MmuINT0150317 @ mm10
Intron Retention
Gene
ENSMUSG00000059625 | Sohlh1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:MGI Symbol;Acc:MGI:2684956]
Coordinates
chr2:25842995-25844000:-
Coord C1 exon
chr2:25843924-25844000
Coord A exon
chr2:25843360-25843923
Coord C2 exon
chr2:25842995-25843359
Length
564 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
GATGTTTCTTTTCCTTCCAGGGT
3' ss Score
10.9
Exon sequences
Seq C1 exon
GTACACCACAGGGGCAGGGTCCGATGTGGTGGATGGAGCACCCTTTCTGATGACCACCAATCCTGACTGGTGGTTGG
Seq A exon
GTGAGTGAGCCTAGGCTGCCTTTCCCCCACACCAGCCCTGGCTCTGGGGCCTGTGTCCAGCCAGCCAGGACCAGGAGACCGTATCCGATCTCAGCTTGCTCTCTGACCCAAGGTCCCCAAATCATCTCCCCGCATCTAGCTATGTTCAGGATGACAGACAGGGACAGAGGTAACGTCTGACCATATGCAATGACGTGAGCACATGATATGTGCAAATGGCTGTGTGAGTCCTGGGTGTTCTCAGTAAAGTTCCTAGGTCGGCACCAGGACAAGTCAGGTGTTCTGCGTCTCCTCAATCTTTAGGATCCGGTGTTGAGTGAACACCTCTGTGGTCCTGGCATGGAGAGCAGCATCTCCTGAGGCATGAGAGTAGGTCACCAGACTTGGCATCATCCTACCTCCCTGGGAGGAGAGAAATGGGGTTCACATTCTCTCACAGAGGGGCAACAGGCACCTAGAATGGACACTGTGCTAGCAGCATGGGAACCCCTACCATGCTGTGGCCAGTCTTTGGCCAGTGTCTGAGGTACATGTCTGCCTTACTGATGTTTCTTTTCCTTCCAG
Seq C2 exon
GGTCGGTGGAGGGCAGAGGAGGCCCAGCCCTTGCCAGGAGCAGCCCAGTGGATGGGGCAGAGCCAAGCTTCATCGGAGACCCTGAGCTTTGCTCCCAGGAGCTCCAGGCTGGTCCTGGAGAGCTGTGGGGTTTGGATTTTGGCAGCCCTGGCCTGGCCCTGAAGGATGAAGCGGACAGCATCTTCCCTGACTTTTTCCCCTGATAGCTGAGTCCCCCAGAGTTTAGTTTGCTGGGGAGCTGTCCTGTGCCTGGGTGTTGTATTTTGGGCTTGGTTTGCAGCTGAGGCCTAATTTGAGGGAGCCTGGCAGGGCTGTGAGTGGAGTTTGTATTAAAGAGGAAAGTGGTTTTTCTGGCAGAAACAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059625:ENSMUST00000076989:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.370 A=NA C2=0.463
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GTGGATGGAGCACCCTTTCTG
R:
AGGCTCCCTCAAATTAGGCCT
Band lengths:
353-917
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