RnoINT0116451 @ rn6
Intron Retention
Gene
ENSRNOG00000008869 | Ppp1r9a
Description
protein phosphatase 1, regulatory subunit 9A [Source:RGD Symbol;Acc:632280]
Coordinates
chr4:30239930-30241911:+
Coord C1 exon
chr4:30239930-30240112
Coord A exon
chr4:30240113-30241376
Coord C2 exon
chr4:30241377-30241911
Length
1264 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TACATGTGTATCCTCTGTAGGCT
3' ss Score
8
Exon sequences
Seq C1 exon
ATCCTTGACGATGGACAGTCTCCCAAACACACTCAGAGTCAGAGCCGGGCCGTCCATGAGTGGAGTGTGCAGCAGGTTTCACACTGGTTAGTGGGCCTCAGTCTGGACCAGTATGTGTCTGAATTCAGTGCTCAGAACATCAGTGGTGAGCAGCTCCTGCAGCTGGATGGCAATAAACTGAAG
Seq A exon
GTAAAGAATCCTCTGTCTTGGTTACTAGTTATGTGTGTGACTCGTAACCGCTGGCGTGCTTTCATTAGCTGAGGGTGTTCTGCAGATCCATGTGGTAGTTACCAGAAAAGACACTGAATTATTTTCAAGAAGCCCACCACAGGTTTTGACTCAAGATAGGTTGCTGACTAAGAGAGTTGGGGGGTGGGGGGAGCTTTTCCTTTGCTTCACCTGGCAACTGCATGACTCCTATATCATAACCACTCACTGCCCACTGTACTGTTAAGTTTTAATAATGACCAGTATGAATCTTCCTTTCTTCCTTTCTCCTCCATGTCCCACCCCCTCCTGCCCACTACTTGAAAACTGAAACGATGACTCCAACTTTCTTCCCCAGTTCATGCAAGCCATTCTCACTGTCACCTCCCTGCACCTTCATTTCCACTCGTCTGGCCCGTCTCTCTTGGAGACTGAGGTGGTACCCAACTCTACTGAGAAAGGGCAAAAGGAAGGTACAGCCAGCGCCACACACCCCTCCCCAGGGCTAGGCTGATGGATAGATAAGTATCTGTTGACAGTCTTTGAAAAGGTTAGAGATCAGTCAATAGTGGTGAATATGAAGGCCCCATTGACAACTGTCCCTGTTAGGGAGAGACGCATCCTTCCTGCTGTTGAGGCTAAAGGTCATGGACCATTTAAATTAAAGCACTGTGCTCTCCCCTCATTCTGAATCGTAAGTCATCTAGCCATCTAGTCATTGTCACGAGGCTTCCTTTACAGCTCTGCCTTAGGGGAGACAATGGGAGAGAGACACTGACATGGGCATCCCCCCACCCCAAGGACATTGTTGCTTCTCGTAGTAAATAACTACATTGGCAGGAAGTTGGCCATTTCATTCTCCCCACCCCTCTTGGAGCCTTCTGTAGCAGCAGGTTCTCTCGGTTACCCTTTCCAAGATGTGGGTAAGTTTAGCAATACTTTAGCTGAAGGTTGGAGAAGCAGGCGCATGCCCCCTTTCTGTTTATTCCCTCCTTAGTCATCAATTTGGAAAGCATTTTCTTAATGACTTCTGGAGTGCATTTTGCAAAGAACTTCAGAGAACAAAGCACAGATCCTTGGTGCTTACAGAATTTAGCACATGTGGTCTGCTTTTCCTCAGCCTTGACCTCCTCCTTCTACGTTTAACTAAGGTCACGAGATTAAACATAGTACGAAGTTTCCCTCATCATAAACAAAGAGGTCAGCAGTTTTTCAGATTCCTTTTGTACATGTGTATCCTCTGTAG
Seq C2 exon
GCTCTTGGAATGACATCATCCCAGGATCGGGCACTGGTTAAAAAAAAACTGAAGGAAATGAAGATGTCTCTCGAGAAGGCTCGCAAGGCCCAGGAGAAAATGGAAAAACAAAGAGAAAAGCTGAGGAGGAAGGAACAAGAGCAAATGCAGAGGAAGTCTAAAAAGTCGGAAAAGATGACTTCCACAACCGAGCAACCGTGAGCAGTAAGGTCTCGCCTCCTCCAGTAGGTGGGAAAGCTTGAGAGAAGTCCCGCCCCTTTCTGCCCCCACTCTCCTGCAGAGGATGAAGAAGAAACTGATGGGGATACACCACTGTAGGCGGTTAAAGAACTGTGTGTTGAATGCACTCTTGATTTTAACCTAAAATGACCCCTCGCCGCCGCCTTCGGTTCATTGACTAACCAGAAGTGTCATTTTTATCTTCTACTTACCAACATCCCATGTTGTGTTAAGTGTGCGGTGCCACTTAGAGGACCAGCCTGACCCAGCCAATGAGAGCAGGACTCTGGTGCTGCGAGTGGAGTACCCAGAATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008869:ENSRNOT00000011756:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.393 A=NA C2=0.976
Domain overlap (PFAM):
C1:
PF0764712=SAM_2=PU(66.2=70.5)
A:
NA
C2:
PF0764712=SAM_2=PD(30.8=29.9)
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:
CCTGCAGCTGGATGGCAATAA
R:
GCCTACAGTGGTGTATCCCCA
Band lengths:
348-1612
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]