DreINT0109580 @ danRer10
Intron Retention
Gene
ENSDARG00000059259 | pabpc4
Description
poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:ZFIN;Acc:ZDB-GENE-030131-9663]
Coordinates
chr17:25297336-25297933:-
Coord C1 exon
chr17:25297796-25297933
Coord A exon
chr17:25297432-25297795
Coord C2 exon
chr17:25297336-25297431
Length
364 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TTGTAAATTTGTGTTTACAGGGT
3' ss Score
8.25
Exon sequences
Seq C1 exon
GCGGTGGAAGAGATGAATGGTACTGAGCTCAATGGTAAGACGGTGTTTGTTGGCCGAGCACAAAAAAAAATGGAGCGACAAGCAGAACTCAAGAGGAAGTTTGAACAGCTTAAACAGGAAAGAATCAGCAGATATCAG
Seq A exon
GTAAAGGAGCTGCTTTGAGTTGTCTTGATGTGTTCAGAGAGAAAAAAAAAACATTAAACACACAATTCATATTAGAGATTAATTTTGGCCCACTTAGACAGAGAAATCTTGAGATTAGTTTTTCAGAACCTAATTACAAATACAAAATACAGTGGACAACTGATTTTTCAAAGCCTTAACTTTAAAAAACAAAGAAATGGCCAGAAAACATCTTGAGCCTTCTTCTTCAGCATCCTATAACTATAAAATGTTTTTATCAAGGCGATAAGTATAATATTAAAAAATAAAGATTTGTTGGTCATTATCGATATGGTTGCTAATATTGTGTGCATCACTAATTAATATTGTAAATTTGTGTTTACAG
Seq C2 exon
GGTGTTAACTTGTACATCAAGAATCTTGATGACACCATCGATGATGAGAAACTTCGTAAAGAGTTTTCTCCTTTTGGCTCCATTACAAGTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059259:ENSDART00000082327:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.152 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(21.4=32.6)
A:
NA
C2:
PF0007617=RRM_1=PU(40.6=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGGTGGAAGAGATGAATGGT
R:
TGGCACTTGTAATGGAGCCAA
Band lengths:
232-596
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]