HsaINT0122163 @ hg19
Intron Retention
Gene
ENSG00000132915 | PDE6A
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:HGNC Symbol;Acc:8785]
Coordinates
chr5:149277926-149279087:-
Coord C1 exon
chr5:149278938-149279087
Coord A exon
chr5:149278070-149278937
Coord C2 exon
chr5:149277926-149278069
Length
868 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGG
5' ss Score
8.98
3' ss Seq
CTCCTTTCTTTCTTTTTCAGTCT
3' ss Score
11.46
Exon sequences
Seq C1 exon
AAAGAACCTCTGGATGAGTCTGGATGGATGATTAAAAATGTGCTTTCAATGCCGATTGTGAACAAGAAGGAAGAAATTGTTGGAGTGGCCACATTTTACAATCGTAAAGATGGGAAGCCCTTTGATGAAATGGATGAGACGCTCATGGAG
Seq A exon
GTATGGCTTGCTAGGAGGCCTTTTGCTGTTGGGATTCAGAGTCAGCTTGCTGGGGGAGGCTGGGTGTCACTGCGCTATCACATGGGGCAGCAACCTGGTTGCTATAACCCTGACTCTGCCTCATCAACCACTTTCTTCACTCTCACTGCTGTACTGCACTGATGTGCTGTCAGAGAAATCCACATTTCCTTTTTAAAAAATGTAATTAAGCTGAGCATGGTGGCTCTCACCTGTAATCCCAGCACTTTGAGAGGTTGAGGCAGATGAATCACTTGAGCCCAGGAACTCAAGACCAGCCTGGCCAACAGGGCAATATCCTATTTCTACAAAAAGTTAAAAAAAGATTAGCCAGGCATGGTAGCGCATATCTGTGGTCCTAGTTACTCAGGAGACTGAAGCAAGAGGATCACTTGAGCCCAAGAGGTCAAAGCTGCAGTGAGCCATGATTGTGCCATTGCAATCCATCCTGGGTGACAGAGCAAGACCCTGTCTCAAAAAAATAAAAAATAAAAAATAATTAACAAACTTTACTTTTTAGAGTAGTTTTAGGTTCTTAGCAAAATTGAGCAAAAAGTACAGCGTTCCTAGATATCCCCTATCCCCACATAGGCAAAAACACATTCTCTTTTTGTGAAGTTATTACACATAAGAATGGTACTTTCTGTATGTTAGTGCTTTATGTACAGTGTGGTCACATCCATTCCTTTATCTTAGCCTTATAAGAACTCCGCAAGGTGGGCAGCACACAGCTTATCAAACCCATTTTATAGCTGAGAAAACAGAGGCCTAGAGACTCTTGCTATGAGTTTTAGAGTCAAGATTAAACTTAGGTGTTCTGTCTCTGATTCCTCCTTTCTTTCTTTTTCAG
Seq C2 exon
TCTTTGACTCAATTTCTGGGCTGGTCTGTCTTAAATCCTGACACCTATGAGTCAATGAATAAACTTGAAAATAGGAAGGATATTTTCCAGGACATAGTAAAATATCATGTGAAGTGTGACAATGAAGAAATTCAGAAAATCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000132915-PDE6A:NM_000440:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(27.5=100)
A:
NA
C2:
PF0159021=GAF=PD(5.1=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAACCTCTGGATGAGTCTGGA
R:
TTTCTGAATTTCTTCATTGTCACACT
Band lengths:
286-1154
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)