RnoINT0106573 @ rn6
Intron Retention
Gene
ENSRNOG00000008639 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:RGD Symbol;Acc:619838]
Coordinates
chr7:75418645-75419139:-
Coord C1 exon
chr7:75418946-75419139
Coord A exon
chr7:75418761-75418945
Coord C2 exon
chr7:75418645-75418760
Length
185 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
AGTGTTCTGTTTTACCTTAGGTG
3' ss Score
9.71
Exon sequences
Seq C1 exon
CGGAACGTGCTTTGGACACCATGAATTTTGATGTTATAAAGGGCAAGCCAGTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGTAAAAGTGGAGTAGGCAACATATTCATTAAAAATTTGGACAAATCCATTGACAATAAAGCACTGTATGATACGTTTTCTGCGTTTGGTAACATCCTTTCATGTAAG
Seq A exon
GTAAGCTGAGATGTAACAGGGCAGTATTTACAGTGTTGTGCTACGTTTAGATTTGGGAGTGACATTTGTGCTGTCTGTTAATGCTGTCCTTATTGTGAAGTTCCCTAGGATTAGGTAGCTAACATTTCTACAAAGTAGAAAAGCAATAGCAGGTAGTAAAAAGTGAGTGTTCTGTTTTACCTTAG
Seq C2 exon
GTGGTTTGTGATGAAAATGGCTCCAAGGGCTATGGATTTGTACATTTTGAAACACAGGAAGCAGCTGAAAGAGCTATTGAAAAAATGAATGGAATGCTTCTAAATGATCGTAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008639:ENSRNOT00000012775:2
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=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
A:
NA
C2:
PF0007617=RRM_1=FE(55.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGTGCTTTGGACACCATGAA
R:
TCAGCTGCTTCCTGTGTTTCA
Band lengths:
258-443
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]