DreINT0109565 @ danRer10
Intron Retention
Gene
ENSDARG00000002597 | pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:ZFIN;Acc:ZDB-GENE-030131-5836]
Coordinates
chr8:45340417-45341352:+
Coord C1 exon
chr8:45340417-45340550
Coord A exon
chr8:45340551-45341249
Coord C2 exon
chr8:45341250-45341352
Length
699 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
TTTTTCCTTTTTTTTTTAAGGTT
3' ss Score
12.44
Exon sequences
Seq C1 exon
CCAACATTGGGACCCAGACTGCAGGCGGGAGAGCTGCGGGAACTGCAGTCAGAGGAGTCAGCCAATACAAGTACTCAGCAGGGGTTCGAAACGTGCAACAGGTCATTAATGCCCCAGCTCCTGTTGTTCATCAG
Seq A exon
GTAAATGAACATGCACACCTTTACTCGAGTTGAACTTAAAGCCCTGCATGCAAAGTTTTAGCTTCTCAGAAAAGACCATTTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAATAACCTAATGCATTGCTTTCAGTGATGGAAAGAGTACTAAAAATCATACTCAAGTAAAAGTACCATTACTTGCCAATAAATGTAGCTCTAGAGGGAGCTGTAAAACAGGAGTTGTATATGAGGGAGAAAGAGAGTAGTCATGAAGAGAGTACAAGGACAACACAGAGTTTTAGGCAGAGTGTGTGTTTGTGTGATTTTCTGACACTTACCAGTAGTTTTACTACAGAAATGTATTGTTCAGGAAAATGCTACTAAACATTTATAGTGGTCGGCATTTGAAGTGAATCAGTTTTGACCAACCTTAAATGTTGACTAAATCGCTGCAACTTTTGTCAGTTCATAGAAGTCTGAAATGCAGTATTTACCATTCATAGTGTTGCAGCACCTTAGTTCAACAAGATACATAGCTGCTACATTAATATAGAAAAATATGTACTTTGAGTATATCAGCCTTTTTTCCTTTTTTTTTTAAG
Seq C2 exon
GTTGTGCAAAATACAGAACCAGCAGTTCATATGAAAGGCCAGGAGCCCCTTACTGCCTCAATGCTGGCAGCTGCACCTTTAAAAGAGCAGAAACAACTACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002597:ENSDART00000134161:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.342 A=NA C2=0.595
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=57.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAACATTGGGACCCAGACTG
R:
TTGTTTCTGCTCTTTTAAAGGTGCA
Band lengths:
230-929
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]