MmuINT0150317 @ mm9
Intron Retention
Gene
ENSMUSG00000059625 | Sohlh1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:MGI Symbol;Acc:MGI:2684956]
Coordinates
chr2:25698517-25699520:-
Coord C1 exon
chr2:25699444-25699520
Coord A exon
chr2:25698880-25699443
Coord C2 exon
chr2:25698517-25698879
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
GGTCGGTGGAGGGCAGAGGAGGCCCAGCCCTTGCCAGGAGCAGCCCAGTGGATGGGGCAGAGCCAAGCTTCATCGGAGACCCTGAGCTTTGCTCCCAGGAGCTCCAGGCTGGTCCTGGAGAGCTGTGGGGTTTGGATTTTGGCAGCCCTGGCCTGGCCCTGAAGGATGAAGCGGACAGCATCTTCCCTGACTTTTTCCCCTGATAGCTGAGTCCCCCAGAGTTTAGTTTGCTGGGGAGCTGTCCTGTGCCTGGGTGTTGTATTTTGGGCTTGGTTTGCAGCTGAGGCCTAATTTGAGGGAGCCTGGCAGGGCTGTGAGTGGAGTTTGTATTAAAGAGGAAAGTGGTTTTTCTGGCAGAAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059625-Sohlh1:NM_001001714:7
Average complexity
IR-S
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
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: