RnoINT0141553 @ rn6
Intron Retention
Gene
ENSRNOG00000033983 | Sohlh1
Description
spermatogenesis and oogenesis specific basic helix-loop-helix 1 [Source:RGD Symbol;Acc:1564440]
Coordinates
chr3:3291084-3291857:-
Coord C1 exon
chr3:3291781-3291857
Coord A exon
chr3:3291287-3291780
Coord C2 exon
chr3:3291084-3291286
Length
494 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
GATGTCTCCTTTCCTCCCAGGGT
3' ss Score
9.9
Exon sequences
Seq C1 exon
GTACACCACAGGGGCAGGGTCCGAAGTGGTGGACGGAGCATCCTTTCTGCTGACCACCAATCCTGATTGGTGGTTGG
Seq A exon
GTGAGTGGGGCCGTGAGCCCAGGCTGCCCTTCCCCACACCGGCCCTGGCTCTGGGGCCTGTGTCCAACCTGACAGGACCAGGAGACTGTACCCAACCCCAGCTTACTCTCTGACCCAAGGTCCCCGAATCATCTACCCCTGCCTGGTGATGATCGGGATGACATGTGCCACCACACAAACACGTGATACTGGAGATGGCTCTGTGAGTCCTGGGTGTTTTCAGTAATGTTCCTAGGTCACCAGGACAAGTCACGTGTTGTGCATCCCCTTGACCACACTTAGGATCCGGTGCTGAATGAACACTGCTGTGGTTCCAGCATGGAAAGCATCTCCTAAGGCAGGAGCCACCAGAGTTGGCCTCATCCTATCTCACTGGGAAGAGAGGGTTCTAGAATGGACACGGTGGTGGCAGCACGGGAGCCCCTACCACGCTGTGGCCAGTCTTCTGCCAGTGTCTGGGGCACGTGCCTTACCGATGTCTCCTTTCCTCCCAG
Seq C2 exon
GGTCAGTGGAGGGCAGAGGAGGACCAGCTCTTGCCAGGAACAGCCCAGTGGATGGGGCAGAGCCAATCTACATTGGAGACCCTGAGCCCTGCTCCCAGGAGCTCCAGGCTGGCCCCGTAGAGCTGTGGGGCTTGGATTTTGGCAGCCCTGGCCTGGCCCTGAAGGATGAAGCAGACAGCATCTTCCCTGACTTTTTCCCCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000033983:ENSRNOT00000051729:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.185 A=NA C2=0.478
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
TACACCACAGGGGCAGGG
R:
CAGGGGAAAAAGTCAGGGAAGA
Band lengths:
278-772
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]