DreINT0109578 @ danRer10
Intron Retention
Gene
ENSDARG00000059259 | pabpc4
Description
poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:ZFIN;Acc:ZDB-GENE-030131-9663]
Coordinates
chr17:25298112-25298418:-
Coord C1 exon
chr17:25298279-25298418
Coord A exon
chr17:25298207-25298278
Coord C2 exon
chr17:25298112-25298206
Length
72 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
AATTTGGTGTCTACCTGCAGGTA
3' ss Score
9.29
Exon sequences
Seq C1 exon
GTTTGTGGGCCGTTTCAAGTCCAGGAAGGAGAGAGAGGCAGAAATGGGTGCCAAAGCCAAAGAGTTCACTAATGTTTACATCAAGAACTTTGGCGATGACATGGATGATCAGAGACTGAAGGAGCTCTTTGATAAATATG
Seq A exon
GTAAGAGTATAAATAATAAATGTTTTCCCAGTGGTTGGGCCTTTTTTCTGAAAATTTGGTGTCTACCTGCAG
Seq C2 exon
GTAAAACACTGAGCGTGAAGGTCATGACTGACCCCACAGGGAAATCTCGGGGATTTGGTTTTGTTAGCTACGAGAAGCATGAAGATGCTAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059259:ENSDART00000082327:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
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:
CCAGGAAGGAGAGAGAGGCAG
R:
ATCCCCGAGATTTCCCTGTGG
Band lengths:
174-246
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]