MmuINT0117062 @ mm10
Intron Retention
Gene
ENSMUSG00000029491 | Pde6b
Description
phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide [Source:MGI Symbol;Acc:MGI:97525]
Coordinates
chr5:108429106-108430706:+
Coord C1 exon
chr5:108429106-108429189
Coord A exon
chr5:108429190-108430549
Coord C2 exon
chr5:108430550-108430706
Length
1360 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCGC
5' ss Score
9.05
3' ss Seq
GACTTCTCAGTTCCCTCTAGGAA
3' ss Score
4.93
Exon sequences
Seq C1 exon
CCCATGATGGACCGGAACAAAGCAGCTGAGCTCCCTAAGCTGCAAGTTGGTTTCATTGACTTCGTATGTACTTTCGTATACAAG
Seq A exon
GTGCGCAGCAGAGGTATTCCATGTTGGCTGGGGTGGACTGGCTCAGAGTGGGTTGGGAATGGACTGAATCCAGCAGGGATCACACAGGGACATTTGTGTGATCTTCACCCTTATTTGATGGGGGAAACCACAACACCCACCTCAACCTGCCCTGCTAATTGTCCCAAAACTTATGACTGTTCCCTCAGAAGCACTAAGTGTATTTCCTAAAATGTCCTTACTCACCTTGAGGTCTCACCTTAAATATCTCTGCCTCAGAGGGCCTCTTTAACCACAATGGGCACACCATCTTCAGGAAAATGGCTACAACTTGTCTACTAGGTATCTGTGAAGGTGATACCTAGTTTTTTGTTGTTTTTTGTTTTTTGTTTTTTTTTGTTTTTTGTTTTTTTGTTTTCCAGACAGGGCTTCTCTGTATAGCCCTGGCTGTTCTGGAACTCACTCTGTAGACCAGGCTGGCCTTGAACTAAGAAATTCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCACTACCTGGCAAGCCTGAGTCTTATCTGTCTCCAATGGCATACCCCAATACAACCTGAAGAACATGATAGCAGCCATGTTCCCACTAGCTGGTCAGGCACCGATGAACTGCCAAGTCGTTAAGTTCTGCTATTTGATCATAGAGTGTAAGACAGGGACTTGAAGAGACTCACAAGATAGTGTCCTCATGTGATGTACATCACACCCAAGCTCCACACCACTCTAGTACTCAGTGGTGACAGACCCCACATTGTAAGGTAGATGCTATGTGACTTCAAGTGAAGTCAATCGTAAGCAGCCAAGGAGGAAGGAAGAGGTGGTCACTGTGGACCCCACTGTTCCTCTGCCCATTGACATCACCTGAAAACAGATGTAGGGCTTGTTAGAGCTTCCAATCCTCCTGCAGGTGACATTCTCTATTCTTGGGATATTCAACCTGCTAGTACTGTATCATAAATACTTATACCCAGCAGCCCCATCTCACAAAAGTTCCTATCCTGTCCCCCTCCTCAGGAATTTTCTGGGAAGGAGACACCTCAGTGGTTCTCTCCTATGCGGGTTAACTATAGATGGCATTGCCTGGTGCGAGCACCAAGTGAAATGAGCTAAGGATCAGGAAACCAAGCTTATGCTGGGCCTCATTTCACTGTCCTTATGACTTCTAAGATAAATATGCCACAGATACCAGAATCCTATAACCAAGATCTATAGCTCCACGATTCTAGAGCATTCTCAGTCCAATGAGTCTGGTGGTAGGGAAGCCTGAGGCCTTTAAGAGCTACCATTTGAGCCCTCCGGGATCAGTGAAACAGCATGGTGACTTCTCAGTTCCCTCTAG
Seq C2 exon
GAATTTTCTCGATTTCACGAAGAGATCCTGCCCATGTTTGACCGACTGCAAAATAACAGAAAGGAGTGGAAAGCACTAGCTGACGAGTATGAGGCCAAAGTCAAGGCCCTGGAGGAAGAAAAGAAGAAGGAAGAAGACAGAGTCGCAGCCAAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029491:ENSMUST00000031456:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(10.8=100)
A:
NA
C2:
PF0023314=PDEase_I=PD(7.6=35.8)
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:
CCCATGATGGACCGGAACAAA
R:
CTTTCTTGGCTGCGACTCTGT
Band lengths:
241-1601
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types