DreINT0109555 @ danRer10
Intron Retention
Gene
ENSDARG00000021140 | pabpc1b
Description
poly A binding protein, cytoplasmic 1 b [Source:ZFIN;Acc:ZDB-GENE-050308-1]
Coordinates
chr19:12202416-12203008:-
Coord C1 exon
chr19:12202910-12203008
Coord A exon
chr19:12202813-12202909
Coord C2 exon
chr19:12202416-12202812
Length
97 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGA
5' ss Score
6.12
3' ss Seq
ATGATGTCTCTGTTTTGCAGGGT
3' ss Score
10.23
Exon sequences
Seq C1 exon
GTCGATGAAGCTGTGGCTGTACTCCAGGCTCACCAGGCTAAAGAAGCCGCTCAGAAAACAGTCACAAACTCTACTGGTGTGCCAAGCGTTTAAGCCAAG
Seq A exon
GTTAGATGTTCTTCGTTATCTGCAGTGTTTTTTATTGCACGCTTCAAATGTTCACTTTGTTTGGGCAAACTGAGGTCATGATGTCTCTGTTTTGCAG
Seq C2 exon
GGTTTGCAACCTTGAATCTTCACTGGGAGGGGAAAAAAAGTAAACATCGAAAAAAATGAAAACACAGAAAACATCGCAAAACATCTAAAACAATATTTAAAAAAGAAACTAGAAGGAGCCAGGTCTAGAGACAAGCATTCTAGGCCTAGTTATGGTATTTTAAAAAAGGAATTAAAAAAAAAAACGAGAAAAACGTAATAAGAAATAAAGTTCGGGGTTTAAAAAAAACTACAGTATAGAGAATAAACAGCCGTAAAGCGTTCCTGCATTGTTTTATTGCTTTTAATTCCTGGCTATGTCACGTTTTTGGAAGGGAGGTGAGAACTGGCAGAACCAGCAATGTGAAGTTATTTTAAATCGAAAATATGCTTGCTCAAATAAAGTTCATTTAAATGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021140:ENSDART00000032474:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.933 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0065813=PABP=PD(9.7=22.6)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACTCTACTGGTGTGCCAAGC
R:
TGCTTGTCTCTAGACCTGGCT
Band lengths:
170-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]