HsaINT0122176 @ hg19
Intron Retention
Gene
ENSG00000133256 | PDE6B
Description
phosphodiesterase 6B, cGMP-specific, rod, beta [Source:HGNC Symbol;Acc:8786]
Coordinates
chr4:660320-661795:+
Coord C1 exon
chr4:660320-660403
Coord A exon
chr4:660404-661644
Coord C2 exon
chr4:661645-661795
Length
1241 bp
Sequences
Splice sites
5' ss Seq
AAGGCGAGT
5' ss Score
2.72
3' ss Seq
GACTTCTCGACTCCCCTCAGGAG
3' ss Score
6.79
Exon sequences
Seq C1 exon
CCTATGATGGACCGGAACAAGGCGGCCGAGCTCCCCAAGCTGCAAGTGGGCTTCATCGACTTCGTGTGCACATTCGTGTACAAG
Seq A exon
GCGAGTGGTTCACGGGTGTTCCGAGCTGACTGGGGCAGGGTGGCTGGGAGCAGGCAAGGGGGCGCGGGCTGGAGTCGCGTGGACTCACACGGGCCCGGCGGTGTCCTCACTGGAGTAGGGATGCCAGTGCCAGCTTCGTGCCGCTCTTGAGTGGGGCAAATGGGGAGGAACATCAGTTTCCGGACCCCCACAGGTGCCCCAGCCCATCCTCACCCTGCTGTGCCCCTGGAAGCTCTGAGCCCTTTCCCAGCCCAGAATGTCCTCTGCTAGCCTCCAGGCCTACCCCAGAAGTTCTCCCTCAGTGCCCTCCGCCGTGGCCAGCACACTGTTTTGGGGGCCTTGGCTGCAGCTCTGTGGGTTCATTTGTTCCATGTTTGTGAACCCTCGAGGCGGGGCTGGGTCGGCCTGTCTGCTGGTGCACCCGCCCACAGGGGCGTTTGGAACAGCAGAAGGAGCCACATCCCTGCCAATCTGCCACAGTCCGATGCCAGCTGAGTCTCTGAGGACGCAAGGCGGACATGGAGGGGGAGACTCGATGGGGCAGGGGTCTGACCGTGGGGCCCTGTGTGATGCCCATAAGAGCCAGCTGCCTCCGGCCACACTCCCTGGTGATGGAATCCACGCCCCAAGGAGGATGCCACGGGTTCCACATGAAGTTGTCCCGGAGTGGGCTGTGCCCACTCCCCGCCCCATCCTACCCACCCCGGGTCGTCAGTGCTGGGGAGAAGGTGGGACAAGGGTGGATATTTGGGCCTGAAGTGGCCACAGGTCACGGCCCCACTGCAGGTGCCCCCCACTGCCTTCCCCACCCCGCCACACTCCATGTGTGATGTGCGCGAGTGCACGCGTGTGCTGTGCTTGCATGATGTGTGCCGTGTGTGTGTGGGAGGGACGGGAGAAGGCACTGCAGGGGCTGCCTGCTGTCCGCCTGTGCCCACCACCCCTCTGCCTGGCACCCTGCCCCCACCCCCTGAGCTGTTCTGCTCATTCTTGGGTTCCTCTCCCTGCAACACTGCACCCTAAGCATGCATACCCTAAAGCTCCCGGCTTCAATGTCACCAACACAGCCCCCGAGGTTTCTCCCTTCACAGGGCTCTGCTGGGAAGGTGCCCCCTCCGTGGCGCTCCCTCCTCCTGCCAGGCAGTTCATCCCCTACGAGGGGGATGAGCTGGGGAAGGGCTATCTTACTCTGGAGAGAGCAGGCAGGACAGGACTGGTGGTGACTTCTCGACTCCCCTCAG
Seq C2 exon
GAGTTCTCTCGTTTCCACGAAGAGATCCTGCCCATGTTCGACCGACTGCAGAACAATAGGAAAGAGTGGAAGGCGCTGGCTGATGAGTATGAGGCCAAAGTGAAGGCTCTGGAGGAGAAGGAGGAGGAGGAGAGGGTGGCAGCCAAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000133256-PDE6B:NM_001145291:20
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=0.031
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(10.8=100)
A:
NA
C2:
PF0023314=PDEase_I=PD(23.5=66.7)
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:
TATGATGGACCGGAACAAGGC
R:
CTTTCTTGGCTGCCACCCTC
Band lengths:
233-1474
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)