RnoINT0106579 @ rn6
Intron Retention
Gene
ENSRNOG00000008639 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:RGD Symbol;Acc:619838]
Coordinates
chr7:75412432-75413025:-
Coord C1 exon
chr7:75412753-75413025
Coord A exon
chr7:75412523-75412752
Coord C2 exon
chr7:75412432-75412522
Length
230 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TGTTCTGTTTTTCTTTACAGACT
3' ss Score
11.61
Exon sequences
Seq C1 exon
GTAATGATGGAGGGTGGGCGCAGCAAAGGATTTGGTTTTGTATGTTTCTCCTCCCCTGAAGAAGCCACTAAAGCAGTTACGGAGATGAATGGTAGAATTGTGGCCACCAAGCCACTCTATGTAGCTTTAGCTCAGCGCAAAGAAGAGCGCCAGGCTCACCTCACTAACCAGTATATGCAGAGGATGGCAAGTGTACGAGCTGTGCCCAATCCTGTGATCAACCCCTACCAGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAG
Seq A exon
GTAAGTGTGAAGAAGAGACAAAGAAAGCCATACTGGTTTCATAATGTATTTTGAGCTCTCCACAATAAAAAAAAGCACTAAGTATTAGAAATTGGAAAAACAAATGGCAAAGGTGGTAGAGTTAATTGTTCTGTTTTTCTTTACAATAAAAAAAGCACTAAGTATTAGATAGAAATTGGAAAAACAAATGGCAAAGGTGGTAGAGTTAATTGTTCTGTTTTTCTTTACAG
Seq C2 exon
ACTCAGAACCGTGCTGCATACTATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008639:ENSRNOT00000012775:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.308 A=NA C2=0.774
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=42.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCTCCTCCCCTGAAGAAGCC
R:
TCCAGCGAGGACTTGGTCTTA
Band lengths:
295-525
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]