MmuINT0117069 @ mm9
Intron Retention
Gene
ENSMUSG00000029491 | Pde6b
Description
phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide [Source:MGI Symbol;Acc:MGI:97525]
Coordinates
chr5:108850507-108852176:+
Coord C1 exon
chr5:108850507-108850554
Coord A exon
chr5:108850555-108852026
Coord C2 exon
chr5:108852027-108852176
Length
1472 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATC
5' ss Score
6.99
3' ss Seq
TCTTTCCCTACTCCCTGCAGGAG
3' ss Score
10.69
Exon sequences
Seq C1 exon
ATCTGTAACATCATGAATGCTTCAGCTGATGAAATGTTCAACTTTCAG
Seq A exon
GTAATCTGCCTACCCATTTAATGAAACTGCATTTTACTAGAAAAATTTTGTTTCAAAAATGATGGATTGAATTAGGTTTTTCCACTTGAAACAACTTTTGGGGGGCTAGAGAGATAGGTCAGCAGGTAAACTGTTTTCTATGATAGCATGAGGATCCATCACCCACATAAATAAAACCCAGGTACATGTACCTATCAATCCAAGTGCTGAGTTAGGGGGATGAGAAGCAGGCAAGACAAAAGGATTCCACAGGCTTAGTAGCCAGCTAATCTAACCAACCAGTGAGCTCCAGTATCAGTTAGAAACCCTGTCTCAGAAAATAGAGTAGCAAGCAACGGAGAAAAACATCCAACATGCACACACATATATGCACACCAATGTATGCAACATACACACATAAAACAACTTCACTTATACCTGTAATCCCAGCACTCAGAAGATGAAGGCAGGAGGTTTGCTGCAAGTTAGCCCAAGGCCAACATTGGCTAAAGAGTGAGATTCTGTCTCGAAAAGCAAATGAAAAATAGAAAAGAACAATTTCATCTCAGTGACTTTCCGGGAAACCATACAAGAAATGTATTTGTACTTCCAGGTTTACAGTTGAGCTGATTTTATGTGGGCTCAGTTAGATTTAATTGATCTTGGCTGGACTCAAATGATCTTGTCTTGTCTCAGCTGAACTTATCTGATCTCAACTGACCTTGGCTGGACTCTGCAGAGCTTATCTGGGCTAAGTGGATCCTGTCTGGCCTCAAGTGATCTTGGCTGGTCTTAGTTGATCTTCACTGGGTTTATCTGGGTTTAGTTGGTTTTCACTGTGTGCAGCAGAAGTCAGCTAATCTTTGAGCTCAATCAATTTTGGTAGGACTCAGCGGAACCTTATCTGTTATCATTTGATTGAATGTGGTATAGTTGAACTTTTCTGTGCTGGAACTATGAAGATTTAGAATTTCTTTGCTCTACCTGTCCTTATCTGGGGTTTAGACAAATGTGCCTATGGCCACATGGCACTTTCCTAAGGGAGGTTATGTTAGTAGGAACACCACTAACAGCCTCTTGGAGGAACTGGTTAAAAATTACCATCCATATTTCATATTGGAAGACAGAATGAACCAACTACATAGTGTTCAAAGTCCAGTGTAAAATAGAAACGTGGATCCATTTGTTGAGCAGTTAGTAAGTTCTTTTTTCAGTTCTTCTAATAAGTATTCATGGGGACTGGAGCCCTTATGTGCCCATGAAGTCTGTATGCTGGGAAAATAGCCTCCTCTAGCCCACAAAATTACCACGCAAAGCCCTTGAACATAAAGTTCACAGACAAGTGAAAGTAAAGAGTCAGCATGCAACCTATTAGCATGGTCGGAGGACAGAAAAAAAAAATGAAGTCTAACCCTGCCCCTCCCCCACCCTGGTCACCAAGTCCTTACCAGAGCACACCTGGAACAGCCTAGTTCTTTCCCTACTCCCTGCAG
Seq C2 exon
GAGGGGCCCCTGGATGATTCAGGATGGGTGATCAAGAATGTCCTCTCTATGCCCATTGTCAACAAGAAAGAGGAGATTGTGGGGGTGGCAACCTTCTACAACAGGAAAGATGGAAAGCCCTTCGATGATCAAGATGAAGTCCTTATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029491-Pde6b:NM_008806:8
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=0.020
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(8.4=100)
A:
NA
C2:
PF0159021=GAF=FE(27.5=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:
ATCTGTAACATCATGAATGCTTCAGC
R:
CTCCATAAGGACTTCATCTTGATCA
Band lengths:
198-1670
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: