DreINT0109552 @ danRer10
Intron Retention
Gene
ENSDARG00000021140 | pabpc1b
Description
poly A binding protein, cytoplasmic 1 b [Source:ZFIN;Acc:ZDB-GENE-050308-1]
Coordinates
chr19:12207755-12208067:-
Coord C1 exon
chr19:12207919-12208067
Coord A exon
chr19:12207840-12207918
Coord C2 exon
chr19:12207755-12207839
Length
79 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TGCTTTACTCTCATCCTCAGCCT
3' ss Score
6.92
Exon sequences
Seq C1 exon
CTACTCAGACCATGGGTCCTCGTCCTTCCACTGCAGCCGCTGCAGCTTCTGCTCCACCAGTGCGTGGCGTGCCTCAGTACAAATACGCCCCCAGTGTCCGCAACCCCCAGCAGCACATGAACACACAGCCTCAGGTTACCATGCAGCAG
Seq A exon
GTAGGACACTCATTTCATCACTTCCCAAATATTTTGAGTAGATTATAAGTTCACTGTATTGCTTTACTCTCATCCTCAG
Seq C2 exon
CCTGCCGTGCATGTGCAAGGACAGGAACCGTTGACGGCCTCCATGCTCGCCGCTGCGCCTCCACAGGAACAGAAGCAGATGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021140:ENSDART00000032474:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.990 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=69.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCATGGGTCCTCGTCCTTC
R:
CGTCAACGGTTCCTGTCCTTG
Band lengths:
178-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]