DreINT0109570 @ danRer10
Intron Retention
Gene
ENSDARG00000002597 | pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:ZFIN;Acc:ZDB-GENE-030131-5836]
Coordinates
chr8:45333264-45333581:+
Coord C1 exon
chr8:45333264-45333358
Coord A exon
chr8:45333359-45333443
Coord C2 exon
chr8:45333444-45333581
Length
85 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAAA
5' ss Score
4.51
3' ss Seq
TTTTTTTCTCTTTGTGGTAGGCA
3' ss Score
8.99
Exon sequences
Seq C1 exon
GTAAAACTCTTAGCGTCTGTGTGATGACTGATGAAAGGGGACGCTCCCGTGGCTTTGGATTTGTCAATTTTGTCAACCATGGCGATGCTAGGAGG
Seq A exon
GTAAAAATGCAAATACAGATGTATCTTCATTATATGATAGTGACGGGTAAACAGAGATTTAACTTTTTTTTTCTCTTTGTGGTAG
Seq C2 exon
GCAGTAACTGAAATGAATGGCAAAGAGCTCAATGGCAGGGTCCTGTATGTAGGCAGAGCTCAGAAAAGACTCGAGAGGCAGGGAGAGCTCAAGCGCAAGTTTGAGCAAATTAAGCAAGAGCGCATACAACGTTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002597:ENSDART00000134161:6
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=0.043
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:
TCCCGTGGCTTTGGATTTGTC
R:
ACGTTGTATGCGCTCTTGCTT
Band lengths:
183-268
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]