DreINT0109557 @ danRer10
Intron Retention
Gene
ENSDARG00000021140 | pabpc1b
Description
poly A binding protein, cytoplasmic 1 b [Source:ZFIN;Acc:ZDB-GENE-050308-1]
Coordinates
chr19:12215263-12215579:-
Coord C1 exon
chr19:12215440-12215579
Coord A exon
chr19:12215358-12215439
Coord C2 exon
chr19:12215263-12215357
Length
82 bp
Sequences
Splice sites
5' ss Seq
ATGGCGAGT
5' ss Score
2.37
3' ss Seq
ACCTTTCCTTGTTTTGTAAGGTA
3' ss Score
8.15
Exon sequences
Seq C1 exon
GTTTGTCGGCCGCTTCAAGTCTCGCAAGGAGAGGGAGGCTGAGCTTGGTGCAAGAGCCAAAGAGTTTACCAACGTCTACATTAAAAACTTTGGAGAAGACATGGATGATGACAAACTTAAGGATATCTTCAGCAAATATG
Seq A exon
GCGAGTTATTTGCATAAGTCTCATGCATTAACTATTTTCATGGTTTATACATTTAAACAAAAACCTTTCCTTGTTTTGTAAG
Seq C2 exon
GTAATGCCATGAGCATCCGTGTCATGACTGATGAAAATGGGAAATCCAGAGGCTTCGGGTTTGTGAGTTTTGAAAGGCATGAAGATGCCCAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021140:ENSDART00000032474:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.047
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=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:
GCTTGGTGCAAGAGCCAAAGA
R:
AACTCACAAACCCGAAGCCTC
Band lengths:
167-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]