RnoINT0106596 @ rn6
Intron Retention
Gene
ENSRNOG00000015642 | Pabpc4
Description
poly(A) binding protein, cytoplasmic 4 [Source:RGD Symbol;Acc:1305015]
Coordinates
chr5:140991554-140993354:+
Coord C1 exon
chr5:140991554-140991681
Coord A exon
chr5:140991682-140993260
Coord C2 exon
chr5:140993261-140993354
Length
1579 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTGCCTCTCCTGGTTCACAGGCC
3' ss Score
9.97
Exon sequences
Seq C1 exon
GCGTCCCTACGGCTGTGCCAAACCTTGCACCTCGTGCTACAGTCGCTGCTGCTGCTCCCAGGGCTGTGGCTCCATACAAGTATGCCTCCAATGTCCGCAGCCCTCACCCTGCCATTCAGCCGCTGCAG
Seq A exon
GTGAGGCACAACAGAGCTGTGAACTGTGAAGGGATTTGTCCTATTTCTGCTCCATTTTAAAGATGCCATGTTTTTTGATTCCTCTTAAGTGTTAACAGGTTCTTACGACACCTGTGCACGCTCAGCTCTTGCCTCTGGGTTACCTTCACATCTGGTGACCTAATTGATCCTTGGCTGTTTTACAGGCAGTTGGTAACCTCTAGCTTTTCTTCAGGCTAGGGACTGACAGCTCAGTGGGCAGCCCGTTAAAGGCGCAAGCTCAGACTTGGATCCCCTGAACCCATATGAAAAGGGGTGGGGAAGTGGACAGTGTGCTGTGTAAGCATGGAGACCTGAGTAGTTCAGGTCCCAAGCACACATGTAAGAGTTGGCATTGTGGGGCCAGAGAGAGATGATGGTTCTTGGATCTGCAGGCTGGCCAGGAGAGCCAGAGTGAGCTCTAGGTTCCACGAGAGACCGAGTCTTAGAGAAGACACCTGACAGTTCTCTGGCCTACGTCTGTGCACATGCCACATATACACACATAACACAGAAAAGGCTGGACAAGGTGAGAAATCTAAACAGGAATCCCTGAGGCCAACCTGGCCTGGCCTACTGGGCAGATTCCAGACCAGGGAGGGAGATGACTTCCTTAAGAAAGTGGTGGTGATGCCTGAGGAACCAGGCCCCAGGGTTGACCTCCCCTACATCGTCAAACACATATACAGAACACCCAACAGAAAGCTTCCCAGAATATTCAGAGGTTAAGGTGCCTAAGCTGTGACCTAAAGCATAGCCACTTTCAGAACTTGGTGGCAGTTTGCTATGACTGGGCCTCACCTGCCCAGACAACTTCAGGAGTAGAAGCTGCTTTGAATTATTCTTAATAATAGTCTCCCTTCTCATCATTCTCTCCAGTGGGGGTTTCTTGGAACTTGGTGCTAATTCACCTGTAACACCTTTTTATGGTTCTAGCAACACTGTTGCATATATTAATGATCCTCAAATAATTGCTAATATATTAAAAACACCTAGACCAAGCCCCAGTCCTGTAAAAGAAAAGGTTGAATTTACCAGGGTATTATTAGCATATCCCAGAATCCAGGTGCTGGGTCAGTAGAGACAAAAGGATTAGGAGTTAAAGGTCAGCACCTACTGAGGCCAGCCTGGGTTCGGAGAGGGTACACAGAAAACCCAAACATCCTGTACCGGGGGATAATGAAGTATGGTTAGGAATGTTTTGATTCTCACTCTTTGGCTCCTGCCTCTGTATGTACTGACAATAACGTAAGGGAGGCATTGAAGAGAAGTGCATAAATACTGTGAAGTACGCACGTGTAATCCCAGCCCTTGGCCCTTGGCAGCAAGGGGATCAAGGCCAGCCAAGACTACATGAAAATCACAAATTATGTCTCCCGGGGCCTGGTTTTGACTGCAGGGCCTTGTGTTGTGAGGCAGGTTTGTTGGTCAGCATCTTCCCCTTCCAATAGCTTACAGTACACAGCTAGCCAGCTTTGTCTTTGAGCACAGGACTGCCACCTCCGCTCCCTTTCACATAGTCTTCCTTAGTGCTAACCCCACTGCCTCTCCTGGTTCACAG
Seq C2 exon
GCCCCCCAGCCTGCAGTCCATGTCCAGGGTCAAGAACCCCTGACTGCCTCCATGCTGGCTGCAGCTCCTCCCCAGGAGCAGAAGCAGATGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015642:ENSRNOT00000056592:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.721 A=NA C2=0.906
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=62.5)
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:
CGTCCCTACGGCTGTGCC
R:
GCATCTGCTTCTGCTCCTGG
Band lengths:
218-1797
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]