MmuINT0117083 @ mm9
Intron Retention
Gene
ENSMUSG00000024992 | Pde6c
Description
phosphodiesterase 6C, cGMP specific, cone, alpha prime [Source:MGI Symbol;Acc:MGI:105956]
Coordinates
chr19:38255266-38258441:+
Coord C1 exon
chr19:38255266-38255422
Coord A exon
chr19:38255423-38258167
Coord C2 exon
chr19:38258168-38258441
Length
2745 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGC
5' ss Score
6.1
3' ss Seq
TTTTTCTGGTCTTTCACTAGCTG
3' ss Score
8.48
Exon sequences
Seq C1 exon
GAGTTCTCTCGGTTTCATGGAGAGATCACACCCATGCTGAACGGCCTTCAGAATAACAGGGTGGAATGGAAATCCCTGGCGGAGGAGTACGAGGCGAAGGTGAAGGTGACTGAAGAAGAGGCGGGAAAGCAGGAAGAAGAAGCCTCAGATGGAAAAG
Seq A exon
GTTGGCTGGATTCAGTGTTTACTATGTGTGCGTTGTGGGGGGTGGGCAGGTGGGGGTCACTTGACAAAAACACAGACCTAATGTACTAACAGGAAGCTGCCTTGCTGGTGCAGGCAGGTAAGGTAAGAAGTTTGTAGTTTTCAGGGTTATTTTACCGCCCAGACAAGATCTTATGCATAATTCTGGGTGGAGGTGACTGGTCCAGACTGGTCCATGTACAGCAAGGGCTACAACTGGGCACTAGCATCGCTCTCGAAGGTGGCCCTAGGGCTTCTCAATAAAACATAGGGCCAGGAGTCAGGAACAGCCAAGAACACAGTGCTTGCTGTGAAATGCTGGACAGCTTGTCTGGAAGTCTGGAAACTCTCTCTAGGTTATACACGGGGTTTTACAGATTTACATTTTAAGGAAGTCCTACAGGTAAAATTAAAGCGGGCCAGCCACTAGGGTGGCTTGAAATCACAACTCCTGTAGTCACCTATCAGGTTTATCATTGTTTTTAGACAGCATGTTAGAATGCTTACAATGAATGAATTATTAGTTGTTCAACTGAATATTCATATTCATAGTGGGATGCTGGGCTCAGTGGTAGAATCTATCCTAGCATATTCAAAAACCCTCTTCTGGATTCCCAGCATTTCAGATAGCAGAATGCTAATTTGATGGTGGTGGTGGGTTGCTCTTGTGTGTGTGTGTGTGTGCGCGCGCACGCGTGCATGTGTGTTGAGGTTGGGGCCTGAGAAGCTGTGTACCTTGTCATTTGAGACAGGTTTTGTCACTGGTCTGGAGCTTACTCAGCAAAGCTGGCTGGCTAGTCTCACATATCTACCTGTCTCTACCCCACAATCCCGCCACCTGAGTACTAGGGGTTACAAGCATCTACCACCATGCTCAGCCTTTTTACATGGATTCTGGGTCTCAAATTTAGGTCCTTGTGCCTGAGCAGCAAGCCCTTTTCCTACTGAGCCTGGGATGTTAATGTCTGTCTGCAAAGGTTAGCACCATAAGCTTTGTAAGCAATTCCTATTGGCAAAGAAACCATCTGTGTGTAGAAGGCCTTGAAAGAAGTTGCTTTTACATAAGTGTACTGCTCGGTCAGATTTTACTGTTCATTGGGAGTGGAGAAACCAAAGTTACGGATGTCCCACAACAGAATAAAGGCAGGGCTTTCTGATTCCTCTGGGCCCACTCATTAAAGCATTCATGGGTGTGTGTTCTCACTGCTGTGCCAGATAAGCCTTAGGGAAAGACAGGACCTTCTCTCTAAGCTCTTAACATCTGAAGGGAGAGCTGGGCATTAAGCAGCCAATACAAAACCCAACGGTGAGCCTTAACATGTGCATGGGGTATGTACTAGGAAGGCTCCCCTGAAAAGGGAGGGTGCCTGTGCTAAGGTCCCAAGACACCAAGTCCCAACTCATGCAAAGGAGCAGAGGAGGGTGAAGGAAAAATAAAATATGTAAAATAGCTACTGACATGGGAATAAGCTTGGTGTAGCAGAATAATTGAAAAGTGTGTCCATGTGTAGTTAAGAGAGGACAGAAACCCAAGTACCAGATGAAGCTGGGAGTGTAGGTGGCTGGCCAACAGCACACAGGCTGCAGCCAGCTGCATTGCAGTCAATGAGGGATTAGCGCAACCCCAGGAATACATGAGAAGTGATTTTGACTAATGTTATGTTGTCGTACACATGAGAATGTGAGTCCATAAGGAGAAAATTTTTTAGGAAAAGGAAATTTGATGATACTGACACCTCTTTGCAGTGACTCCTGACGCTTTACTTAGTAAGTTTATTGGAGGGAAGCCTTCATTCTTTAATACAGCATTTTTATCAGTTCTTTGAGAATTTCACGCATGGACATCATTCACATTGGCTATTTTGATTCCACCCTCTCCCTCAATGCCCCCCAGACTGTACACACTTGAATACATTTATTTCTAACTTTTGTCTATTATTTGGAGAATTCATTGGGAATTAAGACCACTGTGCTCTCTGCAGGCTTCAGGTTCTGTGCCTGTGGCTCAGATTCCAGCTTTGTTTAATCTCAAGGAGACAGACACTGAGATTGTGACTGGGTAACTGCTAATCAAATTTACCTTTATTTTGTTTTTGAGACAGAGTCTCACTATGAATCCTTGGCTAGCCAGATAGAACTCACAGAGATCTGCCTGGCCCTGCCTTCTGGGATGCTGGGATTACAGGTGTATCCACACCTGTTGGTTTTGTTGTTGTTGTTTGAGACAAGACCTCATGTAGCTTTGACCGTCCTGGAATCCACTATTGCCTCAAACTCACCAAGATCCACCAGCCTCTGCCTCCCAAGGGCTGGGATTAAAGACATATGTCACTACACCTGGCTCTTGAATTTTATTTTTCAAATTTTCTCCAATTTAAGCATATGAGGAGTACCTTGCCCGCATGTGTATGTGCACCATGTGTGTTTCTGTTGCCGGTAGAGGTCAAAAGAGGGTATCAGATCCCTTGGAACTGGAGTTACAGATGGTTGTGAGCCATCATGTTGGTGCCGAGAATAAAGGACTACCTCTGCAAGAGCCAGTGCTCTAAACTGCCGGGCCATCTTTCCAGCCCCATGAGTTTGATGTTTAAGTGAGCCAATTGTGAATAAACAATTGGTTTTAAACAGTCAAACCCTATTATAGATCTGATACAAATACCACAGGGATGTAAGAAGACGAGCACTGTATCACACTGACTCCTGATGCTTTTTTCTGGTCTTTCACTAG
Seq C2 exon
CTGCCACAGATTTAGGAGGCAGCGCCGAAGACAAAAAGTCCAAAACATGCTTAATGTTATAATCTAACTGGTCTGTATTTCAAGTATCATCTTAGTTTCCACGAAAAAAAAACATCCAAAAGAGCCTCCTTGATTGAGTTCTGTCCAGTGACCAAGAAGTGACAGAAGAGGAAGAGCCCCAGAGATTCTGCCATGTGACTACCCACAGATTATCCATTGCTGACCTGGAAACCCTGTGAGCTAAATAAAGTTTAGTAAAAACAAAACATGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024992-Pde6c:NM_001170959:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.349 A=NA C2=0.400
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=PD(7.6=35.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: