MmuINT0150311 @ mm9
Intron Retention
Gene
ENSMUSG00000059625 | Sohlh1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:MGI Symbol;Acc:MGI:2684956]
Coordinates
chr2:25702238-25702768:-
Coord C1 exon
chr2:25702651-25702768
Coord A exon
chr2:25702373-25702650
Coord C2 exon
chr2:25702238-25702372
Length
278 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CTTGGCTCTTTTCTCTGTAGCAA
3' ss Score
9.42
Exon sequences
Seq C1 exon
GCTAAGGGCTATCTGCGGCTTCCGGCTTGTTGCTTCCCTCCAACTTCGTGCCAATGGCGTCCGGTGGCCACGAGCGGGCCAATGAGGATTACAGAGTCTCTGGCATTACGGGATGCAG
Seq A exon
GTAAAATTTGGGTTGACGGGCTCTGAGAGGGTCAGGTTCCAAGACCTTTGCCAAAGGGTGACTTACATCTTCACCTTACCTGGCACAGCCAGGCAGAGCTCCCATCTTGGCGTGGAGGAGGTGGGGGAGGGGTCGTGAGCTGGCCAGATGGTATTCCTGGATGACCCAGGCCGGCCTTCACTTCTTCCAGACATCTACCCCAAATGCCCTAGTTCTCCATGTGGGGCACTGGTGCCTTTTGTGAGGTTCATAAGTGGTCTTGGCTCTTTTCTCTGTAG
Seq C2 exon
CAAGACTCCTCAGCCTGAGACTCAGGACAGCTTGCAGACCTCATCACAAAGCTCAGCTCTCTGCACAGCTCCTGTGGCTGCTGCAAACTTGGGCCCCAGTCTTCGGAGAAACGTGGTCAGCGAGAGAGAACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059625-Sohlh1:NM_001001714:1
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=1.000 A=NA C2=0.674
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0001021=HLH=PU(20.8=21.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
CTAAGGGCTATCTGCGGCTTC
R:
CTCTCTCGCTGACCACGTTTC
Band lengths:
245-523
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: