DreINT0128983 @ danRer10
Intron Retention
Gene
ENSDARG00000019778 | rps6
Description
ribosomal protein S6 [Source:ZFIN;Acc:ZDB-GENE-040801-8]
Coordinates
chr1:44347617-44348300:-
Coord C1 exon
chr1:44348229-44348300
Coord A exon
chr1:44347749-44348228
Coord C2 exon
chr1:44347617-44347748
Length
480 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGG
5' ss Score
10.26
3' ss Seq
CTTTTGACCTGTGTATTTAGCTC
3' ss Score
6.95
Exon sequences
Seq C1 exon
TGAGACTACGAGTCGGATATCCGCTCTCTTTTCCGTGGTGGACTCCAAGCGAGAAAGTCCTCCATCATGAAG
Seq A exon
GTACGGTGACAAAATTAGCGCTTTTAAAGTTTTACTATTCACCCTGTCTTCAAAATATCACACGGATTGCATGTTACAGTCTCAGAATCGCCCGACGCGCGCTCGCTTGTTGAGTTTGGCCCAAACAGAATGAAGGATGGACGTTGATCTTGTTAGGCTAGGCGAGCGGCTGTGGATGTGCGGCAACATGGCAGCGCCCGGTTCAGACATGCAATATTATATTAGACCACTTTAAAGATGTCACAAGGTCCGGGTGATTAGTAAACATAACAGCAAATGTTGTAAACCGCAATTAAAACGCTAGTACTTGTGTACGAGAGTGTCAGACTACCGTCAACTGCGCTGTAGCTTTAGCTGTTATTAGCTAGCAGAGACGTGTCAGAGGTAGACCTCACTATTCTGACAGAGGCAGAATGTGTTTCACAGTTTACAACCACAGCAGCAGGCTAATTTCTTCTCTCTTTTGACCTGTGTATTTAG
Seq C2 exon
CTCAATATCTCGTTCCCCGCCACCGGCTGCCAAAAGCTGATAGAAGTTGACGATGAACGCAAGCTGAGAATCTTCTACGAGAAGCGCATGGCCACAGAGGTGGCTGCAGACTCTCTGGGTGACGAGTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000019778:ENSDART00000023336:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0109214=Ribosomal_S6e=PU(0.8=50.0)
A:
NA
C2:
PF0109214=Ribosomal_S6e=FE(33.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATATCCGCTCTCTTTTCCGT
R:
CTTCCACTCGTCACCCAGAGA
Band lengths:
190-670
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]