RnoINT0141549 @ rn6
Intron Retention
Gene
ENSRNOG00000033983 | Sohlh1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:RGD Symbol;Acc:1564440]
Coordinates
chr3:3293512-3294217:-
Coord C1 exon
chr3:3294070-3294217
Coord A exon
chr3:3293637-3294069
Coord C2 exon
chr3:3293512-3293636
Length
433 bp
Sequences
Splice sites
5' ss Seq
TCTGTGAGT
5' ss Score
7
3' ss Seq
TGTGTGTATTTAAACTTCAGGTT
3' ss Score
8.38
Exon sequences
Seq C1 exon
GAGGAGGATCTCCTTGAGCTGTGAGCGCTTGCGGGCACTACTGCCTCAGTTTGATGGCCGTCGGGAGGACATGGCTTCCGTCCTGGAGATGTCTGTGTGTTTCCTCCAGCTTGCCCACAGCATGGATCCTAGCTGGGAGCAGCTCTCT
Seq A exon
GTGAGTCCTAAGCAGGCGGGCCTTGTCAGGCCCCTGCAGCCTGTCTACTATGGGATGTCCTGGTTTGGGATCATCGTACCCCTGTCTTCTCGGTACTGTGTGTTCTGTACCATGACACATTTAAACCATACCAGTTGGCATTCTTCTGAGGGGCAAGTGTCCATTGTGTCTTCCCAATATGGATTGATTAGTTTCCCGTATGTGATACCTGTGTGTGGGAGTTTCAGGGTCTCCACATGTCCAGTTCTGACCAAGAACACTCACACTCAGACTTCTCCCAAGACTGCTGCCTGACTCTCAGTGACGCCTGGGTGGATACAGCCTGACTCAGGAGCAGGGGTGGGGTGTTAGAGGAGTGAGGCTTCAGTCCATGCATACCCTTTCCCTGTGCGACCCTGAGTTTCTGGCTAGTTTGTGTGTATTTAAACTTCAG
Seq C2 exon
GTTCCTCAGCCTCCTCAAGAGATGTGGCACATGTGGCAGGGCGATGTTCTGCAGGTAACCCTTGCGAATCAGATTGCAGACAGCAAGCCAGACTCCGGGATAGCAAAAGCATCTGCCGTGGCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000033983:ENSRNOT00000051729:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.120 A=NA C2=0.595
Domain overlap (PFAM):
C1:
PF0001021=HLH=PD(77.1=74.0)
A:
NA
C2:
NO
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:
GGATCTCCTTGAGCTGTGAGC
R:
GAGCCACGGCAGATGCTTTT
Band lengths:
267-700
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]