MmuINT0036210 @ mm10
Intron Retention
Gene
ENSMUSG00000027107 | Chrna1
Description
cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) [Source:MGI Symbol;Acc:MGI:87885]
Coordinates
chr2:73563215-73566941:-
Coord C1 exon
chr2:73566702-73566941
Coord A exon
chr2:73566308-73566701
Coord C2 exon
chr2:73563215-73566307
Length
394 bp
Sequences
Splice sites
5' ss Seq
AACGTAAGC
5' ss Score
7.35
3' ss Seq
ACGCCCTCTGCTTCCCCCAGGCC
3' ss Score
9.5
Exon sequences
Seq C1 exon
GTTTTTATCGACACTATCCCAAACATCATGTTTTTCTCCACAATGAAAAGACCATCCAGAGATAAACAAGAGAAAAGGATTTTTACAGAAGACATAGATATATCTGACATCTCTGGGAAGCCGGGTCCTCCACCTATGGGCTTTCACTCTCCGCTGATCAAGCACCCTGAGGTGAAAAGCGCCATCGAGGGCGTGAAGTACATTGCAGAGACCATGAAGTCAGACCAGGAGTCCAATAAC
Seq A exon
GTAAGCTGTGTGGCTCCCAGTCCACACCTCCGGGTCTGTCTGTCTGTCTATCTATCTGCCTGCCTCTGCCTTCTGAGTGCTAAGACCAAAGGTTTGCGCCACAACCTCTAAGCTAACACACCTCTGGGTCTAAATGATTAAATGCATAAGTGTGACAGGGAGGTTGACCAATGAATTGGCTTCAAGCTCTAGTTACTAACTTCAGATGCACTGTGTTGACTATCTCTGGCAACTATAGTAAGTCATTTTGGCTTAATTATGCAAAAACTAAAGGTTGTAATATCAGGTGTTGAGGTTTGGAGGTTTACATATTGAAGGCCAGGCCAGTAGGGGGCGCTATGAGCCTGTGTCCCATCTCAGGGGATTCCTATCTAACGCCCTCTGCTTCCCCCAG
Seq C2 exon
GCCGCTGAGGAATGGAAGTATGTTGCCATGGTGATGGATCACATCCTCCTCGGAGTCTTTATGCTGGTGTGTCTCATCGGGACGCTGGCTGTGTTTGCAGGTCGGCTCATTGAGTTACATCAACAAGGATGAGCAGAGGCTGAGCTAAGCCTACCTCTGTCCCAGCCATAGCCATCGCTAGGAAAGATGGAAGAGAGGAAGGTCTGTCTCCTTGAATCCTTTCACACTTACCAAACATGCAGTGTTCTACATGTCCTACATGTTAATGAGAGTGATCTCTGCTCACACGGCTGTATTCTTGAAGTGTCTCCCCTTTGCTTCTGCTTTTAACACTATGGGCCTCCTTAAAGGGCGAACCCTTTGAAGTAAATAAAAGTGAGCCCTCAAAAGAAGTGTTTGCTTCTAAATGGCCCCTGGGAGAGTTTTGCTTGGATACTCAAGGTTTTCTGTTTGTATTGCCATGGCTAGTTGTTTTTGTTTTCTTTCCTTTAATAAATATAATTGTACTTATATGAGTGATCCGCCTACGTGTATGTCTCACATACACGCCTAGTGTCCATGAAGGTCAGAAGAAGGTATCCCATCTCCTAGAACTGGAACTACAAATGGTTGTGAGCGTCCACATGGAACCTGGGAATCAGGCCCTCTGGAAGAGCACCCAGTGTTCTTAACCACTGAACCACCCACCTATCGGGCTCAGTTAATTTTTATTTTTAAAGTGCTGAGAGTCCCTTACTTAAGACACACGGTTTCATACCTACTAGAAAAGTCGTGTCTACCAGATTCCCCAGATTTGATGTGGACACAAAGGAAGTGGTAGAAAGGAAATTAGGTAACTTTAAACTTAAAAAAAAATTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACATACTCGCACACATTGATGAAATTGGGGGACAACTTTTAGGAGTTAGTTCTCATCTTTTATCTCATTTGAGGCAAAGTATCTTGTGATTTCTGCCGCTGTGTTACATTCTCATGTAAAGCTTCCTGGGGCATTTTCCTTTCTATACTTCTCGGCCCATGAACAGAGTGCAGGGATTCCAGATGCATGCCGCCATCTCCAGCTTTTCATAGGTCCTAGGATAGAATTTAGGTCGTTAGGTTTGTCCAGCAAAAAACTACTTTTACCTGCTTAATCCATTTCACTGGCCCAAAGGTAATTTTAGGGCGATCACATACAAATAGTATCAAAACCTCATGGTTTAAAGTAGACTTCTGAAACCAGGAGAGGGAGAATGCTTTCTTAAGTGATTTCTGTTTGAGAGGCCTTCTTGAAAGGGCGCTTGGGATTCCTTGGGATTGTACCTAGAGCTTTGCACACAGAGCTATAACTGAGCCTCAGCTCTCCCAACTTAACGGAGCCCCTGGATTTTGTTCTCAGGACCCGAGGAAGGGCAGATCCCATCCTCATCAAGGGTGTGCCTCTGACCCCATGAGAATCGTCTCGCCCGCATGGGTTTATTTTATCCAAATTGTTTTACACAGTCTCCATAATGTCCCTAATTTACAAATGGAAAAAAAAATTTTTGGGGAAAGTTAAACTCTGCTCCATCTAGAAGTAGAAGAACTGAGATCTGAACCCAGACAGAACTTAAGATTCTAAAACAGGGGCTGGAGAGATGGCTCTATGGTTAAGATCATTCCCAGCAACCACAGGGTGCATGGTGGCTCACAACCATCTACAGTGGGATCTGATGCCCTCTGCTGGTGTGCAGGTGTGCATATACAAAGCACTCACACATAAATACATAAACAAACAAACAAATATTTTTTAAAGATTTATTTATTTATTATATGTAAATACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGCATCAGATCTTGTTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTCAGAAGAACAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCAAATATTTTTTTTAAAAGTCAAAAAGAAAAGGGATTCTAAACCGACTTGCAGCTGATGGGGTCACCTGCTCCCTGCTCTCCCAGCATGCCTGGCGTGATCTAAGTAGTTCTGGTCTGTGTTGGTGGGGACTCTGTGATATCCTATTTCCTGCCTTCTCAATTAAAACCCCTGGCTTTTCCTTCAGTCCTTGGACGCAATCATGTTTGGAGTTCAGGCCCTATGAATGGAACCAGAAACGTATGCACACACCATCACCATTTCTGAAATCTGAAAAATAAATTCTCTGTGCCAAACTCTAGGCTCTAGTACAATTTACCCAGACCAAGAAGCCGTGTGGCTCTGGACGCAGAAAAGGCCTTTGAATCACAAACACATCTGATCCGTCATCTCCAGGGAGAGCTATAAACTGCATAACCAGGAGGCCAGTGCGAGCCCAGGTGGCTTCAATCTCCTGAGGGACTTCCCATCACCCCTGCACCAGTGCTGGGCTCTTTCATCTCAAATAGTTTGCACTTTAAAGTGGAAACAATTGGCAGTTTCTCAGAAAGTCACACTCGGGTCACCAAGTCACTCAGCAGTCCCATTCCCAGGTAGAGAGCCAAAGAAATCGAAAGAAAGACTTACACAATTTGTATGAGAACGCGCACAGAAGGCAAGAGCCAGAGAAAGCGGTCTAGGCTCCAACCCACAGACGACAAGCAAAAGGGATGTGGAGAATGGGTTTTGGGGTGTATGTGTGTAGGCCTGGGGGGCCATCGCCTTTTTGTTTTGTTGTTGTTTTTGAGATAGAGTTTCTCACTGGCCTGGAACTTGCCAAGTAGTTTAGGCTGGCTAGGCAGGCCATTCCGAGATCTGCCTGTCTCCTCTTTCTGCAAACAATTTAGTTGGCATGGGTTCTGGGGCTCTTACTCAGATCTAAAAACAAGCATTTTGTCAGTTGATCTAATTCTTTAGCTTTTTCTACTCACGACCACTTTTTGCTTGAGAAATGTTATGTAGAAATATAAAATATGTATAAAAATAAATAACAAAGAAATTTAATTAAAAAAATTCTCTGACATGCATAGCATTTTATCACCTATTAAGGATAAAAAATAAATTTGCTTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027107:ENSMUST00000028515:8
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:
PF0293211=Neur_chan_memb=PD(31.9=57.5),PF0293211=Neur_chan_memb=PU(52.2=45.0)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(44.9=70.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGGCGTGAAGTACATTGCAG
R:
TACAGCCGTGTGAGCAGAGAT
Band lengths:
348-742
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