RnoINT0141548 @ rn6
Intron Retention
Gene
ENSRNOG00000033983 | Sohlh1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:RGD Symbol;Acc:1564440]
Coordinates
chr3:3294070-3294728:-
Coord C1 exon
chr3:3294594-3294728
Coord A exon
chr3:3294218-3294593
Coord C2 exon
chr3:3294070-3294217
Length
376 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGG
5' ss Score
9.13
3' ss Seq
TTCCCCTTGTCTGGAAGCAGGAG
3' ss Score
4.1
Exon sequences
Seq C1 exon
CAAGACTCCTCAGACTGAGACTCAGGAGAACTTGGAGACTCCCTCACAAAGCTCAGCCCTCTGCCCAGCTCCTGTGGCTGCTGCAAATTGGAGCCCCTGTCTTCGGAGAAACGTGGTCAGCGAGAGAGAACGCAG
Seq A exon
GTGCGGGCAGCCTCGTGGTGGGCAGGATGCCAGTGGGGTGGAGGAGTTTTAGGTCTGTCTATGGTTTAACTAGCTTATACCCGCCTAGACCGACCAGGATTCAAACCAGATCCCCAAGTAAGGTTTGTGGACTAGGTCGGGGTGTTCCTACAGCTTGACTTGGAGTCACCCTTTCATATACCGGGACAGAATTGCTTCAGGGCTGTGCCGTCAGCCCAGAGTTACTGTGTGTCTCAAGGGTTCCGACGGGATAGGCTGCTGCGGCCTGAGCCTTGCTGCTCTGGAGGGAGGCCTTGGGGGCTGCTCAGTGGTGGGTTCCAGAGGTTCTTTGGCTCTCTGGTGAGGGTTGGATTATTTTCCCCTTGTCTGGAAGCAG
Seq C2 exon
GAGGAGGATCTCCTTGAGCTGTGAGCGCTTGCGGGCACTACTGCCTCAGTTTGATGGCCGTCGGGAGGACATGGCTTCCGTCCTGGAGATGTCTGTGTGTTTCCTCCAGCTTGCCCACAGCATGGATCCTAGCTGGGAGCAGCTCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000033983:ENSRNOT00000051729:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.457 A=NA C2=0.120
Domain overlap (PFAM):
C1:
PF0001021=HLH=PU(20.8=21.7)
A:
NA
C2:
PF0001021=HLH=PD(77.1=74.0)
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:
TGAGACTCAGGAGAACTTGGAGA
R:
CTGCTCCCAGCTAGGATCCAT
Band lengths:
262-638
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]