MmuINT0036253 @ mm10
Intron Retention
Gene
ENSMUSG00000029205 | Chrna9
Description
cholinergic receptor, nicotinic, alpha polypeptide 9 [Source:MGI Symbol;Acc:MGI:1202403]
Coordinates
chr5:65970816-65977326:+
Coord C1 exon
chr5:65970816-65971348
Coord A exon
chr5:65971349-65976705
Coord C2 exon
chr5:65976706-65977326
Length
5357 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
TGGTGTTCCTTTCATTCCAGGAA
3' ss Score
9.52
Exon sequences
Seq C1 exon
GGCCGATGACGAGTCTTCAGAGCCGGTGAACACCAACGTGGTCCTGCGGTACGATGGGCTCATCACCTGGGACTCACCAGCCATCACCAAAAGCTCCTGTGTGGTGGATGTCACCTATTTCCCCTTCGACAGCCAGCAGTGCAACCTGACCTTTGGTTCCTGGACCTACAATGGGAACCAGGTGGACATATTCAATGCCCTGGACAGTGGTGACCTCTCTGACTTCATTGAAGACGTGGAATGGGAGGTTCAGGGCATGCCTGCCGTGAAGAACGTCATCTCCTACGGCTGCTGCTCGGAGCCTTACCCAGACGTCACCTTCACTCTCCTTCTGAAGAGGAGGTCTTCCTTTTACATTGTCAACCTCCTCATCCCTTGCGTCCTCATATCGTTCCTCGCTCCGCTGAGTTTCTACCTCCCAGCAGCCTCCGGGGAGAAGGTCTCTCTGGGAGTGACCATCCTATTGGCCATGACTGTATTTCAGCTAATGGTGGCAGAGATCATGCCAGCCTCAGAAAACGTCCCTCTGATAG
Seq A exon
GTGAGTGTATGCTTGGAGCTTAGCTTTGTAGCAGTTGTGATGGCGTGTGTATGTCCCAAGCTAAAGCAATTGAAGCCATTGGCTCTGTGTTTTCGTAAAACCCATTCAGTGCCTGAAGGTGACCTCTTTGCTTATAGCGATGGTTGTTGGAATTAAGTGGTTCTTACGATCTTCACGTTCACAGAAGAACACTTGTTTATTTTGTATTTATCTACTTTTGGATTTTGAGGCAGAGTTTTATAGTGTGGTCCAGGTTGGTCTCAAACTTGTTATTTAGCCAAGTAAGAAGTAGATCTTCTGATCCTCCTTCCCTCCACTGCCTAAGAGCTGAGACTGTAGATGTGTTCCACCAAACCCAGTTTACCTGGTGCTGGGAATCAAATCCAGAGCTTCATACAGGCTGGACAAGCCTCTGCTCAGCAGTGACTTCTGTTACCTGTTCACAGTGTTAGGGTCTTTCTCCTCAGAAGGAAACACAGCAGCTGTGCCAGGAGTTGAGCTGGAGTCTCAAGTCAGATATCTATCCTGCATATAGAAGCCTCATCCCACTTATAAAACAGAGGTTCTGGGGCTGGAGAGATGGCTCAGTGGTTAAGAGCACTGACTGCTCTTCCGAAGGTCCTGAGTTCAAGTCCTAGCAACCACATGGTGGCTCACAACCATCCATAATGAGATCTGATGCCCTCTTCTGGTGTGTCTGAAGACAGGGACAGTGTCCTAACATATAATAAATAAATAAATCTTTAAAAAAAACAAACAAGGGGGCTGGAGAGATGGCTCAGTGGATAAGAGCACCGACTGCTCTTCCAAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGGTCACAACCATCTGTAACAAAATCTGATGCCCTCTTCTGGAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATATTTAAAAAAACAAAAACAAAAACAGAGGTTTCTATGCCCAAAGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATACACACAACCACATATATATAGAGAGAGAGACAGAGAGAGAGACAGAGAGAGAGACAGAGAGGGACAGAGAGAGAGAGAGGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGAGAGAGAGAGAGAGAGGGAGAATCTGGTCATTCTAAAGCAGAATGCATTTTCTCATATTTTGTTTGTGAGCCTAGTGTTCTCTAACAGCTGAGCCATCTCTCCAGCCCACAGAATGCACTTTGAAAAGTCTACAATAATGTAACCTGTAGCCAAGGGTGGCAGCGGAGGCTGAGGCTGCCGTGCCTGCTTGTCTACCTACTTTGTTCTGAGAGCCCTCTGTCACCTCTAACACCTCCTGCTACTGCCACCAAGGAGACCCCTCCGATTCAACACCTTGACCTGCCTGCTATAACAGATGCCTGCCAGTACCAAAAGTAACCCTTCCTTCTTTAAGATAAAACACAAAGAGAAACTGCAAGACATAGAGAATAGTCACCAGGAGCTGTGTGGCCGTGTGTGCTCTATGGAATACAGTTAGCCAGTATTCAGACATGGGTTTTTATGGAGACATCCTTTTTGTTTTGTGCTGTTTTTTGCTTCTTGAGGAGATAGGGTCACATGTAACCCAAGCTGGCTTGTAATTGGTTCTATAACTGAGGCTGGCCTTGAACTTCTGATCCTTCTATGTCCACCTCCCAAATACTGGGGATTTTCCCTTTTTACAGATACACACACACACACACACACACACACACACACTTTCCTTCTAAAATAAGCACAGGTTCTCTTCTCACTAATAGAGACAGGTATAGGAACCTTGGCACTTTTATCCTTTTATTACCTCTCTGGAGACAGAAATGAGTGACACTGGCCAGGCATGGTGATACCTGTCACCCCAGCACTCAGGGGTAGAGGGAGGAAGATCAGGAGTTCAAGGCCTGACTCAACTACATGATATCCTGTCTCAATCAAAAACCAAAACCAAGCCAGAAACAATAACTCTGAAGTGGGATCAGTGACGGGTCCCTCTCTCTTCCTTAGCAGTGACACACAATCACAAGTCAGCAAGTTTCTAAAGAGAGATGACTCACGAGAATTTGGGAAGCATTAATCATTCTGGTTCTACAGTAATATGCAATTTTTTTTCTTAGAATGTACATACAAGGATTTGGAGAACCTTCATTAAAAAAAAAATCACAGCATTTTATTTGTAGCATCTATGAAATGTGCTTCCTGCTTCTGGTTGTCATTGTTATTAGAGACAGCATCTCACCGAACAAGGCTGGCCTTGAATTTAGGCTTCCATTTCCCCTATCTCAGCTTCCCACGTGTTAGGAGGCCAGATGCCTTGATGCCCCTCGTGGTCCCTCCCTCCCTCCCTCCTCACCCTGTAAGTGGAGACTGTACCCAGGACCTCATGTGTGTCAGGCAAGAGCTAAAGCCTCAGACCCTTTGCTCTTGCATTTACAGAAACAAATTTACATCGTCTCTATGACAAGTAGAGTTTCATGAATGTTTCTGGCTCATACTCCTCTTATAATTAATCTGGACTCGTTTTTTTAAAGATTATTTATTTTATGTATATGAGTACACTGTAACTGTCTTCAGACACACCAGAAGAGGGCGTCAGATCCCATTACAGATGGTTGTGAACCACCATGTTGTTTCTGGGAATTGAACTCAGGACTTCTGGAAGAGCGGTTGGTGCTCTTAACCATTGAGCCATCTCTCCAGCCCCTAATCTGGACTTTTTAATAAATAATAAGTGGATGTTAAACAATATTCTGAATGCTGTTCTGGGATGGAGAGCTGAGCCATCCTAACCTTAGAACAGGACTGTTTTCACTTCAGCGCAGGCTGGACTGAGAGCCGGGCCACTGCTGTCTCCCAGCAGGACTGTCAGCTCTCCAGAACTCTCAGCTCTCCAGGAAGACTCAAGCAGGACAAGCCAAGCTCTGGGCATGGCTTACAGTTTAAGATGGGTGGTTGCATTGAGTTGTTTTTGACTCAGTACAAAAGCAGAATTACCTCAAGGCCAGGCTGTCACTAACCACAATAAACCCAGGGACTCCACTGAAGCACTCACTGCCTGGCTGTCCCCTCAAGTCTCCACCCCATAAAAGCTACCCCTCGCTTTCTCTCCCTTGTCTCTCTCTGTCTTGCCGCTGCAGCTATATCACAGTAAAGCTAACACACACTACTCTGCCTCTGTCGTCAATAAGTTTGTTCACGGCTCATTTGTCACAGGACTGTCAACGCTGTCCTGGACCAGGCAATTTCCAAGTGTCTTGTCTCCATTTATAAGATAACCATATACATTTTCTCTTTCACCCATTAATGCAGTGAATTACATCAGTGGGCTTTCCTGTCTCAAATTTTGGATTCCTTAACCCAAGCCTACTTTTTCATGATCTATCACGACACTCTGGGGAGTGGGGATACATGTCAATGGACGAGCACTTGACTAATGTGTAGGAAGTCCCAAATTCAATATAACTACTGAAAAATAAATAAATAAAAAGTCACCATGTAGGGCTCTTGCCTAACATGAAAGAAAACCTGGGTTCAATCCCCACCACCACATACAACCAAGCATGATAATGCACGCCCATAATTAGAGGATTAGAGAGAGGTTCATGATCAACCTCAGCTTTGTGACAAATTCAAGGTCAGTCTGAGCTAATCTGAAATTTTGTCTAAAAAATGATAAATAATGCTGGGTGGTGGTGGCGCACATCTTTCATCCCAGCACTTGGGAGGCAGAGGCAGGCAGATTTCTGAGTTCGAAGCCAGCCTGGTCTACAGAGTGAGTTCCAGGATAGCCAGAGCTATACAGAAAAACCCTGTCTCAAAAAAACCAATCAATCAATAAATACAAATAAAAATATATTAAATAATTTTATTACATAAAACTTTCCAAATATGTCTGTAGGAGAAATGAGGCACTACTCTTTTCTTACCATTTTTCAGGATTAAAACTCCTGCTTTCCTCTCCTCTCCCCATGAGTGACCTTATTAAAGATTTAGCTGTTTGCCAGACATGGTAGTGCTTGTCTTAATCCAAGAACTCAGGAGGCAGAGGTAGGCAGATCTCTGAGTTCAAGGCCAGCCTGGTCTACAAATGAGTTCCAGGACAGCAGGGCTACATAGAAAAATTCTGTCTCAAAACAAAACAAAACAAAACAAACAACAAAAGATTTATCAATTTTATTACTGTTTCTGTTTTTGAAAGTGGCTCTAATGTTGCCCAGGCTAACCCTTACTTCCTGGCACAAGCATCCTTCTGCTTCTACTTCCTGAGATACTGAGATTACAGATGTATATTTTGGTCCAGTCTTATTCCTCTTTTCAAAAGCCTGCCCCTGGCTTTGTTTGTAGGGAATGAGGGTGGGGACTGGGTGGGGCTGGGGCTGGGGATTGGGGGGGGGGGGGCTGAGGCGGGGCTGAGGTGGGGTTGGGGTTGGGGCTGCGGGTGGGGGCCCATGGTCATTCACTCACATCCGGGTCCTGCTGAGGCAAGGGCAGACCTCCCTTTTGCTCTCCATCTTACCGCGTTGAGGCATGAAGGTCACCATTTCCTTTAGGCTGGCTGGTCTGTGAGCCTTGGGGCTCTGCCTGCCTCTGCCCACCAGCGCTGGAGGCATAGGCACGCGGAGCCATATGTGCTTTTCTACTTGGATGCTGGGGACTCAAACTCGGGTTCCGGTGCTTATAGAGCATGTGATCTCACCCGCGGAATCATCTCATCCTTCGGCTTTAATTGCTAGTCTGTTTTGCCTGTTTTGTTCAGTGTTTATTTCATTTACATGTACCTTCCTATGTCTTTCTTCCTTCTCCGCTTTTCCTGTACTTTTGCCTTAGGCAAAGAAATCACATTTAAGGACAGCTGCTAGTTGTCTCCTTTCTCAGGCTATAGGGATTGTTTTCCATAACCATGAGGCCTGGGGGTATTCTAAGAACAGTCAAGGGCCATTGTTGTCTGTTGGATGAGATTGGACTGGTTTTTCACATGCTGGTAAACGTTGGTGAGCTGTTTAGATCACAGTCCAGGGTGGTTGAGAGTGTCATTTCTGTTATGGCTCCTGTACCTTTGTAAGTTGGAGACTGACTACGCTTGTTTTATAGAGCACAAAGTTCAAGTACACACTTTGCTTTGGGTCTGAGTCTGAGTCTAGTCGGGGTAATGATTCTGGATTTCAAACTTAGAAAGTCAGATAAGAAAGACTCTACTGCTGACCACCAGGGTACACCTATTTCTTCGGAATGGTGTCTGGTTCTTTTTTCATTGAATATGAAGAGATATAAAAATGAACTTAGCTGGTGGTGTTCCTTTCATTCCAG
Seq C2 exon
GAAAATACTACATAGCTACCATGGCCTTGATCACCGCCTCCACAGCCCTTACCATCATGGTGATGAATATCCACTTCTGTGGGGCGGAAGCCCGGCCAGTACCACACTGGGCCAAGGTGGTCATCCTGAAATACATGTCCAGGATCTTGTTTGTCTACGATGTGGGTGAGAGCTGCCTTAGCCCCCGTCACAGCCAGGAGCCAGAACAAATCACGAAGGTTTATGGCAAACTTCCAGGGTCCAACCTGAAAGCATCCAGAAACAAAGACCTTTCCAGAAAGAAGGAACTGAGAAAACTCCTAAAGAATGACCTAGGGTACCAGGGTGGGATCCCCCAGAATACTGACAGCTACTGTGCACGCTATGAAGCACTGACAAAAAATATTGAATACATTGCCAAATGTCTCAAGGACCACAAGGCCACCAACTCCAAGGGCAGCGAGTGGAAGAAGGTCGCCAAGGTCATAGACCGTTTCTTCATGTGGATTTTCTTCGCTATGGTGTTTGTCATGACCGTCTTGATCATAGCAAGAGCAGATTAGAAAGAAAGAGGAGGAGTGGGTTGGTAGGCATTCGATATTTGGAGAAAAAAAAATCAATAAATTTCACGTGTGATCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029205:ENSMUST00000031108:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(24.1=31.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(75.4=96.7)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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