HsaINT0122178 @ hg19
Intron Retention
Gene
ENSG00000133256 | PDE6B
Description
phosphodiesterase 6B, cGMP-specific, rod, beta [Source:HGNC Symbol;Acc:8786]
Coordinates
chr4:647641-647943:+
Coord C1 exon
chr4:647641-647781
Coord A exon
chr4:647782-647868
Coord C2 exon
chr4:647869-647943
Length
87 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CTCACCTCTTCTCTGCCCAGGAA
3' ss Score
9.65
Exon sequences
Seq C1 exon
GTGCTGCTGTGGTCGGCCAACAAGGTGTTTGAGGAGCTGACGGACATCGAGAGGCAGTTCCACAAGGCCTTCTACACGGTGCGGGCCTACCTCAACTGCGAGCGGTACTCCGTGGGCCTCCTGGACATGACCAAGGAGAAG
Seq A exon
GTGAGGCTTCCGTGGCTCAGGGACCCCCTGCCTGGCCCGACCCAGGTCCCGCAGTGACCGCCCCACCCTCACCTCTTCTCTGCCCAG
Seq C2 exon
GAATTTTTTGACGTGTGGTCTGTGCTGATGGGAGAGTCCCAGCCGTACTCGGGCCCACGCACGCCTGATGGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000133256-PDE6B:NM_001145291:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.035
Domain overlap (PFAM):
C1:
PF0159021=GAF=PU(18.0=68.1)
A:
NA
C2:
PF0159021=GAF=FE(13.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGGCCAACAAGGTGTTTGAG
R:
GGACTCTCCCATCAGCACAGA
Band lengths:
168-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)