DreINT0109583 @ danRer10
Intron Retention
Gene
ENSDARG00000059259 | pabpc4
Description
poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:ZFIN;Acc:ZDB-GENE-030131-9663]
Coordinates
chr17:25292669-25293581:-
Coord C1 exon
chr17:25293368-25293581
Coord A exon
chr17:25292803-25293367
Coord C2 exon
chr17:25292669-25292802
Length
565 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGA
5' ss Score
6.04
3' ss Seq
TTTCCTCTTGGCTTTACTAGGAG
3' ss Score
9.09
Exon sequences
Seq C1 exon
GCCCAGAACAGAACAACATACTATGCACCAAACCAGCTCACCCAGATGCGTCCAAACCCGCGCTGGCAGCAGCAGGGTGGCAGAGGTCAGGGTGGTTTCCAGGGCATGCCCAGCTCCTTACGCCAGCCAGGGCCCCGGGCTAACATTCGCCACCTGGCACCCAATGCTTCCAACCAAGGCCCACGCGGGATGCCCACAGGTGCACAGAGAGTGG
Seq A exon
GTGAGAAAACCCACCCACTGATGATGATGGCCCACTGTGATCTGCTTTCCTGAAGATAAAAAAAATACTAAAAGCTAGACATTTTTAAGTTTGTTTACCTTACTATAATCACATTAGAATGAAAAGCATCACAAACTACACATTTAAAGGAATAGTTCACCCAAAAGGGATTTTTTACTCACAATTTATTCACCCTGTGAATGAGTTTCTTTCTTCTGCTGAAATTTTGTCATAATTTTGCTCACTCTTTGCCTTATGGTGAACTTATGATGATTTTTTTGAACACAAAAGAAGATATTCTGAAGAATGTTAGAAATCATGGACTAATATGGTACTTTCTACTATGGATGTCAATGGCTACCCTTTTCTAACATTCTTTAAAATATTTTCTTTTTTTTTTTTGTTCAACAGAAGAAAGAAACTCAGACAGGTTTGGAACAAGTGAAGAACAGAATTTGTATTATTTTTGTGCAAACTATCCCTTTATTGATTTTAAGCGTGCTTATTTATTGGTGTTTATTCTATCTGATCATCACATTAATTCTTTTCCTCTTGGCTTTACTAG
Seq C2 exon
GAGGGACTGGCCAACCGATGGGTCCCCGTCCTGCCATGGGGATGACGACCCCACGTGCCATGCCACCATACAAATATGCCTCCACCATCCGAAACACTCAGCCTCAGGTAGTGCAGCCCATCGCTCTGCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059259:ENSDART00000082327:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.968 A=NA C2=0.956
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:
GCCCAGAACAGAACAACATACT
R:
GATGGGCTGCACTACCTGAGG
Band lengths:
336-901
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]