HsaINT0122182 @ hg19
Intron Retention
Gene
ENSG00000133256 | PDE6B
Description
phosphodiesterase 6B, cGMP-specific, rod, beta [Source:HGNC Symbol;Acc:8786]
Coordinates
chr4:650034-650812:+
Coord C1 exon
chr4:650034-650081
Coord A exon
chr4:650082-650662
Coord C2 exon
chr4:650663-650812
Length
581 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCT
5' ss Score
7.33
3' ss Seq
TCTGGACACCGCTCCCGCAGGAA
3' ss Score
6.5
Exon sequences
Seq C1 exon
ATTTGTAACATCATGAATGCTTCCGCTGACGAAATGTTCAAATTTCAG
Seq A exon
GTATCTGTCTGTGCCTTGGTAGAAATTATACTTACTTACAAAAGAGGAGATTTTGATTCAGCGATGATGAAGTGAATTCGTTTTTGCCACTTAAAAAACAACTTCAGCCAGGCATGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGTGGATCACCTGGGGCTGTGACCACAGCCCCCACACACGCCCGCAAGGCCGTGACCGCGGCCCCCACACACCCCTGCGAGGCCGTGACCGCGGCCCCCACACACCCCTGCGAGGCCGTGACCGCGGCCCCCACACACCCCTGCGAGGCCGTGACCGCCGCCCCACACACATGCCCATGAAACCACTCCTGGTGGGAAAACGGCCTCTACCTCCTCCGGTGGGAAAATATCATGACACAAAAACCATGGACACAAACTCCAAATGCAGAGAGGGAGAGAGGGAATGCAGAGAGCAGAGACAGGAACACGAGCCCAGCCGTCACGGCTCTAGGGGAGAAGACATGAGGTCACTCTCCCCGGCCACACGCCCGGGCCAGGGCCAGCCTCAGGGCGGAGCTCAGCTCTGGACACCGCTCCCGCAG
Seq C2 exon
GAAGGGGCCCTGGACGACTCCGGGTGGCTCATCAAGAATGTGCTGTCCATGCCCATCGTCAACAAGAAGGAGGAGATTGTGGGAGTCGCCACATTTTACAACAGGAAAGACGGGAAGCCCTTTGACGAACAGGACGAGGTTCTCATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000133256-PDE6B:NM_001145291:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(10.3=100)
A:
NA
C2:
PF0159021=GAF=FE(27.5=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:
ATTTGTAACATCATGAATGCTTCCGC
R:
CTCCATGAGAACCTCGTCCTG
Band lengths:
198-779
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)