RnoINT0116450 @ rn6
Intron Retention
Gene
ENSRNOG00000008869 | Ppp1r9a
Description
protein phosphatase 1, regulatory subunit 9A [Source:RGD Symbol;Acc:632280]
Coordinates
chr4:30238872-30240112:+
Coord C1 exon
chr4:30238872-30238895
Coord A exon
chr4:30238896-30239929
Coord C2 exon
chr4:30239930-30240112
Length
1034 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TGCATGCATCCCTGTCTCAGATC
3' ss Score
7.58
Exon sequences
Seq C1 exon
AGCCTGGACATGATAGATGATGAG
Seq A exon
GTGAGCTCCCTGTGTGTTGTGCGTGGTGCCTGTCTCGTTCGAACCTGCTTTTTGCTCCTTACAAATGACTTATGAATCCAACACTAAAGAACGCTTTCCTCCGAAGTGGAGGGGGGAAACCCTGCAATTGTTTGCATTTGACTTAAAAGATGTTCCTGGATCAAGATGTCCCCTCCTCCAGAGTCCTAAGCCCCGCCTCCAGAGTCCTTCACTCACCTCCCATAGCCATTACCTGACATGGTCCATTCTTTTTCTTATCCTCTGCCTTTCCTCAGCTCACACTCTTCTTCACATGGCTCTCTCTTTCCTCTGAGACCTGCCACTGCCTCATCTTCTCTCAGCTCAGTGGCTCTGGGAGCTGCCATGCCTCTTTATGCAAATAAAGAGAATGGTCTAGAGTGGACAGAGCCTGGAATTTGCACTGAGCGTCTTGTTAAGCTCTTATTGCTTGCACTGTGTTGTCTAAGAGAGCGTGTGTGGACTTTCTGATCCTCAGTTCCCTCATGTCTTAAAGGAACCGTGGATGCCAGTGTCCCCCTTCACACAGATGGGCTTCTTGCTCAGATAAAACAGTAGCTGTGAAATTTCCCTAAGGAGGCTTGAGAGCTTTGAGACTTTTCTGTAGAATAAAGGAGACCTTGATATTTTCAATGTGTTTTTGTATAACTTTACTGTCTTCCAAAAGGATAAATTTAAGTGATGTATCACATGTGGAAAACTACGCAACAGTTATTTTCCACATCTGATAGTATCTCTAGGGTCATTTATTATAAAATCATCCATGTTAGTGACTACTTTTTCAATTTTTAACTTCCTACATTTTTAATGGCACTTCGTTTATGGGATACTTTTTAACTTTCCGTCTACCAGAATCAGATAGGTAATAGACACGTTTCTTCTAACACAAGTAGAACTATTATCATTTGATGATTTATAAGTAAATGCGGCTCCTGTGACTTGAGAAGTTCCTTTGCTAGCATGATGTACCCTAGTGTCTTCGTCATTTAACAACGCTGCATGCATCCCTGTCTCAG
Seq C2 exon
ATCCTTGACGATGGACAGTCTCCCAAACACACTCAGAGTCAGAGCCGGGCCGTCCATGAGTGGAGTGTGCAGCAGGTTTCACACTGGTTAGTGGGCCTCAGTCTGGACCAGTATGTGTCTGAATTCAGTGCTCAGAACATCAGTGGTGAGCAGCTCCTGCAGCTGGATGGCAATAAACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008869:ENSRNOT00000011756:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.393
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0764712=SAM_2=PU(66.2=70.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCTGGACATGATAGATGATGA
R:
TTCAGTTTATTGCCATCCAGCTG
Band lengths:
206-1240
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]