RnoINT0106576 @ rn6
Intron Retention
Gene
ENSRNOG00000008639 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:RGD Symbol;Acc:619838]
Coordinates
chr7:75414378-75414878:-
Coord C1 exon
chr7:75414784-75414878
Coord A exon
chr7:75414516-75414783
Coord C2 exon
chr7:75414378-75414515
Length
268 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
TTGGTTTTTGTTTCTGTAAGGCT
3' ss Score
4.07
Exon sequences
Seq C1 exon
GGCCTGCCTTAAGTGTGAAAGTAATGACAGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAAGATGCGCAGAAA
Seq A exon
GTAAGAGATTAAATCATTCTTCATTCTATGAAAGAATACTGTACAAAACCGTTGCTCTTGTATTGACGTTTGTGTATTTACATGCCAACATTATTGATGGAGGCTTTACATATCGTAATCACATTTGCATTCTGTTTTTAGAGTTGTGGAGATTGGGGATGGGTCTGTTAATGTTAGTAACTGGATGTTTTCCTTGTTAATGAGATGTATGTACTTTGACAAGCAACTAAGTTTTTATTTTTTTTTTTTTGGTTTTTGTTTCTGTAAG
Seq C2 exon
GCTGTGGATGAGATGAATGGGAAGGAGCTCAATGGAAAACAGATTTATGTTGGTCGAGCTCAGAAAAAAGTGGAACGGCAGACGGAACTTAAGCGCAAATTTGAGCAGATGAAGCAAGACAGGATCACCAGATATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008639:ENSRNOT00000012775:5
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=0.196
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:
GGCCTGCCTTAAGTGTGAAAGT
R:
ATCTGGTGATCCTGTCTTGCT
Band lengths:
228-496
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]