MmuINT0150312 @ mm9
Intron Retention
Gene
ENSMUSG00000059625 | Sohlh1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:MGI Symbol;Acc:MGI:2684956]
Coordinates
chr2:25701729-25702372:-
Coord C1 exon
chr2:25702238-25702372
Coord A exon
chr2:25701877-25702237
Coord C2 exon
chr2:25701729-25701876
Length
361 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGG
5' ss Score
9.13
3' ss Seq
TTTTCCTTGTCTGGAAGCAGGAG
3' ss Score
4.59
Exon sequences
Seq C1 exon
CAAGACTCCTCAGCCTGAGACTCAGGACAGCTTGCAGACCTCATCACAAAGCTCAGCTCTCTGCACAGCTCCTGTGGCTGCTGCAAACTTGGGCCCCAGTCTTCGGAGAAACGTGGTCAGCGAGAGAGAACGCAG
Seq A exon
GTGCGGGCAACCTCGGGGTGGGCAGTATGCCAACGGGGTGGAGGAGTTTAGGTCTGTGGTTTAATGAGCTTGTATTCATCTGGACCAACCAGGATTAAAACCAGATTCCAAAGTAAGCTCAGCTTTGTGGAGTAGGCCGGTTGTTCCTACAATTTGACTTGGATTCACCCTTTCACATACCAGAACAGAGCTGCTGCTTCAGGGCTGGGCTGTGCCGTCAGCCCAGAGTTCTGGCGTGCCTCCTGGGTTCCAATGGGACAGGGCTGAACCCGCTGCTCAGGAGGCCTTGGAGGCTGCTCAGTGGTGGGTTCTTTTGCTATCTGGTGAGGGTAGGATTTTTGTTTTCCTTGTCTGGAAGCAG
Seq C2 exon
GAGGCGGATCTCGTTGAGCTGTGAGCACTTGCGGGCTCTACTGCCTCAGTTTGATGGCCGACGGGAGGACATGGCATCTGTCCTGGAGATGTCTGTGTACTTCCTCCAGCTTGCCCACAGCATGGACCCTAGCTGGGAGCAACTCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059625-Sohlh1:NM_001001714:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.674 A=NA C2=0.120
Domain overlap (PFAM):
C1:
PF0001021=HLH=PU(20.8=21.7)
A:
NA
C2:
PF0001021=HLH=PD(77.1=74.0)
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:
GACTCAGGACAGCTTGCAGAC
R:
AGAGAGTTGCTCCCAGCTAGG
Band lengths:
265-626
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: