DreINT0109561 @ danRer10
Intron Retention
Gene
ENSDARG00000021140 | pabpc1b
Description
poly A binding protein, cytoplasmic 1 b [Source:ZFIN;Acc:ZDB-GENE-050308-1]
Coordinates
chr19:12210273-12210581:-
Coord C1 exon
chr19:12210491-12210581
Coord A exon
chr19:12210384-12210490
Coord C2 exon
chr19:12210273-12210383
Length
107 bp
Sequences
Splice sites
5' ss Seq
AACGCAAGT
5' ss Score
2.98
3' ss Seq
ACATTCAATATTGTCTACAGACT
3' ss Score
5.41
Exon sequences
Seq C1 exon
GCCCAGAACCGAGCTGCATACTACCCTACCAGTCAACTGGCCCAGCTCAGACCAAGCCCCCGCTGGACCACACAAGGCGTCCGGCCTCAAC
Seq A exon
GCAAGTCTATCATTCATTCTAGAATCTTTTATCTACTTTTGAATTCAATATCTCAAGCAAAAAAAGTGCTCATTCATAGTATTGAAGACATTCAATATTGTCTACAG
Seq C2 exon
ACTTCCAGAACATGCCAGGCACGATGCGCCCCTCTGCCCCCAGACCCCAGACCTTCAGCACCATGCGACCAGCATCCCAGGTGCCCCGCATGATGTCCACTCAGCGTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021140:ENSDART00000032474:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.772 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
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:
GAACCGAGCTGCATACTACCC
R:
CACGCTGAGTGGACATCATGC
Band lengths:
194-301
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]