MmuINT0036287 @ mm9
Intron Retention
Gene
ENSMUSG00000026251 | Chrnd
Description
cholinergic receptor, nicotinic, delta polypeptide [Source:MGI Symbol;Acc:MGI:87893]
Coordinates
chr1:89089421-89091575:+
Coord C1 exon
chr1:89089421-89089530
Coord A exon
chr1:89089531-89091374
Coord C2 exon
chr1:89091375-89091575
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-Chrnd:NM_021600:6
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=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(16.7=100),PF0181912=Levi_coat=FE(46.2=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(17.6=57.4),PF0181912=Levi_coat=PD(45.0=52.9),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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: