DreINT0109558 @ danRer10
Intron Retention
Gene
ENSDARG00000021140 | pabpc1b
Description
poly A binding protein, cytoplasmic 1 b [Source:ZFIN;Acc:ZDB-GENE-050308-1]
Coordinates
chr19:12215025-12215357:-
Coord C1 exon
chr19:12215263-12215357
Coord A exon
chr19:12215163-12215262
Coord C2 exon
chr19:12215025-12215162
Length
100 bp
Sequences
Splice sites
5' ss Seq
AGGGTCAGT
5' ss Score
5.85
3' ss Seq
ACTTTGCGCTCTGGTTACAGGCT
3' ss Score
7.93
Exon sequences
Seq C1 exon
GTAATGCCATGAGCATCCGTGTCATGACTGATGAAAATGGGAAATCCAGAGGCTTCGGGTTTGTGAGTTTTGAAAGGCATGAAGATGCCCAAAGG
Seq A exon
GTCAGTTCAGCTTTAATTGCAGTCAGACCAACATTTCTGTAGATTTCTTGGAATGAACGTGAAACCGTGTATTGTCAATGACTTTGCGCTCTGGTTACAG
Seq C2 exon
GCTGTAGACGAGATGAATGGCAAAGAAATGAATGGAAAGCTCATCTATGTGGGTCGTGCTCAGAAAAAAGTGGAGCGTCAAACTGAGCTCAAGCGCAAATTTGAACAGATGAAGCAAGACCGCATGACACGCTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021140:ENSDART00000032474:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.047 A=NA C2=0.290
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(44.3=100)
A:
NA
C2:
PF0007617=RRM_1=PD(21.4=32.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCATGAGCATCCGTGTCATGA
R:
CTGGTAGCGTGTCATGCGG
Band lengths:
227-327
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]