DreINT0156458 @ danRer10
Intron Retention
Gene
ENSDARG00000044655 | st14b
Description
suppression of tumorigenicity 14 (colon carcinoma) b [Source:ZFIN;Acc:ZDB-GENE-061103-613]
Coordinates
chr21:25248364-25248690:-
Coord C1 exon
chr21:25248557-25248690
Coord A exon
chr21:25248469-25248556
Coord C2 exon
chr21:25248364-25248468
Length
88 bp
Sequences
Splice sites
5' ss Seq
ATCGTGAGT
5' ss Score
8.88
3' ss Seq
ACTCTGTCACCTTTCCACAGCCT
3' ss Score
8.8
Exon sequences
Seq C1 exon
GATATGTGGAGAGAAGCCACCTAAAACTGTGTACACAGTCAAATCAAACCAATTAACAGTAAAATTCAATTCTGACCGTTCCTATGTGAGTGAAGGATTTTCTGCAGAGTTTGAGGCCTTTGAACCCACCAATC
Seq A exon
GTGAGTAGAATCATGTTTTTTTTAAAGGGGTTGTTTATGTTCTAAGCCAGTCCACATGCTAAAAAATTACTCTGTCACCTTTCCACAG
Seq C2 exon
CCTGTCCTGGAAGATTTGAGTGTGACAATGATCTGTGTATTTCATCTGACCAGCATTGTGATGGGTACAATGACTGTGGTGATATGAGTGATGAGAGAGGCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044655:ENSDART00000147860:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.005 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(26.7=77.5),PF0005713=Ldl_recept_a=PU(2.8=2.5)
A:
NA
C2:
PF0005713=Ldl_recept_a=PD(94.4=94.4),PF0005713=Ldl_recept_a=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGACCGTTCCTATGTGAGTGA
R:
TGCAGCCTCTCTCATCACTCA
Band lengths:
169-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]