MmuINT0141268 @ mm9
Intron Retention
Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:94975480-94977238:+
Coord C1 exon
chr3:94975480-94975524
Coord A exon
chr3:94975525-94976176
Coord C2 exon
chr3:94976177-94977238
Length
652 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
CCCTCCTTCTTGGTCAGCAGGCG
3' ss Score
6.44
Exon sequences
Seq C1 exon
ATGGAGCGACCGGGAGTCAGTCTGGCCCTGGAGATTCTGCTTATG
Seq A exon
GTGAGTTCTGGCCTCAGTGTCCTGTTCCCTTTCTTGGCCTACACAACCAAATCCATTTGGGCTATAAGCAGACCTTGAACAGTCAGATGAGACTCTGGAATTGTGGACTCCTGGGTTCCAAAGGGGGTGGGGGGGCTCTTGGTGGAGAGCATACGTCTCACTGGCTCTGACCTGGTCTCTGTTACCAGTGCTTCTGGGTCCTGGCCCTTCCCCTGAGACCCCCAGTTCCCCCAGTGATGCCCAACAAGGGCCCCAGTCTTCCACTCTTGGAGCTCACACACAGGGTAAGGGGGTCATCTGGGAGGGACAGTATTGTAGTGTGGAACTGCTGAGTCTCAGAGTTCTAAGCCCGGTACTGATTGGTGTTTGATGCCCACTAACACCTGTTTGGAACCTCCCTTCACCACAGCTGGACTTCCCAGCCAGTGTCCTGCACAGGCAGTTTGCAGTTATTCTTGGCATGGCTACAGGGGCTACAACTGGTACGGGGAATACCCCCGACCAGTGCTCTAGCCCGTGTGTTTAGGGATCCTGAGACTGTGTGGAGTGAAGCTGAGAGGCAGAATGAAAACTTGCTGTTGGCCCCACCTGTGCCCGTTCTGTGCATCACCTACCCTAAAGCTGAGACTCCTCCCTCCTTCTTGGTCAGCAG
Seq C2 exon
GCGTGCGCAGGGACCTTTCCCCAGCCTCAGCCTCCCGATCCATTCCCATCCCACTCCTCCTGGCCTGTGTGGCCGCGGCCTTCGCTTTGGGCGCCTCAGTCTCCGGTCTCTTGGTGTCCTGTGCTTGTCGTCGCGCGAACCGCCGTCGGAGCAAGGACATCGAGACCCCGGGGCTGCCGCGCCCCCTCTCCCTTCGCAGCCTGGCCCGGCTGCACGGTGGCGGTCCTGAGCCCCCGCCTCCGCCCAAGGATGGAGATGCAGCGCAAACGCCCCAGCTCTACACTACCTTCCTGCCTCCGCCCGACGGCGGATCCCCACCGGAGCTGGCCTGCCTACCCACGCCGGAGACGACGCCCGAGCTGCCCGTGAAGCACCTCCGTGCCTCCGGGGGCCCCTGGGAATGGAACCAGAATGGGAACAACGCCTCGGAGGGCCCAGGCCGCCCACCACGGGGCTGCAGCGGGGCGGGCGGGCCCGCACCGCGAGTGCTGGTGAGGCCACCGCCCCCTGGCTGCCCCGGGCAGGCGGTAGAGGTGACCACGCTGGAGGAACTGCTGCGCTACCTGCACGGCCCTCAGCCGCCCAGGAAGGGTAGCGAACCTCTCGCCTCCGCCCCGTTCACCTCCCGGCCGCCCGCCTCGGAGCCCGGCGCCTCGCTGTTCGTGGACTCCAGCCCGATGCCGCGGGATGGCGTTCCGCCGCTCAGGCTCGACGTGCCACCCGAAGGCAAGCGCGCTGCCCCGAGCGGGCGGCCTGCTCTCTCGGCCCCAGCCCCGCGCCTGGGTGTCGGCGGCAGCCGCCGATTGCCCTTTCCCACACACCGGGCGCCCCCGGGCCTGCTCACGCGAGTGCCCTCGGGAGGCCCGGCCAGGTACTCCGGGGGGCCCGGGAGGCACCTCCTGTACCTGGGCCGGCCCGAAGGCCATCGCGGCCGCTCCCTGAAGAGGGTGGACGTGAAGTCTCCGCTGTCGCCCAAGCCGCCCCTCGCCTCCCCGCCGCAGCCCGCCCCGCACGGTGGTCATTTCAACTTCTGACGGAAGCTGCTCGCGCCCGCCCGTCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777-Sema6c:NM_011351:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.906 A=NA C2=0.883
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(12.7=50.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGAGCGACCGGGAGTC
R:
CGGAGGCAGGAAGGTAGTGTA
Band lengths:
344-996
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: