RnoINT0128590 @ rn6
Intron Retention
Gene
ENSRNOG00000053405 | Rpap3
Description
RNA polymerase II associated protein 3 [Source:RGD Symbol;Acc:1303036]
Coordinates
chr7:139193040-139195017:-
Coord C1 exon
chr7:139194859-139195017
Coord A exon
chr7:139193181-139194858
Coord C2 exon
chr7:139193040-139193180
Length
1678 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
ACCCCTGTTCTCCTGTCTAGAAT
3' ss Score
9.98
Exon sequences
Seq C1 exon
GGCGCGATGACCTCGACAAGTAAGGCGGTTGAACTGCAGCTCCAGGTGAAGCACAATGCGGAGGAACTGCAGGATTTCATGAGGGACTTGGAGCACTGGGAAAAGACTATGAGGCAGAAGGATCTGGAGCTCAGAAGGCAGAGTGGCGTTCCCGAGGAG
Seq A exon
GTAAGCGGAGGGTCCCTGCTCGTGTGCAGCAGAACCTGCCTGCCATTGGGGTGTGCACGTACAAGGTGTGTGCACACGAACCAGCAGGCCACAGTGTGTGAGTGCAAGTCAAAGGCCGACTCCCTGGGGTTGACTCTCTCTTGTGGGCTCCAGGACTCGAACTTGAGTCAACAGGCTTTGCAGCAAGCAGGTTGGCCTGCCGAGCCATGTTATCGTTAAATTTAAACTCTAGAAACATATTTTAAAGTAAAGCATGGCCCTGTAAAATGTTGTGAAGTCCTGAAGCTGCCTGCCGTCCTAGTAGTCGGGGGAGGGGGGATGAGTGGCGGTGGAGGCAGAAGGATCTAGAGTTTAAGTTAGGTGGTAATGGCTCACGCCTTTTATCCCAGCGCTTGGGAGGCAGAAGCAGGCGGGTCTCTTAAGTTTGAGGCCAGCCTGGTCAATAGAGCAAGTTCCTGGACAGCCAGAGCTACAAGGAGGAACCAGTTTGAGTCTAGCCTGGGCTATATAAGATCTTGTTAACAAAGACATAAAAAATGCTGAGATTAGAGTGGTTTGCATAATTGTAAACATTTTTCAGAGATCTTGCTTCTCACTAAGCTTTGAATAATTGTGTGTTAGCCTATCGTAAGATCCTCTAAGTCTGGTGGGTATTTACCGAAAGGATGGTAAAGTAAATAAATAACCTTAAAACATGTAGGCTTATCATATCTGAAAATAATGTAATCACGTATTTCATAATTTATAAGCAGTATTGGCCTTAAAATGCAGGTCAGACTCAGGTTGCACTATTCTTACTAAGCCAGGGCGTTGAAACCTGGCTAGGTTTTTATGTCATATTTAGCCCCTGGAGGCATGCCAGGTTGCCTTTGAACTTGTCCGCTCATTCATTCACCATACTAACTGAAAATCAGGTAGTTTTTTAATTTATAGTTGTAAATTTAAAAGCAAAATTCAGATCTCAAGTCAATACTTTTCTTGTGACTGAACAACTTGCAGTGTTCATCAGATAATGAACTGAACTTAAAGACTTAATTACTGCTTTTTTGGGGGGGTCTGTGGAGAGGGTATATGCCCACACGTGTGCACTTATGCATGTGTGCACTTGTGCCATGTGCCCGATAGAGGTGTCTTCCTCTGGTGCTCAGCACCTCATGTTTGGAGACAAGGTCTTTCAGTGAACTGACACACTGTAGGCTGACTGGCTCGGGAGCTCCTGCGATCTGCTTGTTTCTGTCTCCCACTGGGATTACAGGGTGTGTGGCCATGCCTGGCTTTCACCTGGGTGTTGGGGAGTCAAACTCAGGACCTTTCGCTTGCGTGGCAAGTGCTCTTATTCATCGAGCTGTGTCTCTAGTCCCCATAATCAATATTATAAAATGAATCGCTTGAAAATTAAATTGAAAAAAGAATTTCTTATTTGAAAAATTATTTAGTGCCAGGTGGTGGTGGTGCACACCTTTAACCCCAGCTCAGGAGGCAGAGGCAGGCTCTGAGTTTGGAAGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGAGAGAAACCCTGTCTCAGAAAAACCAAAAGGAAAAAAGAAAATATTTCAAACATTGTGTTATACAGAAGTAACAGAGCAAAATGCCAAAGCTTTTTTAAATTTTTTGCCTTTCCCTACCCCTGTTCTCCTGTCTAG
Seq C2 exon
AATTTACCTCCTATTCGAAATGGGAGTTTTAGGAAAAAGAAGAAACGTAAAACTAAAGATTCTTCCAAAAAAACCAAAGAAGAAAACACAAAAAACAGAATAAAATCTTTCGATTATGATGCCTGGGCAAAACTTGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053405:ENSRNOT00000083926:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.843 A=NA C2=0.660
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGACCTCGACAAGTAAGGCG
R:
CACATCAAGTTTTGCCCAGGC
Band lengths:
294-1972
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]