RnoALTA0027870-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000008639 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:RGD Symbol;Acc:619838]
Coordinates
chr7:75410142-75410669:-
Coord C1 exon
chr7:75410539-75410669
Coord A exon
chr7:75410229-75410247
Coord C2 exon
chr7:75410142-75410228
Length
19 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTT
5' ss Score
8.4
3' ss Seq
TGACGTGCTCTCTGAGCCAGTGT
3' ss Score
1.89
Exon sequences
Seq C1 exon
GTGAACGGCTGTTTCCTCTTATTCAAGCCATGCACCCTTCTCTTGCTGGCAAAATTACTGGCATGCTGTTGGAGATTGATAACTCAGAATTGCTTCACATGCTTGAGTCTCCAGAGTCTCTCCGCTCAAAG
Seq A exon
TGTGTTCACCGTTTTCCAG
Seq C2 exon
GTCGATGAAGCTGTAGCTGTACTACAAGCCCACCAAGCGAAAGAGGCTGCCCAGAAAGCAGTGAACAGTGCCACTGGTGTTCCAACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008639-29-25,29-24-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF0065813=PABP=FE(59.7=100)
A:
NA
C2:
PF0065813=PABP=PD(9.7=22.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCAGAGTCTCTCCGCTCAA
R:
GAACACCAGTGGCACTGTTCA
Band lengths:
105-124
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]