RnoINT0141547 @ rn6
Intron Retention
Gene
ENSRNOG00000033983 | Sohlh1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:RGD Symbol;Acc:1564440]
Coordinates
chr3:3294594-3295101:-
Coord C1 exon
chr3:3295037-3295101
Coord A exon
chr3:3294729-3295036
Coord C2 exon
chr3:3294594-3294728
Length
308 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CTTGGCTCCTTTCTCTGTAGCAA
3' ss Score
8.82
Exon sequences
Seq C1 exon
ATGGCGTCCGGTGGCCACGAGCGGGCTACTGAGGATTACGGAGTCTCCGACATTACGGGATGCAG
Seq A exon
GTAAAATTTGGGTTGACGGGCTCTGGGAGAGTCAGGTTCCAAGGCCTTTGCCTAGGGTTTACTTACATCCTCACCTTACCAGAGACAGCTGGGCAGAGCTCCCCATCTTGGCATGGAGGGGAAGGAGGGGGAGGAGGAGGGGGGAGAAGGAGGGGGAGGGGGTCCTGAGCTGGCCAGGTGGTATTCCTGGATAACCCAGGCCAGTCTTCACTTCTTCCAGACATCCACACCAAATGCCCTAGTTCTCTGTGTAGGGCACTGGTATCTTTTGTGGGGTTCACAAGTGGTCTTGGCTCCTTTCTCTGTAG
Seq C2 exon
CAAGACTCCTCAGACTGAGACTCAGGAGAACTTGGAGACTCCCTCACAAAGCTCAGCCCTCTGCCCAGCTCCTGTGGCTGCTGCAAATTGGAGCCCCTGTCTTCGGAGAAACGTGGTCAGCGAGAGAGAACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000033983:ENSRNOT00000051729:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.955 A=NA C2=0.457
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0001021=HLH=PU(20.8=21.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
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:
CCACGAGCGGGCTACTGAG
R:
GTTCTCTCTCGCTGACCACGT
Band lengths:
182-490
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]