MmuINT0036290 @ mm9
Intron Retention
Gene
ENSMUSG00000026251 | Chrnd
Description
cholinergic receptor, nicotinic, delta polypeptide [Source:MGI Symbol;Acc:MGI:87893]
Coordinates
chr1:89092258-89094062:+
Coord C1 exon
chr1:89092258-89092372
Coord A exon
chr1:89092373-89093857
Coord C2 exon
chr1:89093858-89094062
Length
1485 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGTCCCCCTGACTGCTAAAGTTC
3' ss Score
2.73
Exon sequences
Seq C1 exon
GTTCCTGCTTTTCGGCATGGTGCTGGTCACCATGGTGGTGGTGATCTGTGTCATCGTACTGAACATCCACTTCCGGACGCCCAGCACCCATGTGCTGTCTGAGGGAGTCAAGAAG
Seq A exon
GTGAGCTTTTGACCAAAGATGGAAACCAAGTCCTGGCCGGGAGGATCCGTGAGCGTGATGGGTGTGATCTCAGAATCACTGGTCCTGTTGCCCAGAGTGAGGATTCTCAGCTCCACTAAACTCTTTAAAATAATAATAATAATAATAATAATAATAATAATAATAATAATGGACCAGTTAGCTAGCTCAGTGAGTTGGAGCATTTTCCACCAAGCTTGACTGCCTGAGTTTGATCCCTATGACCCATGCGGTATAAGGGGAGGACTGACTCCTGCAGGATGTCCCCTACCTCCTGTAGTAGCACTGTGGCATGTGTATACATGCACACACATATGCCCACATACACGTGTGCATGAATACTATCATTTTAAAATTAAAACAAAATTTAAGAGTAAGCAGGCGAGGACACAGGGGACAGGGTGTTTGGGACAAGACTATCTGTGCTCTAAGATTGTGGGACAATAGGTTCTTCTGGAATAAGTCATCTTCTGGATGGTGATTCTATAGCTCCTTAATGGTTTTTGTCTTTAATTGAAAGGAGAGCCCAACATTTGGGCTTTTATTCATTTGAGACAGGGCCTTACTATATAACTCATAACAGAGGGGGGCACCGGTGTATAGCTCAGTTGGTACAGTGCTTGCCTAGCTTGCACAAGGCCCAATACTGAGTATGAACCCTGCTTGATCCTAGTGGGAGGATCAGAAGTTCAAAGTTATCCTCAGTTACATAGTGAGTTCTGGGCTATCCTAGTATACATGAGACCCTGGCAGGAAGGAAGGAAGGGAGGGAGGGAGGGGAGGGAGGGAGGGAGGGGAGGGAGGGAGGGAGGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGAGAGGGAGGGAGGGAGAGAGGGAGGGAGGGAGGGAGGGAGGGAGGAAGGAAGGGGAAGGGAAAGAGGATGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGGAGAATCAGGGCAGAAGGAAGCTGAGGTGTGTATCAGTGATAAAGCATATGTTCAAACTCTTAATTCTCCTGCCTCAGCCTTCTGAATGCAGGGATTGAAGGCATGTACCCCCATTCTCAGCTTCTTTTTTTCTTTTGGGGGGGTGGGTGTTTCGAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCTGCCTGCCTCTGCCACCCGAGTGCTGGGATTAAAGGCGTGTGCCATCACGCCCAGCGCTTCTTTTTTTCTTAAGATTTATTTTCAGTGACTGAGTTCTGCTGTTGCTGTAAGTAATGAGGGACCGTTGAAAGCATTCTACACCAGTCAGTGGGGAGTCTGGGAAACAGACAATGGGGTCAGCCTGGGAGCTCTATGCGGCAACCAGGGTCCTCAGAATGTGTAAAGATGACTCCACACTTGTGAAATGGCCTGTCTTGTGTCCCCCTGACTGCTAAAG
Seq C2 exon
TTCTTCCTGGAGACCCTGCCCAAGCTCCTGCACATGTCCCGCCCAGCAGAGGAAGACCCAGGCCCCAGGGCTCTCATCCGGAGAAGCAGCTCTCTGGGATACATCTGCAAAGCAGAGGAGTATTTCTCACTTAAGTCCCGCAGTGACCTCATGTTTGAGAAGCAATCAGAGCGGCATGGGCTGGCCCGGCGCCTCACCACAGCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026251-Chrnd:NM_021600:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.188
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(16.0=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(28.7=100)
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:
GTTCCTGCTTTTCGGCATGGT
R:
CCATGCCGCTCTGATTGCTTC
Band lengths:
294-1779
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: