DreINT0156460 @ danRer10
Intron Retention
Gene
ENSDARG00000044655 | st14b
Description
suppression of tumorigenicity 14 (colon carcinoma) b [Source:ZFIN;Acc:ZDB-GENE-061103-613]
Coordinates
chr21:25247951-25248263:-
Coord C1 exon
chr21:25248156-25248263
Coord A exon
chr21:25248068-25248155
Coord C2 exon
chr21:25247951-25248067
Length
88 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGG
5' ss Score
4.2
3' ss Seq
TCATTCGATCTTTTCTGCAGGGA
3' ss Score
9.44
Exon sequences
Seq C1 exon
TGTGTAATGAGACTCAAATCCAATGCAAGAATGGCTTCTGTAAGCCCAGCTTCTGGGGCTGTGATGGGGTGAATGACTGTGGAGATAACACTGATGAGGAAAACTGTG
Seq A exon
GTAGGGATAAAAGGAGCTCTCAAATCAGGAAATACAGCGCAAGTGTAATGGAGACAGCTTCAGGTTGTTCATTCGATCTTTTCTGCAG
Seq C2 exon
GGAATTGCAAAACTTGGGAGTTCAGGTGTCGAAGTGGCCGCTGCATCTCAGCACAGAAGCAGTGCAATGGCTACAACGACTGTGGCGATGGTTCTGATGAATCTCGGTGTGCGAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044655:ENSDART00000147860:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=WD(100=97.3),PF0005713=Ldl_recept_a=PU(0.1=0.0)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTCTGTAAGCCCAGCTTCT
R:
CATCAGAACCATCGCCACAGT
Band lengths:
174-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]