DreINT0109553 @ danRer10
Intron Retention
Gene
ENSDARG00000021140 | pabpc1b
Description
poly A binding protein, cytoplasmic 1 b [Source:ZFIN;Acc:ZDB-GENE-050308-1]
Coordinates
chr19:12207541-12207839:-
Coord C1 exon
chr19:12207755-12207839
Coord A exon
chr19:12207672-12207754
Coord C2 exon
chr19:12207541-12207671
Length
83 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAAG
5' ss Score
4.2
3' ss Seq
TTTATTTTAACCTTTCACAGGTG
3' ss Score
9.42
Exon sequences
Seq C1 exon
CCTGCCGTGCATGTGCAAGGACAGGAACCGTTGACGGCCTCCATGCTCGCCGCTGCGCCTCCACAGGAACAGAAGCAGATGCTGG
Seq A exon
GTAAAGATTGTTGAGGATTTGCTGCCTTTGATTGTCCAATCTTTTTTTGTGTGAGGCTAATCTTTTATTTTAACCTTTCACAG
Seq C2 exon
GTGAACGCCTCTTCCCACTTATCCAGAATATGCATCCAAGCCTGGCTGGCAAGATCACTGGTATGTTGCTGGAAATCGACAATTCTGAGCTCCTCCATATGCTGGAGTCTCCAGAGTCCCTGCGCTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021140:ENSDART00000032474:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.477
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=69.0)
A:
NA
C2:
PF0065813=PABP=FE(59.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGGACAGGAACCGTTGACG
R:
TGGAGGAGCTCAGAATTGTCGA
Band lengths:
167-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]