MmuINT0141128 @ 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
chr1:36612777-36615226:-
Coord C1 exon
chr1:36614861-36615226
Coord A exon
chr1:36612923-36614860
Coord C2 exon
chr1:36612777-36612922
Length
1938 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
AGTTTCTTTTCCTTCAGCAGGGC
3' ss Score
6.65
Exon sequences
Seq C1 exon
GTAAAGGGTCCCCAAGCCTCAGTGCCGGGTAAGCAAGGCAGCGGGTCGCAGCCCCCTCCTGGGCGGGCCTTCGCGTCCCGCCCCCGGCCACCACTCGACACCCTCTGCCTGACGTCAAGGGGTTGGGGGCGGAGAGCGGCGGTGGCGGCGGCTGCAGCGGAGAAAGAACCGGCGCCCGGCGCGGTGGAGCGCCGAATCCGAGCTCAGGGGCGCCGAGAGCCGTGCTGAGACCGAGGGGCGGTGGCACGGGACAGCCTTAGCGTGCTGGCGGGCGGGCGCAGTCTGGAGCGGCGCGGGGGCAGGGGAGGACGGTGGCCGGAGTCAAACGCGAGGGCAGCGCCCAGGGATTGGAGCTGCACGAAAGAG
Seq A exon
GTGAGTGAGGCCGGAGCGGTGGGGCCCCGGGGCCGCTGCTTTGTCCCCTTGCTTGGGTAGGGGCTAGCGCGCGCGCTAGAGGACAGCGTCTAGGGGTGCAGGGCGGGGCGACAGCAAAGACAGCTGTCCGATCCGGGTCCCTCTTGAGTCCGCCGCGGGCTGCCCAGTGGCGATCGGCATCAAGGCAAGCAGTGCCTGCAGCTCCACTGGCCGGAGCAGCGGGAGCCTGGGGGTACGGACAGCGCTAGGGGCAGTGGGGGACCCTTGGGCTGTCCAGCGCGCGGTCCGAATCTTTGCCAGGCTCGCGAACTGCTCGGGTTCCCCCCACCTCGACGGAAAGTTAGGGGCGGGCTTGGACCGTGGCCGATGTTGTGGGATCGGATTTCCCTAGCGCGGCCCCCCGCCCTCCCGTTCTGCTCCGGAGGCGGGCTGGCACTGAGAACCAGCCCCCTAGCCAAAGCTCCGCCGCCCGGTCCCTCTCTGGAGCGCCGCAATCCACGACCGGGTGTGCAAGTGTGGGGTGCAAATCCTGGTCCTGCACCCCTCCATCCCCTTGGCTGTCCGTGTCCCTTGCTTCGGGAAGAGCTTGGGGGTTGGGTCACCGCTACGCCTGCAGATTCTCGGAGCGCACCACCGGGTTTTGACCCCAGCCTAGGGTAATTGGCAGAGAGGAAACTGAGGGTGTGTCAGGGGGGACTGCTCCGGGGAAGGCAGCCCCAGCCCCCCGCCCTTCCCGCGCGGAGGTTCTTGGCCGACAGGGGGCGTCCGCAAGCCCGGCTTTGCCACGCTCCCAGCGCTGCCGCTTTGTTTGCATTCAAATCCCCGGAGCTGGGGGAGGGGAGAGTCCACAGTAGGGAGACCGAGACCGGGTCTTGGCTAGGAACCTTTGTTTTGGGGTGCAATCCTCAGATTCTGCATCTCTGTTCCCAGCCCCTAGCGTCTAGATTAGTGGAGATCCGTTCCGTTTGCCTACTGCCTAGTGCATGGTCCCCGAGGTGCAATCCCGGAGTTAAGAACGTTCGTCAGAGCCGGGGAGGAGGGGACGCAGCCCTTGACGATCATTTGTGGGCATCCCCTGTTGTCCAGGAGAACCCCGCTTCGGCCTCCCCAACCCATTTCACTTCCCTCCACGATCCCGCTCTCGCGGAGGCGAGGAGATTCCCAGACAGAAGCCTGGAACTGACTCGTGGCCCGGTCGCCTCTCTGCGGGAGGGTCAGTGTCTTGTAGAAGGCTGTTGGAGAAACAGGACTGGTCCTGGTCATTTCCACGCCCATCCCACCCACTTCCTGCCTCCCTCTTGGGCAACAAAGGGGCCTCGGAAGCTGGGCCCATTTGGTTCCCGGCCCCACTCCTACTCCAGCCCTGCTGATGTGGAACCGGGTTTGGGCTCTGCCCGGCTATTGTCTGCGCTGGGGGAGGGGACGGGCTGGGGCCGGGAACTCTACACGCTGCCTGCTTCACCAAGTCCCCCACTGAAGCTCTTTGCCCAACCGGCTGCCTGCGGCTGCTGAATAAGGGGTATATCTCCCCGAATTAGGTCTTGGGGCTGGCCTGGGTCCCACTGGTAGCAAGCCCTGTTTTTTATGGTTATTGTAAGAAACTCTGAAACCTTTAAGGCCAGAAGGAGCCAATGAGGGGGAGTCCCTCTTTTATTTTTTTCCACACAACTCCCTGTTGAAGGGAGGGAGTAGGGATGGCCTGGAGGCCACAGGCGGCTTTTGATGACTGCCCACGCCTAGTGCTTGCTGACTAAGTTCCTCTCCTTGCTCTTCTGGGAGACCCCCAGGGCTCTTGTGGGCAGAGGCCAGTTGCAGGATCAGGAGGAGATGTAAAGGCTCTGGGGGAGGTTTGTTCCAGTGTGCGTCCTGTGTTGCTTGTCTCTTGGTGCGGGCCCCCTTCCGGTCTGTGATGCTGACCAGTTTCTTTTCCTTCAGCAG
Seq C2 exon
GGCTGCTGGACTGAAGTTTAGACCCTGGGTGTCTGCCATGGCCCCACACTGGGCTGTCTGGCTGCTGGCAGCAGGGCTGTGGGGCCTGGGCATCGGGGCTGAGATGTGGTGGAACCTTGTGCCCCGGAAGACAGTATCTTCTGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026121-Sema4c:NM_001126047:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGCAGCGGAGAAAGAACC
R:
AAGATACTGTCTTCCGGGGCA
Band lengths:
356-2294
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: