MmuINT0036287 @ mm10
Intron Retention
Gene
ENSMUSG00000026251 | Chrnd
Description
cholinergic receptor, nicotinic, delta polypeptide [Source:MGI Symbol;Acc:MGI:87893]
Coordinates
chr1:87192846-87195000:+
Coord C1 exon
chr1:87192846-87192955
Coord A exon
chr1:87192956-87194799
Coord C2 exon
chr1:87194800-87195000
Length
1844 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTT
5' ss Score
8.17
3' ss Seq
TGTCCTTGTACCTTCCTCAGAGA
3' ss Score
8.41
Exon sequences
Seq C1 exon
TTCACTCAAGTATACAGCCAAGGAGATCACACTTAGCCTGAAGCAGGAGGAGGAAAACAACCGCTCTTACCCCATCGAGTGGATCATCATTGACCCTGAAGGTTTCACAG
Seq A exon
GTACTTCAAAAGTCATGGTGGATGGGCCCCAAAGATGCAGACATCTGTGGAAGTTCACTTACACCTCACACACTCAGCCTGGGGCACCGACACACATACAGGGAAAAATAGGCACCCAGACACAGCCTACACACCTACAGTTACTGATCCAAAGAGATTCTAGAGCAAAGCAAAAGGAATCAGGGACCCCTTCATCACTACTACCCTTCCCCCCAACACACACACAGCAGATACTTGTGAGTATGGCAAGGTCTCTGAGGCTAGACGTAGCTGATGGAGATGGGATCAGGCCTTCTGAAGCCTGAAAAGACTGGGGGTGTGGCTGGGGGTTTCATGGATGGATGGATGGATGAATGAATGAATGAATGGATGGATGGATGCTATCACCAACCCCATCTGTGACTAGCTCAGCTCTGTGGGGCTCTCTGCTCAACCCTGTCCAGAAGAAGAACCCGTGTCTTCCGTTTTCAGGGCTGGGATATCCTAGATGAGAGTATTATACTCACCTAATGTTCTCTCGAAAATCTAAGCCAAGGAACGACAGTCAAGAACTATCACTAGATCTTTGGTTTTTAACTTAGAAGACAAACTCAAAATGGCATGGTAACATGCATGCCTGTAGCCTCAGCCCTTGGAAGGCAGAAACTGAAGAACTGCCTCAATTTTCAAGCCAGCCTACACTACACAGGGGGTTTCAGGCTATCCAGGGTTACACATCAAGACCCTGTTTTAAAAACTAACACAACAGAGCTAGTGAGATGGCTCAGCAGGTACAGGTACTTGCAGCTAAAGCTGAACTCACATTCAATTCCTACAGCCCATGTGGAAGGAGAAAATCAACTCCTATAAGTTATCCCCTGAACTACACATACACACACACACACACACACACACACACACACACACACACACACACCTAACAAAACAAAAAAAAGAAAAATCAATGTAGCTGTGCATACCTGTAATCCCAGTACTCCAGAGGCTGAAGTAGGAAGATCATGAGTTCAAAGACAGCCCTGACTGTCTTTGACATAGTGCTATCAGCATGAACTGCAAATTCAAATTCAAAGTAATACATCTTATTTGCTCTGTGTGTGTGTATGTGCATGTGTGAATGAATACATAGCATATGTGCCCAGAGGACAACTTGCATCAGTCAGTTCTCTTCTTCCCAGAGACTGAGCTCAGGTCGTCAGGCTTGACAGATATTGTCTGTCTGTCTGACTCACGGAGCATCTCATCGGCTCCAGACAGTGATTTTAAAAACTCTCTCTTTAATCGTCATGCCACCTACTTTTGATTTGTTAAAGCTTTCTTTTTTAAAGATTTACTATTTATTTTATGTATTTGGGTGTTTTTCTGCATGTACGTCTTGCATACTAGAAGAGGGCATGGGACGACATGGGACTACATGTGTAGGACTATAGTTACAGATGATTGTGAGTGGCTATATGGGTGCTGGGAATTGAACCCAGGACTTCTGGAAGGGCAGCCAGTGCTCTTCACTGCTGAGCCATTTCTCCAGCCCCTTGTGATAGCTTTTAAGCCAAAACATACTCCTTATTTGAACCCTGTATGGCTTCAGCTTCTGTCTTTTTCCAAGGAGAGAAAGAAACAATAAGCAAACAAATAAAAGAGCCTTCCAGAAAAAGTCAGAAAAAAAACTTCTTCCTCACAGACTGACCCCACAGATGGGCCCCACAGTACCCAGAATTCCTCCAAGCCTTAGACAGCACCCTTGCCTGCCTTGCTCCATCCCAGACCCTCATGCTGTCCCAAGCCTCCTTAGCCCCATGGTTTCCCTTCTCCAGCTTGATCCTCAGCTGTCCTTGTACCTTCCTCAG
Seq C2 exon
AGAACGGTGAGTGGGAGATAGTGCATCGGGCAGCCAAGCTCAATGTGGACCCCAGTGTCCCGATGGACAGCACCAACCACCAAGATGTCACCTTCTACCTTATCATCCGCCGCAAGCCCCTCTTCTACATCATCAACATTCTGGTACCCTGCGTGCTCATCTCCTTCATGATCAACCTAGTCTTCTACCTGCCAGGCGACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026251:ENSMUST00000073252:6
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:
PF0293118=Neur_chan_LBD=FE(16.7=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(17.6=57.4),PF0293211=Neur_chan_memb=PU(8.9=30.9)
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:
TCACTCAAGTATACAGCCAAGGAGA
R:
AGTCGCCTGGCAGGTAGAAG
Band lengths:
310-2154
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