MmuINT0141133 @ mm10
Intron Retention
Gene
ENSMUSG00000026121 | Sema4c
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:MGI Symbol;Acc:MGI:109252]
Coordinates
chr1:36548642-36550576:-
Coord C1 exon
chr1:36550506-36550576
Coord A exon
chr1:36550369-36550505
Coord C2 exon
chr1:36548642-36550368
Length
137 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCTCATTTCTGCCTCTGCAGTCA
3' ss Score
7.97
Exon sequences
Seq C1 exon
GTCCTTTCTGGTCCAACATGTGGCGAACTTGGACACTTCAAAGATGTGTAACCAGTATGGCATTAAAAAAG
Seq A exon
GTGAGCTGTTTTCCTTTTGTTCCCTCATTTTGAGGATGGGCCCCTGGATCACAGCCAGAGTTAGTTTATCACCTCTCACTGTGGGACCTGGGGTTCCTGCATTAACACTGGGTTCTCTCTCATTTCTGCCTCTGCAG
Seq C2 exon
TCAGATCTATTCCCAAGAACATCACCGTTGTGTCAGGCACAGACCTGGTCCTACCCTGCCACCTCTCGTCCAATTTGGCCCATGCCCACTGGACCTTCGGAAGCCAGGACCTGCCTGCAGAACAACCTGGCTCCTTTCTTTATGACACGGGACTCCAGGCGCTGGTGGTGATGGCCGCACAGTCCCGTCACTCTGGACCCTATCGTTGCTATTCAGAGGAGCAGGGGACAAGACTGGCTGCAGAAAGCTACCTTGTTGCTGTCGTGGCCGGCTCGTCGGTGACACTGGAGGCACGGGCTCCCTTGGAAAACCTGGGGCTCGTGTGGCTCGCTGTGGTGGCCCTGGGGGCTGTGTGCCTGGTGCTGCTGCTGCTGGTCCTATCGCTCCGCCGGCGACTTCGAGAAGAGCTAGAAAAGGGTGCCAAGGCATCTGAGAGGACACTGGTGTACCCCTTGGAACTGCCCAAGGAGCCTGCCAGTCCCCCCTTCCGTCCTGGCCCCGAAACTGATGAGAAACTTTGGGATCCTGTCGGGTACTACTATTCGGATGGCTCTCTCAAGATTGTGCCTGGTCACGCCCGGTGCCAGCCTGGGGGTGGGCCCCCTTCCCCACCTCCTGGCATACCTGGCCAGCCTCTGCCTTCTCCAACTCGGCTCCACCTAGGAGGTGGTCGGAACTCAAATGCCAATGGTTATGTGCGTTTACAGTTGGGCGGAGAGGACCGAGGAGGATCTGGGCACCCACTGCCTGAGCTCGCGGATGAATTACGACGGAAACTACAACAGCGCCAGCCGCTGCCTGACTCCAACCCAGAGGAGTCTTCAGTATGAGGGGACCCCCCCACCTCATTGGCGGGGGGGGGTCTCATGGGAGGTGCACTCTTAACTTTTGCACAGGCACCAGCTACCTCAGGGACATGGCAGGGGCACTTGCTCTGCCTGGGACAGACACTGCCCAGCATTTGCCCGGCCGTGAGGACCTGCTCAGCATGGGCACTGCCACTTGGTGTGGCTCACCAGGACTTCAGCCTCACAGGAGACACACCCTCCTCTGTGAATTTGAGACATGTGGGACCCCAGCAGCCAAAACTTTGCAAGGAAGAGGTTTCAAGATGTGGGCGTGTTTGTGCATATATGTGTTGGTATGCATGTGGAAGAATGTGTGTGTGTGTGTGTGTGTGTTGTAACTTTCCTGTCTCTATCACGTCTTCCCTTGGCCTGGGGTCCTCCTGGTTGAGTCTTTGGAGCTATGAAGGGGAAGGGGGTCATAGCACTTTGCTTCTCCTACCCCCAGCTGTCCCAAGCTTTGGGGCAGTGATGTACATACGGGGAAGGGAAGGACAGGGTGTTGTACCCCTTTTGGGGGAGTGCGGGACTCGGGGGTGGGCCTAGCCCTGCTCCTAGGGCTGTGAATGTTTTCAGGGCGGGGGTTGGGGGTGGAGATGGAACCTCCTGCTTCAGGGGGAGGGGTGGGCAGGGCCTCCCACTTGCCCTCCGGGTTCGGTGGTATTTTATATTTGCGCTCTTCTGACAGGGCTGGGAAGGGTTGTTGGGGGAGGGAAGGGAGGAGGTGGGCATGCTATGGATACTGGCCTATCCTCTCCCTGCTCTGGGAAAAGGGCTAACAGTGTAACTTATTGTGTCCCCACATATTTATTTGTTGTAAATATTTGAGTATTTTTATATTGACAAATAAAATGGAGAAAATGAAATTTAACCCTGCCACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026121:ENSMUST00000114991:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.388
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(25.8=100),PF138951=Ig_2=PU(1.1=4.0)
A:
NA
C2:
PF0143720=PSI=PD(34.4=11.6),PF138951=Ig_2=PD(97.8=32.1)
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:
GTGGCGAACTTGGACACTTCA
R:
ACGATAGGGTCCAGAGTGACG
Band lengths:
258-395
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