MmuINT0117058 @ mm9
Intron Retention
Gene
ENSMUSG00000029491 | Pde6b
Description
phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide [Source:MGI Symbol;Acc:MGI:97525]
Coordinates
chr5:108856816-108857262:+
Coord C1 exon
chr5:108856816-108856923
Coord A exon
chr5:108856924-108857198
Coord C2 exon
chr5:108857199-108857262
Length
275 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGT
5' ss Score
8.31
3' ss Seq
TGCTGTCTGTCTGTCCACAGGGC
3' ss Score
13.41
Exon sequences
Seq C1 exon
GAAGAGAACAATGTTCCAGAAGATTGTGGATGAGTCTAAGAACTATGAAGATAAGAAGAGTTGGGTTGAGTACTTATCCTTAGAGACCACACGAAAGGAGATAGTCAT
Seq A exon
GTAAGTAGCAGGTCCACTGCTGGCCAATTAGCCCTGCAGACCTCCCTAATCCCAGGGACCGGAGACGGCACAAGGGTTCATAGGCCTCACCACTGAATCCAGAATCTTCCTTAGCACCCCTGACCACCACTTGCTTCAAGCTCAGCTTTCCTTCTTCACCTACAAGGTGGTGACTTGGGACCAGCACCTTTCCTAGGACTGTCCCAGAGAGCTGCTGAGAAAATGTTTACTCTCTGCTCAGAAGGACAGGTAGTCTGCTGTCTGTCTGTCCACAG
Seq C2 exon
GGCCATGATGATGACTGCATGTGACCTGTCTGCTATCACCAAACCCTGGGAAGTCCAGAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029491-Pde6b:NM_008806:17
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=0.000
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(14.5=100),PF0771711=OB_NTP_bind=FE(25.4=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(8.4=100),PF0771711=OB_NTP_bind=PD(10.6=68.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGAGAACAATGTTCCAGAAGATT
R:
GGACTTCCCAGGGTTTGGTGA
Band lengths:
164-439
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: