MmuINT0141119 @ mm10
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
chr7:80223934-80226527:+
Coord C1 exon
chr7:80223934-80224016
Coord A exon
chr7:80224017-80224595
Coord C2 exon
chr7:80224596-80226527
Length
579 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CATGCCTATTCTGCCCACAGGTA
3' ss Score
11.94
Exon sequences
Seq C1 exon
GCCATGGACCCAGGACATTGAGGGTGCCAGTGTCAAGGAACTCTGCAAGAATTCCTCATACAAGGCCCGGTTTCTTGTGCCAG
Seq A exon
GTAAGATGCCCTGGGAAAGGTGAGCCATATTTGCTTGGAAAACACCTCTAGGTATTTTTAGGTACAAATTTATTCCTCTAGCCCTACAAAGAAGAGTCCAGATCATGAGTCACTTAGTCCCAACCATCGCCCAAGTTACCATTGGTCCTAGTTAGAGTTTCTGTGGCTGGGAAGAGACACCATGATCACAGCTCTTATAAAGGAAAATGTTTAATTGAGGTTAGCTTACAGTTCAGAGGTCAGTCCATTATTGTCATAGCAGGAAGCATGGTGGCATTGCAGGCAGACATGGTGCTGGAGAGGTAGTGAGAGTTCTAAATCTGGATCAGTGGACAGCAGGGAGAGAGAGTGTCACTGAACCTGGCTTGGGCATCTGAAACCTCAAGGCCCAGCCCCAGTGACACACTTCTTTCAGCAAGGCCACACGTCCCAATAGTGTAATTAATTGCCTTTGAGCCTATGGGGCCATTTTCATTCAAACTACCACACTATCATAGCACCAGATTGAGGAGGGTGGGCCTAAGTCTGGAGCTGCTCTGGGCAATGACCTCTTCTACCCCATGCCTATTCTGCCCACAG
Seq C2 exon
GTAAGCCATGTAAACAAGTCCAGATCCAACCAAACACAGTGAACACCCTGGCCTGCCCACTCCTCTCAAACCTGGCCACTCGGCTCTGGGTGCACAATGGAGCCCCAGTCAATGCCTCTGCCTCCTGCCGCGTGTTACCCACCGGGGACCTGCTGCTGGTGGGCAGCCAGCAGGGTTTGGGGGTGTTCCAGTGTTGGTCGATAGAAGAAGGATTCCAGCAGCTTGTGGCCAGCTACTGCCCAGAGGTGATGGAGGAGGGGGTAATGGACCAAAAGAACCAGCGTGATGGTACCCCAGTCATTATCAACACATCACGAGTGAGTGCACCGGCTGGTGGCAGGGCCAGCTGGGGTGCGGACAAGTCCTACTGGAATGAATTCCTGGTGATGTGTACTCTGTTTGTGTTTGCTATGGTGCTTTTGTTTCTGTTCTTTCTCTACCGACATCGGGATGGCATGAAACTCTTCCTAAAGCAGGGCGAATGTGCCAGTGTGCACCCCAAGACTCGCCCTATAGTGCTACCACCTGAGACCCGACCGCTGAATGGTGTCGGCCCTCCTAGCACCCCACTTGACCACCGAGGCTACCAGGCTCTGTCGGATAGCTCCCCAGGGCCCAGAGTCTTCACTGAATCAGAGAAGAGGCCACTGAGCATCCAGGACAGCTTTGTAGAGGTGTCTCCCGTGTGTCCCCGGCCCCGAGTTCGACTGGGCTCTGAGATCCGAGACTCTGTGGTATGAGAGCTGACTTTAGATGTGGTCACCCTGACCTCAGGGGTTGTGAGTGTTCAGTGGAGGTCAGCTACCTCTGCTTCTCACAGAACACAGCCACGGTACCCTGACTGGAGGGCAGCTGGTACCACAGGCCCAACAGCCCAGCCAGCTGCTTCCAGTGTCTGGCCGAGAACTGGGCTGCCTCCAGGGGCCAGAGGGTCCTTGTCTGGGTGGCAGAACTCTGCTACTTAACTGAGCCCTTTGTTTAAAACTGCAAATGTGAAGCCAGAGAGGAAGGAGAAACAGACAAGGAAGACTACAACATAGCCACTCCAGTTCAGCCTGCTGGGCTCTTGGGGACTTCTCCAAAGTGGCTTTGTGAGCAAGCCGAAGTTGAGAATCCCTCCCCGACTGGACTATTCTACCTTCCGCCTTACTCTGCTGCTGAGGCTACCCTTTCTCACTGCAGAATCAGGGCCCTGCTCCAGCTTCAGCCAACCGAGGACATATCTGTGACCGCTGACACCCTACCACCTCAGGGACCAGAGGGCTAGGCTGATTCTGCAGCCCTCCTCACCAGACCCTGGGCTCAGTCCCAGTTCCCGGACTTCTCCAGCCTGTATCAGGCTGTGGCCTCAAAAGCAAGGGAGTGACCCCCAAGGGGGGTTGTGACAGAAGACTTGCCTACTGTCCTTTTCCCAGTCAGAGAACTATGTCCCTACCCATCGACGTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGCTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGTCTCGAACTTAGAAATCCGCCTGACTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCGGCCCCACCCATCTTCTAATTCCTACACAGACTCCTGGATCCTCGTTCCTTGTCCTAGCTCACCGTGCCCGTCACTCTAAGGGATGCTGACACTGCCCATCACAAGGACCCTGAATTTACATGGGTTTTATATTTTTTTTTAATAAGATGCACTTTACTTTCTTTTTTAAATAAAATCCGACAAATTATAGTTATTTGTGGCCCACATTCCTGAAGGGCTTTGCTTTGTGTGTATGTGATATGAATATATGTATATGCGGAGACCAGAGGCTCTCCTTTGCTTTGTGTGTATGTGATAGGAATATATGTATATGCGGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030539:ENSMUST00000032754:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.154
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(32.8=65.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCATACAAGGCCCGGTTTC
R:
GTGCACTCACTCGTGATGTGT
Band lengths:
357-936
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