MmuINT0140987 @ mm9
Intron Retention
Gene
ENSMUSG00000028883 | Sema3a
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A [Source:MGI Symbol;Acc:MGI:107558]
Coordinates
chr5:13451104-13455606:+
Coord C1 exon
chr5:13451104-13451261
Coord A exon
chr5:13451262-13455543
Coord C2 exon
chr5:13455544-13455606
Length
4282 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCT
5' ss Score
7.56
3' ss Seq
TGATTCTTCTGTGTCCTTAGATT
3' ss Score
10.42
Exon sequences
Seq C1 exon
AAATGTTGGAATCCAACAATGTGATCACTTTTAATGGCTTGGCCAACAGCTCCAGTTACCACACCTTCCTTCTGGATGAAGAACGGAGTAGACTATATGTTGGAGCAAAAGATCATATATTTTCATTCAACTTGGTGAACATTAAAGATTTTCAAAAG
Seq A exon
GTATCTATATTCTAATATATGTACTCTATTTTTAAACACTGAAGTTTTTATTATATTTTACAGCTACTTAATATCAGGACAACATACAAAATTATTTCAAAATGATTTTTTCAGACATATACAAAATGAATGACAACAACATGACAGTAGATATAGTAAGCCATATTATCAACAAGGATGAAAAAAATCATAGTACTGTTGATGCTCATTCAAAAAACAAAACAACAATAACAAAAAATCTCTAGCTTATTCTTCCATAAGTATTTATGGAATAAGGTTTTATGCAGAAAATAACATTCAATCTGAAATGCTGGAGGAATATATCATAACTGAGTTTATGAACTATATATTTCCATGTACATATATTTGTGTAAGTTGTCCATCTCTCCATTTGTCAACCAGTGAAAGGTTCATTAAGCAACCACCTGATGACCTTCTTGTACTTGAACATAGTTCTATTTGAATATAGATATTCTCATTCATGTATATATGTCTCTGTATCGCATGTTATGACAGAGGTGAGTAATTGTGTATATACGCCTCTGTATTGCATGTTATGACAGAGGTGAGTAATTGTGTATATACGCCTCTGTATTGCATGTTATGACAGAGGTGAGTAACTGTGACAAACAATATGGATCATAATGCCTACAACATTTTTAATCATTGATTTTAAACAATAAATTTGCAAATCCTCATGTAAAAATCAAATTTCAGGGTATCAATATTCTTGCAAAATTGGTTATCTAGATGTCAGAAGGTTGCTATTTCTCATAATATCCCTTTAGATTTCTGGCTCACTTCAGTCACTCTATGAATCTATATTTAAAACAAACAGATTTTTAAAGTAGACAGAACTGTTTTGCTTTGTCTACATGTATAACCATAAGTCAACCAAATTTTCTTAGTTTTCCAGCCTTAATTCCCTAAGGAGTTAAGAGCAGCTTGCATGAGAACCCCAGAGTGTGCTTCAGCTAGCATGTTTATTGGTATCTCTGGTTTTGGCTTTGTTTCTCTTAGCACTGAAGGCACTAATGTGGTGTGTGGAATATTTATTGAGAACACATTGGTTGGCAACTTCTTAAAAGTGTATGAACTGCTTGGAGACATAACTTTAAATCTGTTTCTTTATCATTATTATTACCTAAACATAGAAGTTTATTTACATATATAAAAGTTTGAATTAAGATACATATTCACAAAACATTGCAGTTCAAATATGATATATTTTATAGTAAAACTGAGGCACTAAATCATAACCTGAGTATGTTTAATCTGATTTTTTTAAAAAAAGAGTCATTTCTAAATGACCACAGGTGATGACCATATAATGATAAAATGTGTCTTTCAAAGACTTTTTTTTTTATTAATTATTCCATTTGTTTCCATCTCAAACAATATTCCATTTCCTGGTTACTCCCCAGTCCACTAATCCCCCATCCCACATCCAATGTCCCCCTCCCCTTTGCTTCTATGAGAATGCTCCACCACCCAACCACACTCTACCGTCCTACCACTCCAGCATCCCCCTATTCTAAAGCATCAAGGGCCTCCGCTCCTGTTGCTGTCAGGCAAGGCCATCCTCTGCTACATGTGAATCTGCAGACATGGATCCTTCCAGATACACTCCTGGGTTGGTAGTCTAGACTCTGGGAAAACTGGGTGATCGTGCCATCCTATTTTGTTCTTCCAAAGGGGATGCAATCCCTCTCAGCTCTCCCAGTCTTTCCGCCAGCTCTCCCATTAGATTCTCTGAGCTCAGTCCCAGCATCCACTTCTGCATTGGTCAGTTACTGACCAAACCTCCTCAGGAACCACCATACTAGGTTCCTGTCAGCAAGGGCCACTTGACCACAGCAACAGTATTGGGTTTGGTGTCTGCAGACATGGTCGATCTCCATGGTAGTCCATGGTTGGCCCCTCCTTCAGTCTCTGTTACTTTTTTTTCCCTAATGCTTTCTTTGGACAAGAACATTTCTGGGTTAAAAACTTTGAGATGGGTGGGTGACACCATCCCTCGACTAGGAGCTGTGTTTTTATCTACTGGAGGTGGTCTCAGTAGGTTCTGTCTTCCCCTTCTCTGCACATTTCAACTAAAGTCATCCTTGTTGGTTCCTGGAAGCTACATGTTTCCCTGATGTCTGGGACCCTCCAGTGGCTATCCCCTGTTCATCACCCCCCTACATATTTTTATTCGATTTCCTGACCCTCTGTACTTCTCTCACATCTCCTCCAGTTCCTGATAGTGCCACACTTATTTTCTTCCCCTACTTCTTCCCTCCATGACCCCTCTCACAATCAACTTTTGTTCAAAAAATAAGAAATTTTGTGTTAATATCTTATACAAAGAAACCATTCTTCAGTAAGTGAAGTAGAAACTTAGAACATTTGCTATTTTAACTTTAGGATAACATATTTGTCAAAATTATGAGGATAACTTGTATTGTTTTGTAAACTTCATATGTATGTAGGTAGAGAGATGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAGATATGCCATGATACTACTTCTAATCATGTAAACTTTATATTTAATACTTTCTTTTAGACACATGTTATAAACTATGCAATGAAACAAATCGTGTCTGAATTTTAAAAGAACCAAATAAGCACATCTAAATGCTAGAACTTTGTAAGTGAGATAGATCCAAGTGCTTTATGGGCAAGCATGACAACCTGCGTTCTGTTTACAGCATCCACTTAAAGTGCCAGGATCATAGAATAGTCCTTGGGAGGTTGAAACAAGGGGAACAAGAAACCTTCTGGTCAGTCAGTCTAGGCAAATCTATGAGCTCATGGTTCACTCACGTTACAGTAAAAATAAAACAGAGAGCAATTAAGAAGTATACCCAACATTAGCTTCTAGAGTCCACACTTCTACATACACATCTTCACATCTTCACATGTAAAGTAGATCATGAAATACCTTAAATAATGGAGTCAGAAACTAAGACATTTGTAGTTAGCTAGTTTTTGAGTAATGAAAAAAAAATGTAATAAGTTTATAAAATACTAATATTTGACAGAAGTGAAAAACACAAAATAAAAGTAATAATTGCTTAGCAAAACTTTAAGAACGAGAAAAATTTAAAAAAAATGTGTCTTCTAAAATCTATTTGTTCTAAAATCAATATATATATAATAAAAAATGATGAGTTACCCGTTCTATTCTTAAACATCATATTTGTTATATGAACTTTAAATGCATTTCTCAAGGAATCATATGTTATTTCAATGACTCCTAAATTTTGTTTATAAGTATGCTGCACTTGGGCTTCCAATTCCCTGAGTTGGAATCTCCATCTTTACCTGAGCTTGTGACCATTTATAGTGAATTATCCTGAGGCTTCAGATGAATGGCAATCCATCATCCTGAGGCTAAAAGCTCTCTAGCACACATAAATAATAAGCTGCCACTGACTCGGGATTTTTATTTAATGTATGACATTTCCCCCTGGATATTAACAAATATAACTCGAATAAAAACTGTTGAAGAAGTAGTACATTGTTTTGTCCAGTGGAGAAAAGACGTATTAAAATTAAAACCCATGGAAAATTTTTGAGACTTGGAACTTGGAAGCTATTATGCTAAATTTTGGTAGAGTATTTATATTGCTATTATAGAGAAAATGTATTCAACTGCCTAAGCAACTATCAGTAGCATCGTGGTTCTTCTACTTTGACTGGATTCATAATAAATGAAAGTCCTTGGAAGTCTTTCAGCTTCCCAAGTACTGTGATTATAGCTAAAAAACACCATGCCCAGTCAAAGAAGCACATTTTCAGAAATATATTTTTTTCTTTGTTTCCACTTTCATCATCTCAAAACATACGATGTTACTTTTAAATATTTCTTATTTTCATTTGGAGAGAAAAAGAAGGCAAACAAGATAGAGATTACTTCATGAGCTGTACCTTCCAAACATTTCAGGTCTTGCGCTTTATTGCCGTGCTAGAGTTTGGCTCAGCAATTCCTCCTGCACTGAACTGCTCACACCTATGAATGCCTTAATAGATTTCCAACTCTAATTTCATACACTGCAAAAATTAGTTTATAGATGGAGAATGCATGACCTTAGTATATAGAAATGTATTAGCTACTGTTAAAAGACAGTCAAATTTGAAAGATTCCTGCATATAATATTTCTTTCCCTAAGCTGTGCCTAATAAATTCAAAAGATTACACAGTAACAAATATCTTGGCAAATTTAATTGCATAAAAATATGATTCTTCTGTGTCCTTAG
Seq C2 exon
ATTGTGTGGCCAGTATCTTACACAAGGAGAGATGAATGCAAATGGGCTGGAAAAGATATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028883-Sema3a:NM_009152:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(19.6=62.3)
A:
NA
C2:
PF0140314=Sema=FE(11.9=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:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: