RnoINT0106569 @ rn6
Intron Retention
Gene
ENSRNOG00000008639 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:RGD Symbol;Acc:619838]
Coordinates
chr7:75410976-75411656:-
Coord C1 exon
chr7:75411502-75411656
Coord A exon
chr7:75411061-75411501
Coord C2 exon
chr7:75410976-75411060
Length
441 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAG
5' ss Score
8.73
3' ss Seq
GTTTTCTGTTTTATATGTAGCCT
3' ss Score
7.61
Exon sequences
Seq C1 exon
CTAACACATCAACACAGACAATGGGTCCACGTCCTGCAGCTGCTGCTACTGCAGCCACTCCTGCTGTCCGCACTGTTCCCCAGTATAAATACGCTGCGGGAGTCCGCAATCCCCAGCAACATCTTAATGCACAGCCACAAGTTACCATGCAACAG
Seq A exon
GTATAGTTTAATCATTTATTTGTAAGGGTCATAATGCTTAGCTGAACTCAAAGGTCTGACCTATGACCATAAACTATCTGGACCATCTTATTAGTTGATTATATGTGAAGAAAGACAGGTGGCCAACAATCTCCCTGTGTGTTTTGTTTAGGATGAATGTGAGGGACATGTTAAGGGAAAATTTATTGGTATTAGATTTAATCTTTTTCCTAGTCCTGCAACCAAAACCGATAACGGTAAAGGAGACTAAAATTATGTATCTCAAGTGCAGGTATGTCAGATGTGATTATCTGTACTTACTGATCTTTAGTTAATATTTCTTTCAGCTTCTCTTGGTCAAATTTAGGTAGCACTCTGTCCTTTCTATGACTGTCCATTATGGACTAGCTGATTTATGTCTCATTACTTAGATATTAAGAGGGTTTTCTGTTTTATATGTAG
Seq C2 exon
CCTGCGGTTCATGTGCAAGGTCAAGAACCTTTAACTGCTTCCATGTTGGCATCTGCACCCCCGCAAGAGCAAAAGCAAATGTTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008639:ENSRNOT00000012775:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.904 A=NA C2=0.966
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=69.0)
Other Inclusion Isoforms:
NA
Other Skipping 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:
CTAACACATCAACACAGACAATGGG
R:
CTTTTGCTCTTGCGGGGGT
Band lengths:
230-671
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]