DreINT0109579 @ danRer10
Intron Retention
Gene
ENSDARG00000059259 | pabpc4
Description
poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:ZFIN;Acc:ZDB-GENE-030131-9663]
Coordinates
chr17:25297796-25298206:-
Coord C1 exon
chr17:25298112-25298206
Coord A exon
chr17:25297934-25298111
Coord C2 exon
chr17:25297796-25297933
Length
178 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
TGAAGATGTTTATGTCTCAGGCG
3' ss Score
4.64
Exon sequences
Seq C1 exon
GTAAAACACTGAGCGTGAAGGTCATGACTGACCCCACAGGGAAATCTCGGGGATTTGGTTTTGTTAGCTACGAGAAGCATGAAGATGCTAACAAG
Seq A exon
GTACAGCAAAATTGATGCTTTAGCAACTGTGCAAAAGATATCTATTAATTAAAAATATTTGGTAATTTACAGGTCAGGAATTATGAAATATGCACACAATTAATTAAGGAATTTTTATAGTACATAGATAAATGAATGAAGAATACAGTGACTGATTGTGAAGATGTTTATGTCTCAG
Seq C2 exon
GCGGTGGAAGAGATGAATGGTACTGAGCTCAATGGTAAGACGGTGTTTGTTGGCCGAGCACAAAAAAAAATGGAGCGACAAGCAGAACTCAAGAGGAAGTTTGAACAGCTTAAACAGGAAAGAATCAGCAGATATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059259:ENSDART00000082327:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.152
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(44.3=100)
A:
NA
C2:
PF0007617=RRM_1=PD(21.4=32.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAACACTGAGCGTGAAGGTC
R:
ATCTGCTGATTCTTTCCTGTTTAAGC
Band lengths:
226-404
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]