RnoINT0106567 @ rn6
Intron Retention
Gene
ENSRNOG00000008639 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:RGD Symbol;Acc:619838]
Coordinates
chr7:75418946-75421874:-
Coord C1 exon
chr7:75421483-75421874
Coord A exon
chr7:75419140-75421482
Coord C2 exon
chr7:75418946-75419139
Length
2343 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGC
5' ss Score
9.89
3' ss Seq
TGAAAATGTATTTTTCGCAGCGG
3' ss Score
6.89
Exon sequences
Seq C1 exon
CTGCCGCCCGGACCCAGCACCGCCAGCCTCGCTCCCCCGGTTCCACGGCCGTTGAGTACGCGTCGATTCCGGTTGAATTTTGTCCCTCTGCGCTCGCCCCCGCTCCCCTCCCCCCGGCTCCGTCCCCCGGCCCCGCACTCGCTCTCCTCCTCTCACGGGAAAGGTCGCGGCCTGCGGCCCCGCGGGCAGCCGTGCCGAGATGAACCCCAGCGCCCCCAGCTACCCCATGGCCTCTCTGTACGTGGGGGACCTGCACCCCGACGTGACCGAGGCGATGCTCTACGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGGGTCTGCAGGGACATGATCACCCGCCGCTCCTTGGGCTACGCGTACGTGAACTTCCAGCAGCCGGCGGACG
Seq A exon
GTAAGCGGCAGGCCGGAGGGTGGCGGGCGGGCGGCCATGCGGCCGGGGCGGCGGGCCTAGCGGGCCGGGCCGAGGGGGCGGGAGGGCACGGCGCCGCAGCCCCTCGCGGGCCGGCACTTCCTCCTCTGCGACCATTTTCTCGCCATCGGTCGCTCTCAAACTTTAGGGCGATGACGCGCCGGGAGGGTGGGTAAGGTAGCCTTCCCGGCGCTCCCGCCACAAGCTGTGGGGTTCGGGGGTTTCGAGCCCCCTCTGGAGTGGAGCAACGGGTGGAGGCGCCCCTCCATCTCCTTCCCTGGCCCGGCATTCAGGCTGGGGAGGAAGTACGATTCAGTGTTGGGAAATACCACGTGTTGAACCCTGTAACCTCACAGGCCCGAGGCCTGTTCCTGCGGGTGGCTCAATCGCTGGGAGGAGCCCCAGGCTTTAGAAGAAAGTTAATAGGGAGATGCCTGTTGGTGGTCCTTAGGGTCATGAGCTCCTTCCTAATAGCATACCCCTGGCTTGTGGACCGCGAAAGGGACATTATACCATGTGCACTGCCTGGGGTTTTCCCTAGATGAAGTATTTTCTGTCTTTAACCCTGCAGTGGAGGAGGGGATGTGGAAGACTCTAGGGCACCAGACACCTTGGCTCATTTTCAAACAAATTAGTTGGATATTAAGTTTAATAGAAGTGATTATTTAATGTATACATGCATATTTTTTCTAAAATAGCACCAGTGGTTATGAATTTTAAACTGCTGACCAGTTTTGGTCGTAAACATTAGGGTAACCTGGATAGGATTATGCTGAATTAGTAGCAGACAACTAATAATAGCTTCTTTGATTTTTTTTTGTGTGTGTGTGTGAAGTGTTTCAGAATCTTGGAGTAGTTGAGAAGTAACACATTGAGTTTATATTCTTAAGTTTGACAGTTCACTGAAACAGAAATCCAAGAATCAGATAAGGTCTACAGTCTGATGTTAAGTTTTTAAGTCTAGATGACCCTGACTAGAAGTCAGTTCTGTCTGGCTTTTATTTTAATAAGGAAGACTGGGGTTGATCAGTTTTTCATAGATAAAGGTGATACTGAGATTTTGAGTAAACAGCATCTTAGGTGATCGGAAGCCACAAGTTACAAGTTGTAAAAGTGCACTGCAGGTGGCCTGCCCTTTTGCTCTCAAAGGGCACTTTTAGTGTCACTTCATTAGAGCTCTCAACTCACAGGAGATGACAGGATGTAAGCTAAAGAAGGTAACTTGAGCAAGTAACCGAAAGAACTTCTATGAAAAGAAAACTTAAGAGACTTGAAACTTAGTGGTTTCTTTTTTTTTTAATTCAGAAAAACCCAGTCCTGACATTTGAAAAGTTGAGTTTCAAATTAACTTTATAAATTCATGTCAGTGAACCAATATTCTAACCGCTCAGAATCTTGCCTCTACATTCTTCATTTATTTTGTGGCTGTATGTTCAATGTTCCATCTTTTGAAATAGTTTTAACCAGTTTTTTCCTTTTTATGGTATTTTCTTATGTATTGCAGTAGTTGACTAGGGTTCTGCTAGTGACCAGTATTCAGTTTAGTAGGAAGATGTGACTCATTAGAAAAGAAACCAAGCTGGAGCACAGTCAGCGTGACCAGGGGTGCTTAGGAGGTGTGGCCAATTGATAGTGAGCTGGCTGCTGACTGTCACTTACTCTAGGAACTGGAATTCATTTATAGGAAAGCGGTTGGGGGGCTGGGTAAGGTGGTTTCTGCACTTATTCCCAGCATGAGAATCCCAGCATGAGTATTTCAGAGGTCTTGGCCAGCCTGAGCTACATGAGTTCCAGGAAAACTAAAGCGACACAGGGAGACCTTAAAGAAAAGGTTGTTGAAAAACTTGTTCTGTCAATAACTACATTTATTAGTGAGATTTGAAATTTGCTTCAGGGATTCAAGTGGACTGTTCCCCTAGAAGGTCTGGTTTCTTAGGTAGCATTTTTCCATTTAAGACAGGGCAATGGATACATAATTTTTGAAGGCAGGGACTCGGCCAGATTGGGCTTAATAGAGACCCTGTATCCAAAAAATTGTCTCAGCCTCAGCATTTCTTTTACAAGTATACATAAATCAATCTTTTTGGAGGTCTCAAAATTGTAGAGTAGGATTTTTTGATGTGAAGCATGCCTATCCAAAAATAACTGGAATAAATTGTTGGTTACGATGATCAAGGTAAAGGTCACGCATGGGTAGTGAAGTTCAGAGGAAGATGAGCTGAGGCCACGTGACTACCCTTTTACTCGAGGTCACTGGTCATTTTATAAAAAGTGGCTAATGGGATGTTACAAGTGATACTTACTCTGAAAATGTATTTTTCGCAG
Seq C2 exon
CGGAACGTGCTTTGGACACCATGAATTTTGATGTTATAAAGGGCAAGCCAGTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGTAAAAGTGGAGTAGGCAACATATTCATTAAAAATTTGGACAAATCCATTGACAATAAAGCACTGTATGATACGTTTTCTGCGTTTGGTAACATCCTTTCATGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008639:ENSRNOT00000012775:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(73.2=80.0)
A:
NA
C2:
PF0007617=RRM_1=PD(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]