DreINT0109560 @ danRer10
Intron Retention
Gene
ENSDARG00000021140 | pabpc1b
Description
poly A binding protein, cytoplasmic 1 b [Source:ZFIN;Acc:ZDB-GENE-050308-1]
Coordinates
chr19:12210491-12210931:-
Coord C1 exon
chr19:12210659-12210931
Coord A exon
chr19:12210582-12210658
Coord C2 exon
chr19:12210491-12210581
Length
77 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TTTAATGTCTTGTATCTCAGGCC
3' ss Score
7.95
Exon sequences
Seq C1 exon
GTCATGATGGACGGTGGTCGCAGCAAAGGCTTCGGTTTTGTCTGTTTCTCTTCTCCTGAGGAAGCCACTAAAGCTGTGACTGAGATGAATGGCCGTATTGTGGCCACCAAGCCACTGTATGTGGCTCTTGCTCAGCGTAAAGAGGAACGGCAGGCCCATCTCACCAATCAGTACATGCAGAGGATGGCCAGTGTCCGTGCAGTGCCAAACCCTGTTATCAACCCCTACCAACCTGCACCTCCATCAGGATATTTCATGGCTGCCATTCCACAG
Seq A exon
GTAAAGCGGTGACCTTTTTGTTCATAGCTCTTCGATTTTAACTGCTACTTATTTGTATTTAATGTCTTGTATCTCAG
Seq C2 exon
GCCCAGAACCGAGCTGCATACTACCCTACCAGTCAACTGGCCCAGCTCAGACCAAGCCCCCGCTGGACCACACAAGGCGTCCGGCCTCAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021140:ENSDART00000032474:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.297 A=NA C2=0.772
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=42.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCTCTTGCTCAGCGTAAAG
R:
AGGGTAGTATGCAGCTCGGTT
Band lengths:
179-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]