HsaINT0122167 @ hg19
Intron Retention
Gene
ENSG00000133256 | PDE6B
Description
phosphodiesterase 6B, cGMP-specific, rod, beta [Source:HGNC Symbol;Acc:8786]
Coordinates
chr4:654256-656030:+
Coord C1 exon
chr4:654256-654402
Coord A exon
chr4:654403-655922
Coord C2 exon
chr4:655923-656030
Length
1520 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGA
5' ss Score
4.3
3' ss Seq
TGTCCTCTCGGCTCCCCCAGGTC
3' ss Score
11.14
Exon sequences
Seq C1 exon
AAGGAGGAGCTGCCAGGGCCCACCACATTTGACATCTACGAATTCCACTTCTCTGACCTGGAGTGCACCGAACTGGACCTGGTCAAATGTGGCATCCAGATGTACTACGAGCTGGGCGTGGTCCGAAAGTTCCAGATCCCCCAGGAG
Seq A exon
GTGGGAGACACCGCAGGGCGCATAGTCAGGTCCCTGAGGCCGCCCAGGACATGGGGGTGGGGATGTGATCAGGGCCTCAGGTGCCCCAGAAGGTGAGGGGGATGGGATTGGGGGTTCCAGATCCCACAGGAAGTTTAGAGGGCCGACATGTTCATCACAGAACAGGTAAAATGCACACGGGAAGTAAGCATAAAACAAATAATTGGATGGCTGGGTGGATGGCTGGATTGATGGATGGCTGGATGGGTGAAAAGCAGGGAGGAAGGAGGGAGGTTAGGAAGGAAGGAAGGCCAACAGGCAAGCAGAAAGAAACAAAGGAAGAATAAATGAATGGATGGGTGGATGCCAATGGTAGTTGGATAGTTGGATAAATGGATGGGTGGGTGGGCCAATGGTAGTTGGATGGTTGGATAAATGGATGGATGGGTGAGTGGGCCAATGGTAGTTAGATGGTTGGATAAGTGAATGGATAGGTGGATGGATGGAGAAGTGGGTGGATGAGTGATAGATGAGTAGGTGGGTCAATTAATGAATTAATAGATGGGTCAATGAATGGGTGAATGGATGGGTGGACAGCAGATGGATGGTGAATGGATAGATTTAAAGTTTTATTATTAGGAGTTCCAAGCAATTTGATCATTAGGCACATCATCTGGCAATAACAGGGGATTTGGTGTGGGGTGCTGAGGAGATAGAAGCATCCCATCACCTAAACAGAAAGCACAAAGTGGCCCCCCTGGTTTGGCCACAGCAGCACTCCTCGGAGACCCCCTGGGGAGGCGGGATGGCTTTCCCAGCCCTCGTCCACAGCTCTGTGCCCTCCCTGGGTTCTCCTGCCCTGCCCTGCTTCCAACATCTCAAGGGGCTTCCCACAGCCCTAGGAAGAGAATCCTCTTTTCTCATGCCCCTCTGAGAACAGGTGCAGCAGGCCAGCATTTTCAAAAGAAGTTTTACTAAATACTAAGGGAAAACACTCAAGAAAAAATGTATAGAAAATATTTGCAGAATAAAAAATATTTCCAAATAATTTTCTGACCCTAAAAATCACAATGGCCGCAGGAAGAGCCTCCTGGCGATGTCCGCAGGGCAAGAGAGACCAGCATTCTCTTGCCCTGCGGACATCGGTTCTCCCACCCCAGCCTGCAGCCCACACATTCTGCTCATTCAAATGTCCATGCCTAAAACCAACATCTTAAAATATGCTGCATCCCCAGGGGTCCTCCTCCCAGCTTGAGGCCAGGCAGTCGGATGGAGGCTGGGCGGCCCCTGAAGGCTGGGGCTGTTCTCAGCTCCTGCCCTACCTGGCTCCACCCCATAGGTGCCAATGTGGCAGCCCCTACCCAGGAAGGCCAGCAGAGGCCAGTGGGAAACGCAGGGATGGGGAAGATCGGGAAGTCCAGGAGACGGTGTGGGGATGATGGCACGGAGCAGGGCTTCCACTGTGAAGTCAGCCACAGGTGCCGCTCTGGCGGGACTTACACGCTTGCCGCCGGAGCCCTGTGTCCTCTCGGCTCCCCCAG
Seq C2 exon
GTCCTGGTGCGGTTCCTGTTCTCCATCAGCAAAGGGTACCGGAGAATCACCTACCACAACTGGCGCCACGGCTTCAACGTGGCCCAGACGATGTTCACGCTGCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000133256-PDE6B:NM_001145291:12
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0023314=PDEase_I=PU(7.2=50.0)
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:
AAGGAGGAGCTGCCAGGG
R:
ATGAGCAGCGTGAACATCGTC
Band lengths:
254-1774
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)