RnoINT0128582 @ rn6
Intron Retention
Gene
ENSRNOG00000053405 | Rpap3
Description
RNA polymerase II associated protein 3 [Source:RGD Symbol;Acc:1303036]
Coordinates
chr7:139194859-139196416:-
Coord C1 exon
chr7:139196363-139196416
Coord A exon
chr7:139195018-139196362
Coord C2 exon
chr7:139194859-139195017
Length
1345 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGG
5' ss Score
10.19
3' ss Seq
GTGTGCTCCCGAGTTTGCAGGGC
3' ss Score
2.12
Exon sequences
Seq C1 exon
GAAGGCGCAGACCTCCGGCGGTGGTGTAGGACGCCGTGCGTCTCCCTGGAGCCG
Seq A exon
GTAAGGGTGGTGGCGGCTGTGGCGGGTGAGCAGGTTTTGCCGTTACTGCCAGCTGCAGGGGCGCTTGGGGTGCGGGGCCGGGCCGGGAACAGCGGTGGGCCCGTTCCCGAGTGCGATCTCCGCGCGCCGCCCAGGGTTCGGCCTGAGCTGGCTCTGCATCCGGACTCGGGCCATCTGCGGTAGCCGGACCTCCAGAGCCACAGTCCCGAGAGGGCCGAGGACCAGCCGCCTCCTTCAGGCCAGGGTGTGCAGGCTTGCCTTGGATACGGGCCGTGAAAGTGTTTCCCCAGGCTCTGGAAGTACCTGGTTGCCTGCGGAACGAACCCCGTCCTGTCAGCTTGGGCTGCCTAAAGACCCAGGGGTGGTAGGTGAATGGAAGGAGAGCTGTCGCCCCTACAGCATCTCACGGTCTGTTTGTGTTTGTTTCTTTGGTTAGAGACAGGGTTTCTCTGTAGCCCAGGCTGCCCTGCAATTCGCTGTGTAGTAGAGCAGGCTGGCTTCGAACCCATGCCTCTGCCTCCCTCCGGAGTGCTGGGTTTGAAGGCGTGCAGCGTTTAAAGGGTTTCGTTTTGCGTGTGTACGAGTTTGTGTGGAGCAAAGCATTATGCTAGATTTGTTTATGAATGAAATGCATGCGTATAACCAAATATTGACACTGCCTGACACTACTTTTTTTTCAAAATTTTATTTTTACTGTATGTGTATGTGATGTGTGATGGTGCATGCAGGTGTCACACATATCCGAGGACAACTTTGTGGAGTCAGTTTTCCCTTTGCACCATTGTGAGTTTACCAGGGATTGTGTGGGTACCACCAAGCCTTACATTGTCAGGCTCAAGCGGGGAGCACTTTAGTCAGGAGTCACCTTTCCAGCCCCTCAGAATTGGAATTCTTGACTTAATATCATATTACCAATTTCTACCAAGCAGAGATCTAGAACACTGTTCTAGATCTTTCTCTCCTTCCCAGTGTCTCAACCTAATCAGTCATCAGGTTATTTTTATATCAGCCAATACCTTTACGTGGCTTTTAGAATGTCGGCTAATACTCCCTGGCCTGGTGTGTTACGGGCTGTCCCATGTCTACTTCTGACTTCTCCTTGTCCCTCGGAGTTCTCTCTGCTCCCTTTTCCTCCCCACTCCTCACTTGATTGGCCTGCTCTGACCTTGAACCTTTTTGATACTATTGGGCTTACAGACGTGTACTGTCACACCAGGTTTAAATGCAGTTTTTCCACTTAACAGTGCGTTTAAGTGGCGATGGTTTTATAGGGATGCACCCCCGTCTTAAATAGAAGCACCTGCCGCCCTGATTCTCGAAACCTTGTGTGCTCCCGAGTTTGCAG
Seq C2 exon
GGCGCGATGACCTCGACAAGTAAGGCGGTTGAACTGCAGCTCCAGGTGAAGCACAATGCGGAGGAACTGCAGGATTTCATGAGGGACTTGGAGCACTGGGAAAAGACTATGAGGCAGAAGGATCTGGAGCTCAGAAGGCAGAGTGGCGTTCCCGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053405:ENSRNOT00000083926:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.843
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGGCGCAGACCTCCGG
R:
GGAACGCCACTCTGCCTTC
Band lengths:
206-1551
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]