RnoINT0106570 @ rn6
Intron Retention
Gene
ENSRNOG00000008639 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:RGD Symbol;Acc:619838]
Coordinates
chr7:75410539-75411060:-
Coord C1 exon
chr7:75410976-75411060
Coord A exon
chr7:75410670-75410975
Coord C2 exon
chr7:75410539-75410669
Length
306 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
GAGTGTCCTTTTGTTCCTAGGTG
3' ss Score
9.31
Exon sequences
Seq C1 exon
CCTGCGGTTCATGTGCAAGGTCAAGAACCTTTAACTGCTTCCATGTTGGCATCTGCACCCCCGCAAGAGCAAAAGCAAATGTTGG
Seq A exon
GTGAGTGACTTCATTGTCTTGACCTGTCAGAGTTGACAAAAATAAAGATCACTTAGACTCTTTGCACCTAAAATGAGATGGTGGTATGTGAAGGAATACTGGAAAGTGGTGGGCTGTTGTTTGCCATTGACATTCCACTCTAGCCTTGGAACAAGGAAACGTTTATATGTAATACTAACACTTGGGAAACTACTGTTCATATGGGTATGGTAGCAGGCACACACAGTACTATGTATTACATACGGTTCCTAAACCCAGGTTGATAACAGCATTACTGCTTTCATCAGAGTGTCCTTTTGTTCCTAG
Seq C2 exon
GTGAACGGCTGTTTCCTCTTATTCAAGCCATGCACCCTTCTCTTGCTGGCAAAATTACTGGCATGCTGTTGGAGATTGATAACTCAGAATTGCTTCACATGCTTGAGTCTCCAGAGTCTCTCCGCTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008639:ENSRNOT00000012775:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.966 A=NA C2=0.250
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=69.0)
A:
NA
C2:
PF0065813=PABP=FE(59.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCGGTTCATGTGCAAGGTC
R:
TTTGAGCGGAGAGACTCTGGA
Band lengths:
214-520
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]