MmuINT0092734 @ mm10
Intron Retention
Gene
ENSMUSG00000030201 | Lrp6
Description
low density lipoprotein receptor-related protein 6 [Source:MGI Symbol;Acc:MGI:1298218]
Coordinates
chr6:134457658-134459468:-
Coord C1 exon
chr6:134459232-134459468
Coord A exon
chr6:134457769-134459231
Coord C2 exon
chr6:134457658-134457768
Length
1463 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTA
5' ss Score
7.52
3' ss Seq
TAAAACTGCCTTTTTTCTAGTGC
3' ss Score
6.65
Exon sequences
Seq C1 exon
AGCCTCCAACGTGTTCTCCTCAGCAGTTTACCTGCTTCACTGGGGACATTGACTGCATCCCTGTGGCTTGGCGGTGTGATGGGTTCACTGAGTGCGAAGACCACAGCGATGAACTCAATTGTCCCGTGTGCTCAGAGTCTCAGTTCCAGTGTGCCAGCGGGCAGTGCATTGATGGTGCCCTTCGATGCAATGGCGATGCGAACTGCCAGGACAAATCAGATGAGAAGAACTGTGAAG
Seq A exon
GTACTAAGTCCCTCGGTGCTTGCTTTATGGTTCTTTGCATCAAGTTATTTAAAATTCAGTGTCCTTTTGTTGTTGTTTTTGTTTGTTTTGGCTTTTTGGCTCAATAATTTGAGTTTTATATTTGACTATGCCTTGCACATTATATATGTTGCTAATTATTTGAACCATTTTATATGTGTAAGTTCTCTACAAATTAATGTGTTTATTTTGCTACTTGATCGAAATACCTTGGTGGTGAGTGTCTTTGGCTGTGATAAAACACTCTCACACTGTCCAAGGGCACCTTAATGAAGAAAGAGTTTATTTTGGCCAAAAGTTCCTGAGGGAGAGTCTATAAAGGCAGGGAAGCTGAGAGACCACATCTTCTGCTTCAAGATACCAAGCAGAGGAAATGAGCTGGGAGTGGGGTGAGACTGTAAACTTAGCTCTTCCCTGCCCGATGTACCTCCTCCAACACTGCAACTCCCATAACCTCCCAAACAGCTCCACCAAATGGGAACCAAGTGTTTAAATATTTCTCTTGTAATGAGACATTGCTCATTCAAGTCACCACAGTGACATTTTTATAGAGGTGTATTTAGCTCCCATTCTGAAATGTCAAGGGCAGGTGCTGGCTTTAGTTGGGCTCTGGTAAAAACTTCCTGGCAGAAGGCAGCACAGTAGTGAGAGCACTTGGGAGAGTGAGGGCACACATCTATACTACGGAAGGCAGGGTGAGAGGAGGGGCAGGCTTGTTCTCTTGTTCTCCCTTTAAAATGTGTAGGTGTTTTACCCAAATGGGAAGGACTGACAAAAAGAATAGTGGTCACACAGAGATAGGACAGTCATAGCCAAGGGACCTCAATAAAAATATATAGACACCATTTTACAATACATAGACTTTGTAACCTGCTTCATGCACAGATACTTATATGCATGGCGCCTAAGGAAGCCTTAAGAAGCTGTCAGACCTCTCAGTATTGGAGTTAGATGGTTGTGAGCATCTGTGTAGGTGCTGAGGAGGGACCTCTGGAAGAGCAGCCAGGGCTCCTTAACCATGGAGCCTGCTCTCCAACCACAGGCGTGTTTTTGTATGACTAGTTTTTCTCAAGAGCTAACACAGGGTACATTGAGCATTCCCTAACATATTCTGAGAATGAGGTCCAGTTACCTGCCACTATGCTCCCTCTACCTCCAAACTACACGAAGGACCAGGGCTCCAACGTATGAACCTTAGGAGGAAGGAATACATTTAGACCATCCAAACCACACCAGTAAGTTCTGAAAATTGAGAAATAGCACCAAAAGTTAAGTGAAATAAAAAATTTGATAACAAAGCAGAGAATATCATTTTTACCAGTGGGAATCCTTAGAGGTAGCACTCACCTGTGTCTGAGCCTGATGTGTTTTTAGATTATACTTAGAAAGCATTTGATAGAATTTGTCTTTTCATGGTGATAAAAATAAAACTGCCTTTTTTCTAG
Seq C2 exon
TGCTTTGTTTAATTGATCAGTTCCGCTGTGCCAATGGTCAGTGCGTTGGAAAGCACAAGAAATGTGACCACAGTGTGGACTGCAGTGACAGATCTGACGAGCTGGACTGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030201:ENSMUST00000032322:18
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=0.000
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=WD(100=48.8),PF0005713=Ldl_recept_a=WD(100=46.2),PF0005713=Ldl_recept_a=PU(0.1=0.0)
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=97.4)
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:
CTCCAACGTGTTCTCCTCAGC
R:
AGTCCAGCTCGTCAGATCTGT
Band lengths:
342-1805
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