MmuINT0036251 @ mm10
Intron Retention
Gene
ENSMUSG00000029205 | Chrna9
Description
cholinergic receptor, nicotinic, alpha polypeptide 9 [Source:MGI Symbol;Acc:MGI:1202403]
Coordinates
chr5:65967782-65969269:+
Coord C1 exon
chr5:65967782-65967927
Coord A exon
chr5:65967928-65969114
Coord C2 exon
chr5:65969115-65969269
Length
1187 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
CATCTGGATTCATTGCTTAGGAC
3' ss Score
5.36
Exon sequences
Seq C1 exon
CCGTAGAGACAGCAAATGGAAAGTATGCCCAGAAATTGTTTAGCGATCTTTTTGAAGACTACTCCAATGCTCTGCGTCCAGTAGAAGATACGGACGCGGTGCTGAACGTCACTCTGCAGGTCACGCTCTCCCAGATAAAGGACATG
Seq A exon
GTGAGTCTTTTTAAAAAGATTTTTATTTATTTATTATGTATACAGTGACCTTTGATGGTGAGGGCGACAGTGAAAAACAGGCGTTTTCTTCTCAATGGGTGTGACAGAAATGTCCTTGAGTTAGGTAATTGAGATGATTATGCAGTGTGGTAGGTGACTGGAAGCCCCTGACAGTTATAGTGTGGCTAAGATGATGGGTTTTAGTATTTTAATTTAATTTAATTATTATATGTACATGCCTGTGTGTTTGAGCATGTTAGTGCAGTGACTGCAGAAGCCGGAAGAGGGCGTCAGGGACCCTGAGCTAGAATTACAGGCAGCTCCCCACTGCCTGACAGGTGCTGGGAGCTTATCTCAAGATACTTGGCACACACCTTTAATCCCAACACTTGGGAGGCAGAGGCAGACAGATTTCTGAGTTCAAGGCCAGCCTGGTCTACAAAATGAGTTCCAGGACAGCCAGGACTATACAGAGAAACCCTGTCTCGAAAAACCAAAAAAAAAAAAAAATGGAAAGAACAGTACAAACTTTCCAGTCCCCTAAAATAGTACTTTAAGGTTATGTGGATTTTACTACAATTTTTTAAAAAGATTTTTATTTATTTATTATGTATACAGTGTTCTGCCTGCATATATGCCTGCAGGCAGAAGAGGACACCAGATCCTGTTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTTGGTGCTCTTAACCTCTGAGCTCTATCTCCAGCCCTTAATCACAATTTTAAAAGAGGAAGGTGGTGTTTTAAAATGACATGGCTGATTTCCTCCATATACATATTTAATTACACAAGCTATCAGATTTAAATGATGTTTTCTTTTGTACCTGGTAGACATTTCACGTCTCCTGGCTCCAGTGTATCATTAGTTGGTCCGCTTTCAGAGAAAACTTAGCAATTAACCTAAGGAAAGATATAAAGATGCAAGTACTGGTCTCCTTTACATTTTGTACACTACATCAGGAAGGCATTGAATGCGGCCTTGATAATCAATCAATCAGGTAGAATTTTAAAAGGTCTCCTTTATGGGTTGAAAATAAGTGGGCACCCTGGAGATTCCTGCTATCAAGAACAAGTATCCCAAAGCTGGAAGTGTGTACAGAATAAGGTGACATCTGGATTCATTGCTTAG
Seq C2 exon
GACGAGAGAAATCAGATTCTGACAGCCTACCTGTGGATCCGCCAAACTTGGCACGATGCGTACCTCACGTGGGATCGAGACCAGTATGACGGGCTGGACTCCATCAGGATTCCCAGCGATCTGGTGTGGAGGCCGGACATTGTCCTCTACAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029205:ENSMUST00000031108:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.030 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(18.8=79.6)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(24.6=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:
CCGTAGAGACAGCAAATGGAA
R:
CAATGTCCGGCCTCCACAC
Band lengths:
288-1475
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