MmuINT0150315 @ mm9
Intron Retention
Gene
ENSMUSG00000059625 | Sohlh1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:MGI Symbol;Acc:MGI:2684956]
Coordinates
chr2:25700006-25700915:-
Coord C1 exon
chr2:25700782-25700915
Coord A exon
chr2:25700193-25700781
Coord C2 exon
chr2:25700006-25700192
Length
589 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACC
5' ss Score
8.66
3' ss Seq
CCTATCTTCTCCCTGTTAAGAGT
3' ss Score
6.19
Exon sequences
Seq C1 exon
GGTACAGGATCCCCCATGCTTTGGGATGCTGGATACAGACCAGAGCCAGGCTACTGAGAGAGAGTCAGAGCTGCTGGAGAGACCTTCCTCCTGCCCTGGTCATCGCCAGAGCGCGTTGTCATTCAGTGAGCCAG
Seq A exon
GTAACCTATGGCCCTGAAATGACCATCGCTGTGGCTGAAAGGGCTACCTCCCCCATGTCCAGAGTCTAGAACAGCTGACTGTCTCGCCTCTGCCTCTGCTGAAATCGGGGCAGTTGTGAGGCCTGCAGCTTTTCTAGCTGTTTTCTAGTGCACGGGGTCTTGTTCTCCAGTGCCAAGCCCTGGTCAGGAGGTACCAGTGAGTCACCAGGTGGGCTGCTTCTCATGCCAGTTTGCCCTTCTTGGATGTTAATGTCTCCCATCATTTATATTTGCCGTGTCTACAAGTCTCAGCTGGCCGGCAGGGGTTCTAAGCAGCCGCATACACAGGGGCTGGGGATAGTCAGCTGGTCCGAGGGAGGAAGGAGCTTGACCAAGCTCATAGGAGCAGTGCTGAGGGGACTCCTGACTGGAGCCCATGTGAGCAATCCAAGGCCTAGAGACTACTTTTCCAGGAACCTGCCCTGACACAGAGTTGGACATTGCCCTGCGTGGTCACCTGTTGTCAAGTACCTTTGGCTTTCATATGCACACACTGTAGGACAGTAGCTGGCCTAAGCCATGTGGGCTAACCTATCTTCTCCCTGTTAAG
Seq C2 exon
AGTCTTCCAGCTTGGGTCCTGGGCTCCCACCCTGGATCCCTCACTCATGGCAGCCAGCCACTCCCGAGGCAAGTGACATTGTTCCTGGTGGGTCACACCAGGTGGCATCCCTGGCCGGGGACCCTGAATCTTCCGGCATGCTGGCTGAGGAGGCCAACTTGGTCTTGGCATCTGTGCCTGATGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059625-Sohlh1:NM_001001714:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.935 A=NA C2=0.889
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
Human
(hg19)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
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:
GGTACAGGATCCCCCATGCTT
R:
CTGGCATCAGGCACAGAT
Band lengths:
321-910
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: