MmuINT0036235 @ mm10
Intron Retention
Gene
ENSMUSG00000035594 | Chrna5
Description
cholinergic receptor, nicotinic, alpha polypeptide 5 [Source:MGI Symbol;Acc:MGI:87889]
Coordinates
chr9:55004336-55007779:+
Coord C1 exon
chr9:55004336-55005159
Coord A exon
chr9:55005160-55006413
Coord C2 exon
chr9:55006414-55007779
Length
1254 bp
Sequences
Splice sites
5' ss Seq
GAGGTTTGT
5' ss Score
6.36
3' ss Seq
GTATTTATTTTTTTTAACAGGTT
3' ss Score
10.47
Exon sequences
Seq C1 exon
ACGGACGTTTCGAAGGGGCCAGTACGAAAACAGTTGTCAGGTACAATGGCACTGTCACTTGGACGCAGCCAGCAAACTACAAAAGTTCTTGCACTATAGATGTGACCTTTTTCCCATTTGATCTCCAAAATTGCTCCATGAAATTCGGCTCATGGACGTATGATGGATCCCAGGTCGATATAATCCTAGAGGACCAAGATGTCGACAGAACAGACTTTTTTGACAATGGAGAATGGGAAATCATGAGCGCAATGGGGAGCAAGGGGAACCGGACGGACAGCTGCTGCTGGTACCCCTGCATCACCTACTCCTTCGTGATCAAACGGCTGCCTCTCTTCTACACCCTGTTTCTTATCATACCCTGCATCGGGCTCTCGTTTCTGACTGTGGTTGTCTTCTATCTCCCTTCAAACGAAGGTGAAAAGATTAGCCTGTGCACTTCCGTGCTGGTCTCTCTGACTGTCTTCCTGCTGGTGATTGAGGAAATTATACCGTCATCTTCCAAAGTCATACCTCTGATCGGGGAGTACTTGGTGTTCACCATGATCTTCGTGACCCTATCCATTATGGTGACTGTCTTTGCCATCAACATCCACCACCGCTCTTCTTCCACACACAATGCTATGGCGCCGTGGGTTCGTAAGATATTTCTCCACAAGCTTCCCAAACTGCTCTGCATGAGAAGTCATGCCGATAGGTACTTCACTCAGAGAGAAGAAGCCGAGAAAGACGGTGGACCTAAATCTCGGAATACTTTGGAGGCCGCGCTCGATTGCATTCGCTACATCACGAGACACGTAGTGAAAGAGAACGACGTCCGCGAG
Seq A exon
GTTTGTGGCGAGCATAAACACCCCCGCAAAGTGGGGTATCTACATGAATCTCACCCTCCATTTCCCCAGAGCATCTTGAATGACCCTGAAGAAAGTTTAGTAGTATGCATTTGAAGGGATAGTAATATTGACTTAGTTCTTTGGCTCTGGAATAGTTTACTGATTTAGATTTATCTTCCATAACTTTGTTTCTGAATTTTTACATTATAGTTTATCAAAAATTACCTTTTTTGAAGAATGAGTCTAATATAAACCTTAAGATACTTTGCATAGAGATATCTTTTGTAGCTTGTTTACAAATGAATATTAGTAAAATTGAAAAGAGCAAGGTGCATGGCTATAATTCTACCATTCAGGGGCTGAGGCGGGAGGATTGAAAGTTAGAGTCTATATTGATGTACTTTAGGAAGTTCATGGTTAGCATGGGCTACATAGGGAGATTATGTCTAATAAAAGCAAAGTGAAATAAATAGCCATAAAAATAAAGAAAAGGAATAAGGTGTGCCCATGTGTTATTTTATACTTTAGAGTTTTCAGGAAAGCAGTAATAGTATCCCTGCCTTCCTCCCTCCCTTCCCCTCTTCATCCCCTTCTCTCCTCCTTCCTTCCTTCCTTCCTTCTTTCCTTTTTTTTTTTTTTTTTGAGACAGTCACTTTATAGTCCTGGCTAGACTGGAATTTGGTATGTAGACCAGGCTGGCTTCAGACTTACAGAAATTCCCCCTTTTGGATTAAAGTCGTGTTCCATTATGCCAAAGCCCCCACCGTTCACTTTTTAAAGAAAATTTCACTATGTAGCTCAGGTTAGCCTTGAACTGTCAATCCTTTTACTCCAGCCTCCTGAATGCTGAGATTTCAGCAAATACTGCCATGTGCAGGTTATGACTTTGAACTAACTCTTTGTTATTGTTCCAAGGTGCTGGCCTTGAACTTCTGATCCTCCTGCCTCAGTCTTCCAAGTAGCTGGTACTACATGCTCCTACCACTGTGGCCAGTTTACTTTTAACAAATTAGTACTTGTTAACTGTAGTATTCTATGGCAGTATAATTGAATTATTGTAGGGTTTAAGATATTGATGGAATCTTAAAAGGTAAGAATTTATTGAATATAAATTCCAAATTTAAATTTAGAATGGGATTTAATAAATTATACTAGTCTGTCTTAGAGATCTGGGCATAGGAGACAGCAAATGATTATCTCTCTGTTTTTTATCCTAAAATACAGCTTTATATATGTATTTATTTTTTTTAACAG
Seq C2 exon
GTTGTTGAAGATTGGAAATTCATAGCCCAAGTTCTCGATCGGATGTTTCTATGGACGTTTCTTCTGGTTTCAATCATTGGGACGCTAGGGCTTTTTGTTCCTGTTATTTATAAATGGGCCAATATAATAGTCCCAGTTCACATTGGAAACACAATTAAGTGAAACCAAGAAATTACACTGGACTTAGTGAGCAGTCAAGCAGCTCTTAGGACACGTATGCCATTATGAAAATATTTACAATTTGATATAGGCAGTAACAGATTAGCAGTTTCTGACATTGGCTTAATGTTGTCCATTAGAACTGTAGTAATAGCCTTGAGTACCAACACTGTCCGCCTGCACTAGTGAAGGCCTACCATCGCATCCTGGCAAATCCTACTAACTTGCAACCAGTGACGAAGGGCATCTTTGGAGTACTGGAAAATGCAACTATATTTGAAGACTGTTTAAAGCTTTTCTCCCCACATTTAGTAAAAGCATATATTTGTGTGGTTTTGAATTTTCAGAATGGGTCTTGTTAAATTGTCCAGGCTGGCCCTAAACCTCCTGAGTAGCTAGGACTATGGGTGTGCTCCATTTTGCCCTGTTCTGTATTCATGGATATAAAACACATCATACTTTTATAGGAGATAAGCCGATTACTTGGTTTAATAATAACTATTTTTGTGAAGAGACACCATGATCAACAACTCTTATAAAGGAAAACATTTAATTGGGGCTGGCTTACTGGTTCTGAGGTTTAGTCCATTATTGTCATGGCAGAAGCATGGCAGCATACAGGCAGACATAATGTTGAAGACAAGAGTTTTCTACATCTGGATTGGCTGGCAGCAAGAAGAGAGAGTGACCCACTGGACATGACTTGAGCTTCTGAAACCTCAGAACCCACCTCCTGTGACACACTTTCTTCAACAAGGCCACACCTCCTCATAGTGCTACTCCTTGGTGATCAAGCATTCAATCTATGGGTCTATGAGAACCATTTCTATTCACACCACCCTTGATAGGATGCTATTCTTACTGACATTTTTAATATGTGAAAAATGGTAACTAGAAACTCCTTAAGTCTACTTTATTCTTCATATGGCAATATGGAATGGCTTTTGTGCTAACTAACTTTGCAGCTTACTGTCCACTGAAAACATATAACAGGCATCTCCTGCAGACATTCTTTGTAATGACTTTATAATCCTGCAGTGACACATTTTTTGTAATGACTTCAGTCGCCTTGTCCATATTCTTTGGTTAGGAGAGCTACTTATTTATCTCTGATTTCAGAATAATACTGCAGTTGTACAGATTCCCGTCTCAAAACGGGATGTTATGTCTCTGTCTTGGTAGTTCTGTGGAAAAAATCATTCTGGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035594:ENSMUST00000217408:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(89.4=40.0),PF0293211=Neur_chan_memb=WD(100=49.1),PF0293211=Neur_chan_memb=PU(54.2=14.2)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(43.1=57.4)
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:
TTGCCATCAACATCCACCACC
R:
CAAAAAGCCCTAGCGTCCCAA
Band lengths:
342-1596
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