HsaINT0122171 @ hg19
Intron Retention
Gene
ENSG00000133256 | PDE6B
Description
phosphodiesterase 6B, cGMP-specific, rod, beta [Source:HGNC Symbol;Acc:8786]
Coordinates
chr4:657559-658010:+
Coord C1 exon
chr4:657559-657659
Coord A exon
chr4:657660-657902
Coord C2 exon
chr4:657903-658010
Length
243 bp
Sequences
Splice sites
5' ss Seq
CAAGTGCGC
5' ss Score
4.41
3' ss Seq
CCCTTGTTCCCTGGGTTCAGGAA
3' ss Score
8.87
Exon sequences
Seq C1 exon
ACCCTGAACATCTACCAGAACCTGAACCGGCGGCAGCACGAGCACGTGATCCACCTGATGGACATCGCCATCATCGCCACGGACCTGGCCCTGTACTTCAA
Seq A exon
GTGCGCGCCTTCCGGGAGGGGGCGCCTCGCGGGGCGGGCGGGTAGCCTGGGACCCCCGGCAGACACGGGGGCGCAGCGGCGGCACAGCCCGGGGGACGCAGCCCCGGATTCCGTCCCTGCCCGCCGGCCCCGCGCACCCCGGATGGGGCCTCGCTCGGGCTCCGCGCCTCCCTGCAGACGGGCGCTTGGGGCGGGGTCTCCACACTTGCTCCCACCTGCACCTCCCTTGTTCCCTGGGTTCAG
Seq C2 exon
GAAGAGAGCGATGTTTCAGAAGATCGTGGATGAGTCCAAGAACTACCAGGACAAGAAGAGCTGGGTGGAGTACCTGTCCCTGGAGACGACCCGGAAGGAGATCGTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000133256-PDE6B:NM_001145291:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(13.3=100),PF0771711=OB_NTP_bind=FE(23.6=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(14.5=100),PF0771711=OB_NTP_bind=FE(25.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCCTGAACATCTACCAGAACCT
R:
ATGACGATCTCCTTCCGGGTC
Band lengths:
209-452
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)