MmuINT1030856 @ mm10
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:95171791-95174024:+
Coord C1 exon
chr3:95171791-95171886
Coord A exon
chr3:95171887-95172254
Coord C2 exon
chr3:95172255-95174024
Length
368 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CCCTCCTTCTTGGTCAGCAGGCG
3' ss Score
6.44
Exon sequences
Seq C1 exon
TGCTTCTGGGTCCTGGCCCTTCCCCTGAGACCCCCAGTTCCCCCAGTGATGCCCAACAAGGGCCCCAGTCTTCCACTCTTGGAGCTCACACACAGG
Seq A exon
GTAAGGGGGTCATCTGGGAGGGACAGTATTGTAGTGTGGAACTGCTGAGTCTCAGAGTTCTAAGCCCGGTACTGATTGGTGTTTGATGCCCACTAACACCTGTTTGGAACCTCCCTTCACCACAGCTGGACTTCCCAGCCAGTGTCCTGCACAGGCAGTTTGCAGTTATTCTTGGCATGGCTACAGGGGCTACAACTGGTACGGGGAATACCCCCGACCAGTGCTCTAGCCCGTGTGTTTAGGGATCCTGAGACTGTGTGGAGTGAAGCTGAGAGGCAGAATGAAAACTTGCTGTTGGCCCCACCTGTGCCCGTTCTGTGCATCACCTACCCTAAAGCTGAGACTCCTCCCTCCTTCTTGGTCAGCAG
Seq C2 exon
GCGTGCGCAGGGACCTTTCCCCAGCCTCAGCCTCCCGATCCATTCCCATCCCACTCCTCCTGGCCTGTGTGGCCGCGGCCTTCGCTTTGGGCGCCTCAGTCTCCGGTCTCTTGGTGTCCTGTGCTTGTCGTCGCGCGAACCGCCGTCGGAGCAAGGACATCGAGACCCCGGGGCTGCCGCGCCCCCTCTCCCTTCGCAGCCTGGCCCGGCTGCACGGTGGCGGTCCTGAGCCCCCGCCTCCGCCCAAGGATGGAGATGCAGCGCAAACGCCCCAGCTCTACACTACCTTCCTGCCTCCGCCCGACGGCGGATCCCCACCGGAGCTGGCCTGCCTACCCACGCCGGAGACGACGCCCGAGCTGCCCGTGAAGCACCTCCGTGCCTCCGGGGGCCCCTGGGAATGGAACCAGAATGGGAACAACGCCTCGGAGGGCCCAGGCCGCCCACCACGGGGCTGCAGCGGGGCGGGCGGGCCCGCACCGCGAGTGCTGGTGAGGCCACCGCCCCCTGGCTGCCCCGGGCAGGCGGTAGAGGTGACCACGCTGGAGGAACTGCTGCGCTACCTGCACGGCCCTCAGCCGCCCAGGAAGGGTAGCGAACCTCTCGCCTCCGCCCCGTTCACCTCCCGGCCGCCCGCCTCGGAGCCCGGCGCCTCGCTGTTCGTGGACTCCAGCCCGATGCCGCGGGATGGCGTTCCGCCGCTCAGGCTCGACGTGCCACCCGAAGGCAAGCGCGCTGCCCCGAGCGGGCGGCCTGCTCTCTCGGCCCCAGCCCCGCGCCTGGGTGTCGGCGGCAGCCGCCGATTGCCCTTTCCCACACACCGGGCGCCCCCGGGCCTGCTCACGCGAGTGCCCTCGGGAGGCCCGGCCAGGTACTCCGGGGGGCCCGGGAGGCACCTCCTGTACCTGGGCCGGCCCGAAGGCCATCGCGGCCGCTCCCTGAAGAGGGTGGACGTGAAGTCTCCGCTGTCGCCCAAGCCGCCCCTCGCCTCCCCGCCGCAGCCCGCCCCGCACGGTGGTCATTTCAACTTCTGACGGAAGCTGCTCGCGCCCGCCCGTCGAGGCGCTGGAGGCCGCTGGCCTTCCCGGACTCCGAGACTCTCCCGGGGCCCCCCCTCTCGCCTCGGTTTATTTATTGACTTGTCTTTCCCCTGTCCTTTGGCGAGGAACTCGCCCCTCGGAGCGCCAGCATTTCAGGGGACCTGGCCGACTCCCACTCCCCGCTCCCTTCCAGCCACGCTGCCTTAAGTCGCCGCTCCGGACTCCCGCGGACTGAGCCCCGGGCGGGCCGGCCGGGGCTGGAGCCGCGCGCTGTGTAGAGTCCTCGGGCCTCCCGGGGCCGGGACGTGCCTCCTCCTACTGTGTAGGAGCCCCCTGCTTCCCAATACAGCCGTGTCCCCAAGCCGCTGCCTGACTTTCCTCGCGGTGCGGGAGGGGAAGGAGGGCGCGGCGCCCGGCCCTCTGGGTAACCGTGCTCCTGAAAGTCGGCCTCCACTGCAGCTCGGCCCCCAAGTCTCTCCGGAGCAATTGGCTTGGCGGGTGTCCCACCGGGGTTAATCAGGAAAGGTTTCCTGAAGGAGGCAATCAAAGACCTGGTGTGTGTGGGCTGAGCCGGGGCCCAGGAGAGCAGTGGGTACTGATTGGGGGTGCCGGGGAAGGCGCTCAGCACGTTTCTGGATAGAGGTCAGGCACCTTTCCACGGCCTACACTCTGGGGTGGGAGAGGGAACTTTTGGAGAAATAAAACGAAGCTGCTGCGTGATTTGAATTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777:ENSMUST00000090823:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.888
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAACAAGGGCCCCAGTCTTC
R:
CGGAGGCAGGAAGGTAGTGTA
Band lengths:
342-710
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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