MmuINT0036282 @ mm10
Intron Retention
Gene
ENSMUSG00000026251 | Chrnd
Description
cholinergic receptor, nicotinic, delta polypeptide [Source:MGI Symbol;Acc:MGI:87893]
Coordinates
chr1:87197575-87200070:+
Coord C1 exon
chr1:87197575-87197693
Coord A exon
chr1:87197694-87198579
Coord C2 exon
chr1:87198580-87200070
Length
886 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TGTCTTGACCCTACTTATAGGAG
3' ss Score
7.4
Exon sequences
Seq C1 exon
GCAGGCCTCCAGCAAGCTCTGAGCAGGTCCAACAGGAGCTCTTCAATGAGATGAAGCCAGCTGTGGATGGGGCAAACTTCATCGTCAACCATATGAGAGACCAAAACAGTTACAATGAG
Seq A exon
GTGAGCGACCTGAGACACCATAGAATCAGATGTTCAAGTAGACTAGGGATCAAGTGGATTCTGTCTCCCCCTCATAGACACATGTCCACTTAGATGAAGAGATGCATGGTGGGTAAGGGACCCTTGGCATACATTCTCCAGGAAGGCAGAATTCCTTCATGAAATCCCACAGCATCACCCTGGACCAAGCTCAGGGGTACACACAGACAGACAGCCTTAACATGACCAGGACAAATTTTAAATACATGTCCTTTCTGCTCAGATATTCCAGATAGCATCTATTTATTATATTTATTTATTTTTATAAATGGGTATTTATGCATATTACATATTTATTATACAATTCTTATATTATTATACAATATAATGGATATATAATATGTAAGTATATTATTTTATAAAATATGAATAAATAATATATAACAAATATTTTAATTTTATGTGGTATAGTATATATAAATATATTTTATATTTTGGTTATATATTTATTTATAACATTTGTTTTATTGTTATGTTACTTTTGCAGTGCTAGGGATTAGACTCAGGGCCTCTGTAAATCATTAACCACTGATCTACACTCCCAGCCCAGCACCAGACCTTTCAAAGACAGCCATACTGGGCTGTCTACTCTTAAGCAACTTTTTAACGGTTCTCCATTGTATCCTCCTGCTCACATGTGGCTCAAAGCAGCCCTGAGTGGCTTGGGTCCCTACTAAGGGTAATGGCATTCTGTCCTGCCCCACCCTACTGCTATAAGCCTGAGGTGGCCCCCACAGACACAGAGGAATGGAGCCTATGTGTCTCCATTTCCAGGCCCTAGCTTAAGGGTGTGAGCCTGCATTCTGAAGACTTCCCTTACCCCATGGTGTCTTGACCCTACTTATAG
Seq C2 exon
GAGAAGGACAACTGGAACCAGGTGGCCCGCACAGTGGACCGTCTCTGCCTGTTTGTGGTGACACCCGTCATGGTGGTGGGCACAGCCTGGATCTTCCTGCAGGGTGTCTACAACCAGCCCCCACTCCAGCCTTTCCCTGGGGACCCCTTCTCCTATAGCGAACAGGACAAGCGCTTCATCTAGAGCAGGCATGAGTAGACAGCCAGGCAGACAGCAGTCTGAGAACGGCACGTAGTTCCTGCCCTTGAGCTTGTGCCTAGCGGGTGCTGTGTGGCTGGGCAGAGGCCATGGTCGGGAGAGCTCCCTTCCGGAAACAATTCCTTTCTAAATAAAGGAGGGAGACACTTGAGATGGGCTAAGGGTGGACGTGGTGGAGAGGGAGGCTCCAGGGTTGTGAGGAGAAGCAGGGGCCTTGCTCAGGGGGCCAGAGAGGTGACCTTGGGACTGGCTTCCTGGGAACAGTCCTGTGAGAGATCCCCCAACCTGAGCTGCTCCTCCGCCTGACTGTCTTCCAGAGCAGGTCAGAATTCTGAACTTGCAATTTCCTTGCCTTCCTTCCCTTACCTACCTGGGGCCCAGAGAGGGTGACTACTCTCCATTCCCCAGGGAAGGAGGTTTACTGGGATGGTGGGCTGTCCAGGTTGTCATCTGTCAGCCCCCGATGCCTTGGTCGTTCTGTCTGAGTCCTTCTGAGAAGCGGGGGACTGGTGTGGGAGGATGACACTTGGCATCAAAAGCCCCATCAGTGTGTGTTCTCACATCCTAGAGCATCAGGACCCAGCAGCCCCTCTAAGAGACCCCCACATTGAGTCCCTTCCTCCTAGCCCCAGGCTCTCCAAACCAGGGTTGCCTAGCAATATTTGAGGTACACTTGGGATAAAGATTTATCCGTCGTTCATCTGAAGCTCAAATTTAAATGTGCACCCAGTGTTCTTATTGAGTCTGGTCTTCAACCCTATCCTAAAGGAAGGCACATTCAGAACTATCCTGAGTCCTATCAATCACAGGAGCAAGGAGACTAGGTCTTAGTGTAGCCTGCAAAGCCCACCTCTCAAATCGTGTCTTGAGACAGTCCCTGCTCTCTGTACCTGGCAGTTCAGAGTAACCAATAGAATGAGGTAGAAATGATGCTATGCTCCTTCAAAGAACAGCTTCTGAGATGGCTGCTCCTGCAGAGTAATGGCGCACACCTATAACCCCAGCACTTAAGAAGCCGGAGCAAACAGATGAGACCAGCCTGGGTTGCACACACACACACACACACACACACACACACACACACACACACAGCACTGCGGCCTCTCCCTTCCACTCTCCCACTCTCTTTGGAAGTCAGCCACACTGCTGAGACTCTGTAAAAGGGTCCACCTATCAAGAGCCACACAGGCAGGTAGACTAGAAAGGGGGTCTTTCTACCCTGGGAGGACCTCTAGATGAGAGCTGTTCAGGACCCTCAGAAACTGTCGGGGATAATAAATACATTTGGGAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026251:ENSMUST00000073252:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.475 A=NA C2=0.117
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(16.5=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.1=50.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGAGCAGGTCCAACAGGAG
R:
CAGGAACTACGTGCCGTTCTC
Band lengths:
343-1229
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