RnoINT0106584 @ rn6
Intron Retention
Gene
ENSRNOG00000012750 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:RGD Symbol;Acc:1563142]
Coordinates
chr3:160443126-160444528:+
Coord C1 exon
chr3:160443126-160443219
Coord A exon
chr3:160443220-160444397
Coord C2 exon
chr3:160444398-160444528
Length
1178 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TATTAGGTTGTTCTACACAGGGG
3' ss Score
4.62
Exon sequences
Seq C1 exon
GTCCAGGAGTCGACCGTGTATGTCCCTGGCCATCAGCCTCTGACTGTGTCCATGCTGGATGCTGCACCCCTGCATGAGCAAAAGCAGATGATCG
Seq A exon
GTGAGTCGCTGGCTCTCCCACACTGGGGCAGGCAGGAGGGCTGACTAGCCTGCCGAGAGCACCTTGAGTGAGAACAGACTTGGGAACAAGGACTTCTTCCATCACTGGGAGACTAGGTAGCTTCACCCAAACTGCCTCTTTCTAAGCCTCTGTCCTTTTGTCTTGAAAGATCAGTGGGCTGACGCTCCCAAGGCTTTTTTCCAGCTTGCTCTCTGGCTCCTACTTTAGGTGGGAAATATCTGGATATGGGATCAGGACCGAGAAGCAGGGTAGGAGAATAGCCTTGGGTTTTTACTGGGCCAGAGCGGTCATTACCCATCTCTTAGAATGTGGGGAAGCTTTGGTCAAATTTCATCTGTCTCTCCGTGCTCATGGTGGGAGGCAGGAAAACCCTGTGTGCTGGGAAAATGCAGGTTGTTCCCTCTGGACTCTGAGCTTCAAGAGTACTTCTCTCCAGCCCCAGAGTTTCTGACAGGCTCTATGAGAAGACAGCAACCGTGGGGACTGGAGGTATGGCTCAGTAGATAAGGGTGCTTCCTGTGTAAGTTTGAGGACTTCAGCTTGAATCCCTAGCATGCACATAAAGCTGGCCACAGCTGTGTGTGCCCTGACTCCAGAGTTGGAGGTTGGAGATGGGAAGACAGCAGGACTTGTTGGCTAAGCAGCCTGGATGAACAGCAGCTTCACGGTCAGTGAGAGACACTGTCTTCAGGGGCTAATGTCTCCAGTCGAGTATTACATCCTGTCTGGCCAGCATCTCAATGTGTCCAGTCAGAACCACTTCTCACGAAACAAACAAATGGAGTTTCAAAACTCAACTGACTTTGCTGTAGATCCCTTTATATAGTATTGCTTATATTTATATATTATCATTTTATTATGTTTATATTATTTACCTCACTATATATTTATAACTATATTTATAATATATACTAAATACACATACTTATAGGTTATATATAATATTCAACCTGACCCTTCCTCTAAGGTGGGGTTGCTATGCCCACTTTATAAAGTTGGAAAGAAGAGATTCTAGTAATGTTACATGATATAGCTTGGGGTGACAGGTTCTAGGACAAGATCCTAGACACCCTCATTGCTCCACTCGGCGATGCCACTCTTGGAACACTGGGCTTTGAGGCAGGTGTGTGTGTAAGCTATTAGGTTGTTCTACACAG
Seq C2 exon
GGGAGCGTCTCTACTCCCTTATCCACGATGCCTGCGCCCCACTGACTGGCAAGATCACGGGCATGCTGCTGGAGATGGACAACCTGGAGCTTCTGTTATTGTTGGAGTCCCCAGAGTCCCTCCACGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012750:ENSRNOT00000055172:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.281 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=62.5)
A:
NA
C2:
PF0065813=PABP=FE(59.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCAGGAGTCGACCGTGTAT
R:
GGGACTCTGGGGACTCCAAC
Band lengths:
214-1392
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]