGTGTGCAGGGTCTGTCATCAGTTAGATGCAGAACTGGGAACCCAGTCAGTGTGTCGAGGAGACTATGAGAAGACGTACTGGTTCGCCACAGACCAGCAGAAGAGACAGCCGTGGCTCATTCTCTGAGGACCACGAAGCCGGTTCTACCACTCTTCCTGTGGGCACAGCCCAGCCTGGGCAGGACAGGCAGGGGCCACCCCAGGGCCTACCTATGCCCCAATTAATCCTCATTAGGAGCAATCATATTTCAGATCCTGCGATGGGCTTCCAGACAGGCCTTAGGTCAGGGTCAGGGAACTCTGTGGGGCTGTCAGGTCCTTATCACCATCAGCAAGGAAAAAATAAGCCTCCAGAGGTTGGCCTGGCTCCTACCCTCTAGGCCGGCTGGGATTCCACTGGGGCTGGAGAGGCAGCCAAGGGAACCACAGTGAATGTCTTCTCTGGCTGTCTTCAG
Seq C2 exon
GCAGGTTGGCGGGACCAGGAGCTCAGCAGTCTGTGCCTTCTCTCTCACGGACATTGAGCGAGTCTTTAAAGGGAAGTACAAGGAGCTGAACAAGGAGACCTCCCGCTGGACCACTTACCGGGGCTCAGAGGTCAGCCCGAGGCCAGGCAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064:ENSMUST00000029700:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.216
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(13.7=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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGACGTGGGCGGTGAAAAG
R:
CCTCGGGCTGACCTCTGAG
Band lengths:
313-1851
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