MmuINT0141134 @ mm9
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
chr1:36611097-36612922:-
Coord C1 exon
chr1:36612777-36612922
Coord A exon
chr1:36611246-36612776
Coord C2 exon
chr1:36611097-36611245
Length
1531 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TCTAATATCTGTTTCTGCAGAGC
3' ss Score
8.43
Exon sequences
Seq C1 exon
GGCTGCTGGACTGAAGTTTAGACCCTGGGTGTCTGCCATGGCCCCACACTGGGCTGTCTGGCTGCTGGCAGCAGGGCTGTGGGGCCTGGGCATCGGGGCTGAGATGTGGTGGAACCTTGTGCCCCGGAAGACAGTATCTTCTGGGG
Seq A exon
GTGAGTGCCTGAAGCATGGGAGGCAGGGCCAGAGGGAGGCTGGGATAGACTGCTGGGGGAAGGGCGAGGAGGGGAGTGATGCTTGCTTGCAGGAAGGAGCTGCTGCTGAGGAATTACCCCCAAGCATGCACCTTTACACCGATATGTGTGGCTGTGGCTTTCTAAGAAACGCGAGTGGCCCCAGGGGCCCAGAACTGGTAGTGCTGGTCTAGACCTGGGCTTTGCCCCCTTCTGACACTGGGATAACTTTATGGGATCTCTTACCAGCGCACCCCCACCCTCACCCAGACCTGGCTGGCCTGGTGTGCAAGGGAGGTAGTTTCTGAATCAACCTCCCTGTTCCTCACTTGAATTGTCTCTCTTGCTTGGAAGCCTAGAGAGAGAAACCTGAACCCCAGGGCAAGTGTAAACCTAACCCTATCTCCAGTCTTTCTAGCTGTCTGTCCCTAGAAGCCCCTTTAATTCACCCTAATGGTCTCCTCTGCTGCTCTAACACTGGAGCCTTCTGATGGCTCTGGGTGGACACATATAAGCTCGCGCTTCGTGGGGGAGGAGACAGAGTGAACCAGACAGCTCTCCTTTGCTTTCGCGCACACCTGTATGGAGAGGTGATGTCAGGTGTTTGTATCATCTCTGTGCTCCTGGGACATGGGATGAGCTCACCTCCCACAGGCTACACTCAGCTGCTATTAAAGCCCCTCCCATGTCGACCCAACTCTCGTTGGTCACTGCCTCCCGACCCTGAAGCTGGCTTAAGTAGGGATCCTGTGAACAGGTGTGCAGGTATACGGTCCTCTGACAGGTTACATGACTGTATGTATGATCACGCCCTACGTGTGCTGGCCGGAAGCACAACTTCCCAGGCTTCAGCACCACCTCTGAGTCTCAGGTTCCTTTTATCTCCCAGTCCTAACCTCTTCTTCCTTCTCCACACGCCACTTTGCCAGTCCCCTGCCCATCTGTGCGTGTGTCTCTGAAAGCCTGGATTGGTGCCTGCTGGGACTTCTTAGACAAGGAATGCTTACAACTATTCTGTGCCTCCTGATGCAGTAAATCCGCCACCAGGGTCTGCCTAGACCTTGCCATGGTCAGCAAGTAGCAGAGCAGGAAATGGCAACCGAGGAAGCGGGGCTGGGGGTGGGGGGGAAGTGTCCAGTTCTGTGCCTGAGGTACCGCTGACCCTGAGGGAGCGTCATCAGTCAGATGGCTTCCTCTGGCCGGAAGCTTTGGCTGAGGTATCCTTCCTTCCCCGTTACCAGCCCAGATTACCTCCTCCCAGGCTGAGGAAGGGCCTTGGAAGCCTGGGTAGGATGGAGCTGTTGAGCCAAAGGCTATTCAGAAAAAGTCCTTTATGGCCCATAGAGGTTTGGTTGTCGTCTGTGTGTGTGTAGTGGTAGCTTTTGTGGAGAATCGTGATGACGAGGCCCAGGGGAGCCTTGGACAAAGGAAGATTGATGGATTCCTGGAACCCCAGGGAGGATGTCCTCTGCCCCTACTCATCCCCACCTTGTTCTAATATCTGTTTCTGCAG
Seq C2 exon
AGCTGGTCACAGTAGTGAGGCGGTTCTCCCAGACAGGCATCCAGGACTTCCTGACACTGACCCTGACAGAACATTCTGGCCTTTTATATGTGGGGGCCCGAGAGGCGCTGTTTGCCTTCAGTGTAGAGGCTCTGGAGCTGCAAGGAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026121-Sema4c:NM_001126047:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(7.7=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTGCTGGACTGAAGTTTAGA
R:
GCTCCTTGCAGCTCCAGAG
Band lengths:
294-1825
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: