MmuINT0117055 @ mm9
Intron Retention
Gene
ENSMUSG00000029491 | Pde6b
Description
phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide [Source:MGI Symbol;Acc:MGI:97525]
Coordinates
chr5:108855817-108856213:+
Coord C1 exon
chr5:108855817-108855926
Coord A exon
chr5:108855927-108856125
Coord C2 exon
chr5:108856126-108856213
Length
199 bp
Sequences
Splice sites
5' ss Seq
GAAGTAGGC
5' ss Score
3.93
3' ss Seq
TTAAATAAAATAAACAACAGATC
3' ss Score
1.85
Exon sequences
Seq C1 exon
ACAGGCAAACTGAAGAGCTATTACACTGACCTAGAGGCCTTCGCCATGGTTACAGCTGGCTTGTGCCACGACATCGACCACCGTGGCACCAACAACCTGTACCAGATGAA
Seq A exon
GTAGGCTGTGGGGAGGGCAGGCTTGTGGTGGGCATGGTAAACCATAAATCACGCGTCCTTAGGGTGAGTCTTTGCAGTCTGGCAATCAGTACTGAGATGGACCACCTTGAAGATGCAGTGCCACATGGGTCAGACCTCATCCTACTGCCTTCTAACATTGCTTTTGTTGTGTTCCCCTGTTAAATAAAATAAACAACAG
Seq C2 exon
ATCGCAGAATCCTCTAGCCAAGTTACATGGCTCCTCAATTCTGGAAAGGCACCACCTGGAATTTGGGAAGTTTCTGTTGGCAGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029491-Pde6b:NM_008806:14
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=PU(19.0=73.0)
A:
NA
C2:
PF0023314=PDEase_I=FE(11.6=100),PF0771711=OB_NTP_bind=FE(20.4=100)
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:
AGGCAAACTGAAGAGCTATTACACT
R:
TGCCAACAGAAACTTCCCAAA
Band lengths:
190-389
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: