MmuINT0141131 @ 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
chr1:36550668-36551838:-
Coord C1 exon
chr1:36551726-36551838
Coord A exon
chr1:36550829-36551725
Coord C2 exon
chr1:36550668-36550828
Length
897 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGTA
5' ss Score
5.69
3' ss Seq
TGTGCTTTGTTTTACTGTAGAAG
3' ss Score
8.43
Exon sequences
Seq C1 exon
GAGATGGCTGGCTGCTGAAGGCTGTGAGCCTGGGGCCCTGGATCCACATGGTGGAGGAACTGCAGGTGTTTGACCAGGAGCCAGTGGAAAGTCTGGTGCTGTCTCAGAGCAAG
Seq A exon
GTAGTAAGACTGGGCCACACGCACCTCCCTCTCTGTTCTCTGCTCCATTGTCTATCTGGCGCCCAGGCTCTATGCCATCCATAGTTGGGCTCATGTAGCTCTCGAGTTCCCAGAAGTAAGAGATCTAAGGTGGCCAGAACCTGTCCTCTGAAGGTTCTCTTATAGAGCCAGTCCCTGTGGGGCCCCCATTCCCAGAATCCAGCCTTGGCAAACTCCTTCCAAGTGGGGCTGCAGCTCTATCTGCAGTCTCTTCTCGGTCAAGATGTTTTGGTACCCAAGCAACAGAGACATCCGATTTCTTTGAGTCCCTAGTGGGTGTCTGAGCCAGGCCCTCAGTCTCCGGGCTCATTTAAGTGTTCACGTTTTTTCTTTTCTTTCTTTCTTTCTTTTTTTAACACCTTTATGCAAAACTCATATTCGCATCACCCTCTGGATTCTGATTTGCTTGCCCTTTACCAGCTACTATGACTCAAAGTTGCTCCCTACAACGCTGAATAATGAGATGGCAGCAAGGGAATTGTGGGGCTGAGCAAGCATGCAGATTGGCAGTCACCATTCAAACAGAGGAACCCCACCTTCCATAGGCACTGCTGTCACTGTGCTGGCTCCGGGGGCCGGGGGAAACTGAGTTTCCTGGCCCGAGTGTGAGCAAGTGAGCGTACGCCTCAGCCTCACGGGTCTGCCGTCCGTCCCTGTCTAAGAAGGTCATGTCTGTAAAGTGATTAGGATTTTGATGGCTTGTCGTAAGCCCTCATCAAAATTGTTCCTCTGGCCTGGATTTTTCTTCCGCTGCCTTTTTCTTCCTTGGGGGACCTAGTATGTTTATGCTCTCTGAACAAATCTCAGCCATCACCCCGAGGCGTGGTGTGGCTTACCCTGTGCTTTGTTTTACTGTAG
Seq C2 exon
AAGGTGCTCTTTGCTGGCTCCCGCTCTCAGCTGGTTCAGCTGTCTCTGGCCGACTGCACAAAGTACCGTTTCTGTGTAGACTGTGTCCTGGCCAGGGACCCTTACTGTGCCTGGAATGTCAACACCAGCCGCTGTGTGGCCACCACCAGTGGTCGCTCGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026121:ENSMUST00000114991:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(8.6=100)
A:
NA
C2:
PF0143720=PSI=PU(38.7=66.7)
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:
GAGATGGCTGGCTGCTGAAG
R:
CCCGAGCGACCACTGGTG
Band lengths:
274-1171
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