MmuINT0036229 @ mm9
Intron Retention
Gene
ENSMUSG00000027577 | Chrna4
Description
cholinergic receptor, nicotinic, alpha polypeptide 4 [Source:MGI Symbol;Acc:MGI:87888]
Coordinates
chr2:180762903-180768734:-
Coord C1 exon
chr2:180768625-180768734
Coord A exon
chr2:180764278-180768624
Coord C2 exon
chr2:180762903-180764277
Length
4347 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
TTTCTCTCGCTTCCTGCCAGCGC
3' ss Score
8.43
Exon sequences
Seq C1 exon
GAGTGGCATGACTACAAACTGCGCTGGGACCCTGGTGACTACGAGAATGTCACCTCCATCCGCATCCCATCTGAACTCATCTGGAGGCCTGACATCGTCCTCTACAACAA
Seq A exon
GTAAGCCGTGTGGGCCCTGGCAGGTGAGATCAGGCCCCACCCAGCAAGGAAGCTCTAGGAACAAAGAGGAGCAACTGGAGAGGAAGCCCAATGGGCTTGGTGTGGGGGACCTGGGGATACCTGCTCTCAAGTCTGGAGGACTTCCAGCTCTGCTTGTCTCCTAAGGGCAGAGAATGGATTGGACATCCTCCTCTGGCAGTGGCTGCAGGTCCCATCCTTAAACTCTTCCATGCACAAGTCACAGTTTGGTTACCCAATGAGGCAGGGGATTCAGGGAGTAGATAAAGAACAAGAGAAGTGGCTGCTCCACAAAGCTTAGCCTCTGCTCTTCTTGGGCCCGCCTTCATGCTGTATCCAACACTGGGCATCCAGCCAGTAGATAAACCTCTCAAGATCAGCTCACACCCTGTCTCGGCCCCTGGAAGCTGAAGTCCACGTGGAGACAAACCCAGTTAGTGGTGACAAGACAGGAGGTAGGCATTTTCACACTTGTCTTTCCGGGGGACCTGGACTAGGAGCAGCTGGTTTTCGAAGCTGAGTAGGTGATGTTCTATTCCCTCGGGGTCTGGGTGGGCAGCAGCTTCCACAGTGCTTACAGACAAAGCAAACCGAAGATCTTCTACCCCCCCAGTCCCAGCCATCTGCCAACAGCCCCCTCCAGGCCCTGGGGTGCCTGTCTGACCTACAAATGCTCCCATTTGATTAAGAATGACTGAGATTCTCTTCCTCTTTAATTGAGTGGAGTACTAGGCACATCCTCGGCGTGTAGAATGAGCTGAGGGTGGTTTTCTAGAATGTGTTATGGATGGACTTAAGAATGAGCATATGCCAGGGAATGGAAGTCTCCAATTCCCGCTCTTCCCTCAAAATGCCTGTCTTCTGCAGCAGCAATCCAGCTGAACCTTGAGCCCTGGAAAGTTTCTAGCTAGTGCTTGTTCCACCCTCGAACCCTGGGATCAAGGACTGAATCTACTCTGGGCAGCCTATTGAACCCATGGCAAGGAAGGACATGTATTTCCTGAGTGGTATTTGTTAGGCAGAGGAGTATCAGCCCAGCACTAAGCTGAGAACAGGCACTCAGAAGACCTCACCCGTCTAAGGTCACCTTTTTAATCTCTCGTACATGCTAGGATACTGTGAAAGGGGCAGCCCCCCTTTTTTTGTGGGGCTGGAGATGAGCATTTGAGGTCTATCTGAACAGGACTTGGAGCTGGCGAGGGTTGATAGGACTCTGGTGCCAGCAGGGAAGAAGGCCATTTCCAGCAGTCATCAGCAGTTGCTAGCCAGATGGCTGGTCCCAGTGCTGGACACGGGAGTCCCCACTGTTGTGTTGACTTGGGGCTCCCTCTCCTGGAAGCCCAGAAGCTCTCCACCTGGTACAGGGCAAACGGAGGGTCTCACACTTGCCTCTGGAATGCAGCCTCATATGATGAGGCCTCTTAGGGGAAGATAGGATCTGGGACCCACCCTCCCCGAGCTACTGGCTGGCTCATTGAATCCACTAACTCACACTGGAAGGCTCTAGAACCCAAATGCCTGTGCTTCCTCTGGTTTCCTGGGGACTCTAAGGTGCAGAACTGGAAACCGAGGACCCATATCCTTGCCCTGCATCAGCAACCTTGGCAGAGAAATGCTGACAGCCTATTCAAGGAATTTGCTATCCTGGTACATGGGCTGCTAGTGGTTCCTGGGACTGCAATATCCTTTGAGCATTCTGAGTACCTTACCCTTGGCACTAGGAGAAGAAAAAGCAGCCAGAAGTAGCACACAGAGTGCTGAGCCCTGTAGACTCTACTGTCACCTTCTCCATAACTGGGGCTTTGTGGCAGTGTCATGTGGAAGCAGGGCCGGAACCTGAAGGAGATGGGCTGCACTGCTACCCTCAGAGAACTCCGTCCTCAGAGAGTGTGCACTTGGGATCTCTCTGCAAACACAAGCCCAGAAGCATTCTCAGAGGGAAGCGTACACTCAGGTTTAGGAGCTCTAGAAAACTCAGAAAGGGGACCCAGCCAGGCTAGGCAGGGCAGGGAGAGCAGTTGTACTAGCCCCAATTGTGACTAGTACTGGTGAAGGCAGATGCAACCACAGTATCCTGAGCTGAGTCCCCAGTGTGTCTCAGGGGTGGGAAATCTAGACTCAGCAACCCAGGCTGCAGATGGGAGCTACGGATTCAAGTGAGCCCTGAGGGCCCCCTGTCTGCCAACTGGTTGCAGCATCTCCTGCCTGCCCTCCAGAATATTTGCAACACAGAAGATCCACTCACTGACAGTAGGAGAATTTAAATTTGTGCCTGGAGTGTTTGGGCTTTGATTTTTGGAGAGATGGGACTGAGAGAAGGAAATGAAACCAAGCCTGATTCCACACGGCCCGAAATGTGCCGCAAGATCCACCCCCGTGTACCCGGAGGGAACCTCTGCTTCTGCGGAAGCCAGGCTGTGCTCTGTGCAACGCGCAGCCAGGAGCCCTGTTGGGGTGCACGTAGAGAGCAGTGTTTCCAGCTTCTTCCGTATGCATCACAGCTACACAGGAGAAAATTGGTGGCATTAACTCAGGATGTGTTAACGTGCAGGAGGGTCCAGGGTTGCCACCTGCTGAGACCATGAGAGGCTCAAGTCTTCTGGACTTGGGAATGGTGTTGTAGGATTTTTGGCTAGCATAGGAAGGGCCACTAAGATTCCCAGGAGGCTACCGTGGGCCCTGGTCTAGACCTGAGAAGCTGGTCAGGAAAGCAGGGCCAGTTAGCTGATGAAATTCAGGAACCTGGATTCTTCTGCCTAAGAACCCTGAAGGACACTAGCCAACGAGCCGGGCCTGTGAGAGGAGGTGGGAGAAGAAATGGACAGAGGAGGTCTGGGCAGCTGGGTAAACAGAAGGTTCTAGAGCCCATGGCTCTGAGCTACACTGTCTTATGAGTGTCGAGACCAAAGGGATGCGTTGCTAGTGCCATTGCTGAGGAATTTAATCAGGCTTCAGAGAACTCGTTAGCTATAAATCGAGGTTTCCTGTCAGCGTTTCTGAGCTGAAGCTGGCAGTGTTTGCCCAAGCGCGTTAGTGCATTGCTCTCTCACGGTCTGTGAATGCTAATCTAGGACCAGAGTGATCAGCCCGGGCCCGTGAGGAAGCCAAGACCTAAAGAGTGGCATTATGGCCCAGGTTTCACAGGGCAAATAGAGTAGAGGCGCCGCTCTGAAGATCAGTTCTGGGGAGGGTTGTGGAGGCAAGCAGGGTGAGGAAGGCTTCATGGGAGCTGCTACCCAGTGTCACCAAGTCATAATGTGTAAAATGAGGTGTAGCATCACCATTCATGAAGCTCAGGGGTCAAGGCTGGAACTCTGCTTGAGAGGAGGGGCCTGAAGGACAGCAGCCCCATTGCCACTGCTCAACCTGACACACATTCCCCAAGTCAGAGAGGCAAGAAGTCAACAATTGACACTGGCAGCTGGATTAGACAGCTGGAGTCCACATCCAGCCTGTGCCATGACCTGTAGGGAGGTAGCCTCCAAATTCTTGGTGCCAGTGGAAAGAAAGACGCCTTCTCAGGCTCCAGCGGCAGAAGTTCAGGGTTGATCCATCCTGAGTGTGGGCTCAGTCCAGGGGTATTTGTCCTGAGAGGTACTGTGGGTACCTATACATTGCTATTTCCATACCTGGGGTCTTCTGAATGGATAAGATGGGCAGAGAGGCCAACTGGCTTCCAGCAAGATGATCCATTAACCAGGACACAATGAGCAGGGATCAGGCCTCTGGGCCCTCTTGTCCTGCCACTGTGGGCACATGCTCTCCATACTCAGTGGGTTTGCTATGGTCCTGCAGGGACCTCCGGGATATCCATAGCACACTACAGGGGCCAGTTGTCAGCTCCTAAACTGAAGAAGACAGGCACAGCCCCTCCCCTTAGTACATGAGATGCTCAGGTGGGAACCAAGGGAAGTCAAAGGGAAATTCCCATGGTGCCTCAATAAGCAGAGGTGACCCAGGCCCCTCTGAATGGAGGTACAAATGCAAATTCATGGAGGCAGTGGGTGCTCAGGGGAAGCCAGTGGTTTGGTCCCACCCTGCGCCCTCACAATAGCGATGAGTAAGAGCTGTAACACTAACTCTGCTCACTGTGGGCTCCATTCATCCTCTTCTTCTCCGAACCACATGTCACCTTGACTCAAGGGTGAGAAACTGAAGTGCACAGGTGAGTGACGGCCCAGTCCACATGGACCACCACACACAGTCCTGCACTCTGTGTGTGACTGGTGGAGCTGTCAGTCAGGCTGGGAGGCTTTCTCCACAGTAATGTTCGTGGGTGTGGTGTATGGAGGGGCAGACCTCATTGCTCTTTCTCTCGCTTCCTGCCAG
Seq C2 exon
CGCGGACGGGGACTTTGCAGTCACCCACCTAACCAAAGCCCACCTGTTCTATGATGGGCGTGTGCAGTGGACACCCCCGGCCATCTATAAGAGCTCCTGCAGCATCGACGTCACCTTCTTCCCCTTCGACCAGCAGAACTGTACCATGAAGTTTGGGTCCTGGACCTACGACAAGGCCAAGATTGACTTGGTGAGCATGCACAGCCGTGTGGACCAACTGGACTTCTGGGAAAGTGGGGAGTGGGTCATTGTGGATGCCGTGGGCACCTACAACACCAGGAAGTATGAATGCTGTGCCGAGATCTATCCTGACATCACCTACGCCTTCATCATCCGCCGACTGCCACTGTTCTACACCATCAACCTTATCATCCCGTGCCTGCTCATCTCCTGCCTCACCGTGCTGGTCTTCTATCTGCCCTCGGAGTGCGGCGAGAAGGTCACGCTGTGCATCTCGGTGCTGCTTTCTCTCACCGTCTTCCTGCTGCTCATCACCGAGATCATCCCGTCCACCTCGCTGGTCATCCCGCTCATCGGCGAGTACCTGCTCTTCACCATGATCTTCGTCACCCTCTCCATTGTCATCACGGTCTTCGTGCTCAATGTACACCACCGCTCACCACGCACACACACCATGCCCGCCTGGGTGCGCAGAGTCTTCCTGGACATTGTGCCCCGTCTCCTCTTCATGAAGCGCCCATCTGTGGTCAAAGACAACTGCCGGAGACTTATCGAATCCATGCACAAGATGGCCAACGCCCCTCGTTTCTGGCCAGAGCCTGAGAGTGAGCCCGGCATCTTGGGTGACATCTGCAACCAAGGCCTGTCACCTGCCCCAACTTTCTGCAACCGCATGGACACAGCAGTCGAGACCCAGCCTACATGCAGGTCACCCTCCCACAAGGTCCCTGACTTGAAGACATCAGAGGTTGAGAAGGCCAGTCCCTGTCCATCACCTGGCTCTTGTCACCCACCCAATAGCAGTGGGGCCCCAGTGCTCATCAAAGCCAGGTCCCTGAGCGTCCAGCATGTGCCCAGCTCCCAGGAAGCAGCCGAGGGCAGCATCCGCTGCCGGTCTCGGAGTATCCAGTACTGTGTTTCCCAAGATGGAGCTGCTTCCCTGACTGAGAGCAAGCCCACTGGCTCCCCAGCCTCCCTGAAGACCCGTCCATCCCAGCTTCCAGTGTCAGACCAGACCTCTCCATGCAAATGCACATGCAAGGAACCATCTCCTGTGTCCCCCATCACTGTGCTCAAGGCTGGAGGCACCAAAGCACCTCCCCAACACCTGCCCCTGTCACCAGCCCTGACACGGGCAGTAGAAGGCGTCCAGTACATTGCAGACCACCTCAAGGCAGAAGACACAGACTTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027577-Chrna4:NM_015730:4
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=0.192
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=25.1),PF0293211=Neur_chan_memb=PU(91.1=73.2),PF113173=DUF3119=WD(100=20.0)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: