MmuINT0141126 @ mm9
Intron Retention
Gene
ENSMUSG00000030539 | Sema4b
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B [Source:MGI Symbol;Acc:MGI:107559]
Coordinates
chr7:87361834-87363950:+
Coord C1 exon
chr7:87361834-87361985
Coord A exon
chr7:87361986-87363768
Coord C2 exon
chr7:87363769-87363950
Length
1783 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TGTCCCCTCTTCTCCTACAGGGC
3' ss Score
13.32
Exon sequences
Seq C1 exon
ACCCTGCCTTTGTGGCCTCGGCCTACGTCCCCGAGAGCCTGGGCAGCCCCATAGGTGATGATGATAAGATCTACTTCTTCTTCAGCGAGACGGGCCAGGAGTTTGAGTTCTTTGAGAACACCATCGTGTCCCGAGTTGCCCGAGTCTGTAAG
Seq A exon
GTGAGTGGGAGGGCGCAGGGTCATCCACCCAAGGTGCACCCACATCTGTCACCTTCCAGAACCAGTCCCCAGGGAGTTGCAGCCCAAAACCAGTCTGTGGCTCCTCTTCCTTCTCATCCTTGCCTTGAATCTGGAGTGTCTGGGCTCTGGACAGTGTGTCCCGGGGCTGAGCTGGCGTCTCCATGCTACACTGCTGTCCTCTTTTGTTTTTTGTTTTTGTTTGGTTTTTCAAGACAGAGTTTCTCTGTGTAGCCCCGGCTGTCCTGGAACTTACTCTGTAGACCAGGCTGGCCTCAAGCTCAGAGATCTGCCGCCTCTGCCTCCTGAGTGCTAGGAGTAAAGGTGTGCACCAGCACTGCCTGGCTTCTTTTGTTTTTGTTTTTGTTTTTGAGACAAAGTTTCACTATATAGTTTTGGCCATCATGGGACTCACTCTATAGACCAGGCTGGCCTCAAACTCACAAAGATCCGTTTGCCTCTGCTTCCCAAGTGCTGGGATTAAAGGAGGGTACCAACACTCCTGGTTGTCCTCTCTTCTTTTAATTGAGAAAATCTCACATTGAAGGTAGGTGTGAAGGCGCATACTCCAAATCCTGACACTCAGGGAGCCGGGGAGTGGAGGTCTCAAGTTTAAGGCCATCCTGGATAACTTAGCAAGGTCCTGTCTTTTTTTTTTTTTTTCATTTTTTCCTTTTGGTCCTGTCTTTTTGTTTGTTTCTTTTCCAAGACAGGGTTTTTCTTTGTAATCCTGGCTGTCCTGGAACTTTCTCTGTAGACCAGGCTGGCCTCAGATTCAGAGATCCACCTGCCTCAGCCCACAGATTCTATCTTAAAATTTTAAATAGGTATTCCTCTCTTAGGGTCTTGAGTTCAGCTGCCTTCAAACATCCTGTGTCACTCAGGCTAACCTTGAACTTTTGGTGTGCTATCCCACTTAGTTTATATATTGCTGGGGATCAAGCCCAGGGTTATAAACATAAGAATTATAAGCTACTTGGAAAAGAAGTCCTTGGCTTTCTCTTAAACTGGAAACCCAGGAAAGTGTACAAAGAAGTGACCTAGAGTGAACAGCCAACGGCATCACTGTGTAAGAGCCCAGATTCTCAAGTTTGAACTTCCAGGTTCCAACTTAGCTGTTAAATGGCAGTGATAACATCACTAGCTGTTGCATGAATTAAATTCTGCCGTGTAAAGCTCTTAGGGCCCCTGCTATCACAAGAAGAAGCCATTGTTAAAGTGTTCTTTGCTGATCTGTTCAAACTAATGTATTTGTATTAACTCAGTTACAAACCTGAGACCTGAGTTGTGCTATTTCTCCCTGTTTGCTCAGTAATCCGTCAATCATGGACACCTTTTCCTATTATTTATTCATTTATGTGTTCATTGTGTTGAAGCCCTACTTCACTCCCTCCCTGGCTGACTGCAAACTCTTAGACTTGAGCAATCCTCCTGTCTCATCCTCCTGAGTAAACTCAAGCTTCAGGTTTCTGACATGGCCAGTGATGCTAGCATGCCAGATAGCACTGGCCATCGAGCGCTCTCCTGGCCCTTCCCTATTTGGATGGTTTCCCCTGGTCCTTCTTTGCTCGTTGTCCACAGTAGGGAACACACTTTCCTGATGAAAACATACTCAATTTTAGGTGCACATCTGTCCTGGTGCTCTCTCTCATTCTTCATTCCTGTGTGACTCAGCTACTGCTGAGGAGGGCTGGCAAGGAGACACTGTGCCTCCGAGAATGGCCCTCAGCTTGTGACTAAGCCCGTGTCCCCTCTTCTCCTACAG
Seq C2 exon
GGCGATGAGGGTGGAGAGCGGGTGTTGCAGCAACGCTGGACCTCCTTTCTCAAGGCTCAGCTCCTGTGCTCCCGGCCTGATGATGGCTTTCCCTTTAACGTGCTACAAGATGTCTTCACCCTGAACCCCAACCCTCAGGATTGGCGCAAGACCCTTTTCTATGGGGTCTTTACCTCCCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030539-Sema4b:NM_013659:8
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=FE(11.4=100)
A:
NA
C2:
PF0140314=Sema=FE(13.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTACGTCCCCGAGAGCCTG
R:
GGTAAAGACCCCATAGAAAAGGGT
Band lengths:
304-2087
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: