RnoINT0108904 @ rn6
Intron Retention
Gene
ENSRNOG00000017816 | Pde6a
Description
phosphodiesterase 6A [Source:RGD Symbol;Acc:1306835]
Coordinates
chr18:56611356-56613309:+
Coord C1 exon
chr18:56611356-56611439
Coord A exon
chr18:56611440-56613161
Coord C2 exon
chr18:56613162-56613309
Length
1722 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
ACTTCACTTCTCCTCTCCAGGAA
3' ss Score
10.31
Exon sequences
Seq C1 exon
CCCATGATGGACAGAAACAAGGCAGATGAACTCCCCAAGCTTCAGGTCGGCTTCATTGATTTTGTGTGCACCTTTGTCTATAAG
Seq A exon
GTAGGTTTCTTCAGAGTCCAGCAGACCGCAGGGCGCACGTGGTGTATTTCCCACTCTGTGGAGGGGAATGATAACCTCCAGCTGAAGCCTGGAGCTCGTTTCTCCTCCTTGCTCAACAAATACCCATGGGACAAATGACGAAGCATGCTTGTATGGACAGAATGTCATTGTGAAAAGGCCAGTTCAGGTTAGATCCTTCTCAAGAGGCCACCAGCGACAAACCCATCTCTACTGTCTACCTGGCTGCCTCTTCATTTTTGAGACTTGGTCTGGCTATGTTGCCCTGGTCTGATCTCCAACTCATGATCCTGTTGCCTTAGCCTCCAAGGTGTTGGGATAACATCTCTGCATCACCATGCCCGCCTCCACCTCCCATGAATTAGTTTTCTTTTGGCCACATTATATATAAGGAGACAGAGGTCAGAAAGGATGTGACCGAGCTAACATTTCTGGATCCACCTGTGGAGCAGGACTGAAGCTGGCTCACCTAATACCCAGGCCAGGGCTTTCCACAAGTATCTACGTCCTCACACAGACCGAGGGCCCTCTGCTTAACAGGACAGCATGCCTCTGCTCACACTGCCGGCAGTAGAGTTATAAATGGAGATTTGCCTGCTTAATCCCAACTATGCTAGGGTAGGTGCCATTACCACCCCACTGTCTAGATGAAAGTGAGCTTCAGCAGTGACTATCCCAAAGTCACACAGGTCCTGGTAGAACCCAGACCACAACTCAGGCATCTCTGGGCACGGTAAGCCCTGCCTGGCTCCCGCTGCAATGGGTCCCTCCTCACTTCAGCAAACCTACTTCACCAATCTGCACTTCCGTCTCTCCTCACTACAAGTGAAGGAGTGGCGGGCAACCCACATTGGGGGCGGGGCTCGAAAGACCAGAAGAGATAATTGCCCCATAGATTGCAGGGTACTGTGTTCAAGGTGTTATTCAATTCCTAGAGTTGCAGGAGCCCATAGGAGTCATCTCAATAACCGAGTGTCATTCACTGGGTATTTATGAAGCAGCTGTGTGTTCCAGACCAGTGCTAATTCAGAACCAACTGAGGTGCTCCTGCCATCTCTAGGTGCCATCCTCTGGGAGAGGCAGGCAAAGAGAGTCATTATAGGGAAGTGGACATTGATTAGAGAGGGCTTTGGGGCCATCCAGTGGGGACTCAGTTTACCTACAGGGTCAGAAAAGGTTTCTCTGGGCGAGTGTTAGGGAAGTAGGGACCTCAAGGAAAGGTGGAAGGGTAGAATGTTCCATCAAAAAGAACAGCTGCACAAGGTCCACAGATGGGAGGAAACACTCATGAAGTGAGGTTTGGGTGCCTGGGACTTCTGATGTGAAAGAGTAGACATCAGTGAATGACATGCTAAGACTTACATTGCACGCTGAAGGAGTGGCCATACGGGAAGGTTCTAAGCAGGGGAAGGAGGGGCTCCCTAGTGTCAGCAGCCATGAGAGGCAGCTCACTCCAATGCCAGGCAGAACATACCCCACCTTGATCCAGGGTCCTAGGGCAATGCCCTTGTTTCACTGAGGCATTTCACTGAGATGAAAGGTCACAAAGTCAGTATGTGGCAAAATCTGGTCCCTTACTAGAGGCTGTGGGATGCTCTAGGGTCCTTTAGTTGAACATAGACTCCCCCTACCCCCTTCTCTTTCTCCTCCCTCCCTCTGTCCCTTTATCCCTCCTGTTCATTGTACTTCACTTCTCCTCTCCAG
Seq C2 exon
GAATTCTCCCGGTTTCATGAGGAGATCACACCCATGTTGGATGGGATCACTAACAACCGTAAGGAGTGGAAGGCGCTGGCTGATGAGTACGAGGCCAGGATGAAAGCATTGGAGGAGGAGAAGCAGAAGCAGCAGGCAGCCAAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017816:ENSRNOT00000024171:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.320
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(10.8=100)
A:
NA
C2:
PF0023314=PDEase_I=PD(7.6=38.0)
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:
CCATGATGGACAGAAACAAGGC
R:
CTTGCTTGGCTGCCTGCT
Band lengths:
231-1953
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]