MmuINT0141251 @ mm9
Intron Retention
Gene
ENSMUSG00000001227 | Sema6b
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:MGI Symbol;Acc:MGI:1202889]
Coordinates
chr17:56262508-56264814:-
Coord C1 exon
chr17:56264756-56264814
Coord A exon
chr17:56264341-56264755
Coord C2 exon
chr17:56262508-56264340
Length
415 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
TTCTCCCCATCTGTCCCCAGGAC
3' ss Score
11.97
Exon sequences
Seq C1 exon
TGCCACGTTTGAGCAAGATGTGTCCGGGGCCAGCACCTCTGGCTTAGGTGACTGCACTG
Seq A exon
GTAAGCTGAGAAAGGGAATCCTCTGTGTGCTGTGTGACACAAGCCAGAGACACTCAGTCCTGGAGATAGAGGGTGGACACTCAATCCTGGGGATGGAGGGAGACTTCCTTAGTTAGATGGAAGCCATGGAAAGCTGAGCTCACCCAGTGCTCACGGTCGCCCTCTGGTGGCTGCTGCAAGGAAGGGTGAAAATGAGATCCACCTAATAGAAAAAAAAAAAAAAAAAAAAAAAAAAAACACGCAAAAGGGTCATGGCATAGAGTCCTTGCCTAGAATTCCCTTGTGAGAGGCATGAGGCGTATCATGGACGGAACCCCGCCTAGAATAGAGCCTGGCTCAGTGCCTATCTAGCAGACTTTCAGACTGGTTTCCAAGGCGGAAATCGCACTGCCACTTTCTCCCCATCTGTCCCCAG
Seq C2 exon
GACTCTTGCGCGCCAGCCTCTCAGATGACCGCGCAGGGCTGGTGTCGGTGAACCTGCTAGTGACGTCCTCGGTGGCAGCGTTCGTGGTGGGTGCCGTGGTGTCCGGCTTCAGTGTAGGCTGGTTCGTGGGTCTCCGCGAGCGGCGGGAGCTGGCCCGGCGCAAGGACAAGGAGGCCATTCTGGCGCACGGCGGCAGCGAGGCAGTTCTGAGCGTGAGCCGACTAGGCGAGCGCAGGGGGACCGGGCCCGGGGGTCGTGGAGGAGCCGGCGGCGGTCCCGGAGGTCCCCCGGAGGCCCTGCTGGCCCCGCTTATGCAGAATGGCTGGACAAAGGCAGCGCTGCTGCATGGTGGCCCTCACGACCTGGACACGGGGCTGCTGCCCACCCCAGAGCAGACGCCTCTACCCCAGAAACGCCTGCCCACGCCACACCCACACGCCCACGCCCTGGGGTCTCGAGCCTGGGACCACAGCCACGCGCTGCTGTCGGCCTCAGCCTCCACCTCCTTGCTCCTACTGGCGCCCGCCCGCGCCTCTGAGCAGCCCCAGGTGCCAGCCGAGCCGGGCCCGGAATCTCGCCTCTGCGCCCCCAGATCCTGCCGGGCCTCTCACCCAGGCGACTTCCCGCTCACGCCCCACGCCAGCCCGGACCGCCGGCGGGTGGTGTCCGCACCCACGGGCCCCTTGGACCCTTCGGTGGGCGACGGCCTGCCCGGGCCATGGAGCCCACCTGCAACCAGCAGCCTGCGGAGGCCGGGTCCCCACGGGCCCCCCACAGCCGCCCTACGGCGCACACACACATTCAACAGCGGCGAGGCTCGGCCCGGGGGTCATCGTCCTCGCCGCCACCCACCCGCGGACTCTACACACTTGCTGCCCTGCGGGACGGGCGAGCGGACTGCACCCCCGGTACCCTAGGCCAGGCGGATGCCTCGACGGTGCCAACCACAGCGACCCGGGCGCCAGCCCAGGTCACCGAGCCCTACTGGCGCCGAGTGGGGCGCGTTTGTTCCTCACCCACGCGCGTGGGGATCCCCTCGCCACAGGGAAGCACAAGAACCCCCTCCATCCCGGAGGATGCAGGACACGAAGCCCCGGGGTGGGCGGGAGGAGGCTGACCTTTTACCTGCGCATAGACTTTGATTTTTGTTTATTTTGAGTTTTTTTTTTTTTCTAAGAAATTGCACAGCCCCATTCTTACTTGGGGTGGCGGCCGGGGTGGGGGTTGAGGACGTGGGGTGAGGGGAGGCAGCTGCAGACATGAGCCTTCCCGCCTCAACACATCCTCCGTAGAAGGGACCCCCTCCCTGCTCCTGGGTCCCTGCGTGTGTGGGTGTGTGTCCGTGTGCATGGCCTGTTTGTGTGCAAGGGCCCAGGACAGAAGTATGTGTGCGTGTGTGTGTGCGTATGCGTGTGAGACAGGGCCGCCGTGGGTGTGCGTGTGTGCGACTCAGAATGTGGGTGGTGGCGCCCTCAGAGACCCTGGCATTGGCTGAGCCAATGTTGGGCCTTCTGAAAAGAAGCCCAGGGGATGGGGCCTTCAAGGTGCCGGTTTGGAGTTCAAATCCTGCTCCTGCAGAGGGGACCTGGGGGTCCAGGCTGGGAGATGGGGGAACCTGCTTCTAAAGGGCTTGTGGGGGTTTTGGGAGGGTGGAGGTGGGCAGACGCCCCTGTAAATACAGCCCTGGGGTGGTCAGAGAGGCCCATGCCACCCGTCCCCACTTGTGACATCCCCTTCGACCACCAGCTGACCATGCATGCCACGTGGCCAGCTGAGTCCAGGACCCTCTCCAGCCCTATCCCCATCAATAAAACTCTGTTTACATCCACCGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001227-Sema6b:NM_001130456:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.095 A=NA C2=0.738
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(35.7=100)
A:
NA
C2:
PF0143720=PSI=PD(0.1=0.0)
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:
CTGGCTTAGGTGACTGCACTG
R:
TCCAGCCATTCTGCATAAGCG
Band lengths:
348-763
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: