HsaINT0156584 @ hg19
Intron Retention
Gene
ENSG00000165643 | SOHLH1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:HGNC Symbol;Acc:27845]
Coordinates
chr9:138590175-138590972:-
Coord C1 exon
chr9:138590841-138590972
Coord A exon
chr9:138590323-138590840
Coord C2 exon
chr9:138590175-138590322
Length
518 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGTTTCTTGACCGGAACCAGGAA
3' ss Score
3.17
Exon sequences
Seq C1 exon
CGGCTCCCTGTCTGGTGCCCTCTCCTGCTGCGAGGACTCGGCCCGGGGCTCGGGCCCGCCCAAGGCCCCTACGGTGGCCGAGGGTCCCAGCTCCTGCCTTCGGCGGAACGTGATCAGCGAGAGGGAGCGCAG
Seq A exon
GTGAGTGGTGGTGCCTCCCAGGGGTGAGGGCGCTGTAAAGGGGTGGAGCGGGTGAGATTATGTTCGGGGCTGCCACCAGGTGTCAGGCAGCTGGGAGGGGCTCGTGGCCTGTGCCCAGGAGAAGGACAGACTGCACATCTCCAAGTAAACCAGAAAAGCCCTGTTGGGGAACATCCTGCAGCCCCTCTTTATCCTGAAGCCTTGGCCTCTTGAGGCTGTGCACCTGTGACCCTCTGTGCTTCTGACTGCCTCTGACCCTCGCTGTCTTTTCCACACCGCAAAGCAGCCATGGTTTGGGCCTGGGCTGGACAGCCTGTCGCCGAGGTCCAGGGGTCAGGCCCAGGCTGTGCTCTGATGTGGATCTCGGGGCTTCAGACCACGGGGGCAGCTCTGAGTCATCTTGTAGCCCCCTCTGCCTGACAAGCGCCCAGGGTCTATCTGGCAGGTTCTAGCAGTTGCTGTCCCTTCTCGGGGAGGGCAGGAGGGCCCAGAGGTATTTGTTTCTTGACCGGAACCAG
Seq C2 exon
GAAGCGGATGTCGTTGAGCTGTGAGCGTCTGCGGGCCCTGCTGCCCCAGTTCGATGGCCGGCGGGAGGACATGGCCTCGGTCCTGGAGATGTCTGTGCAGTTCCTGCGGCTTGCCAGCGCCCTGGGGCCCAGTCAGGAGCAGCACGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165643-SOHLH1:NM_001101677:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.489 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0001021=HLH=PU(20.8=22.2)
A:
NA
C2:
PF0001021=HLH=PD(77.1=74.0)
Main Inclusion Isoform:
NA
Other Inclusion 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:
CGGCTCCCTGTCTGGTGC
R:
GCGTGCTGCTCCTGACTG
Band lengths:
279-797
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)