MmuINT0036230 @ mm9
Intron Retention
Gene
ENSMUSG00000027577 | Chrna4
Description
cholinergic receptor, nicotinic, alpha polypeptide 4 [Source:MGI Symbol;Acc:MGI:87888]
Coordinates
chr2:180757016-180764277:-
Coord C1 exon
chr2:180762903-180764277
Coord A exon
chr2:180759585-180762902
Coord C2 exon
chr2:180757016-180759584
Length
3318 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
ACCCATGTCTGTGTTTGCAGGTG
3' ss Score
10.07
Exon sequences
Seq C1 exon
CGCGGACGGGGACTTTGCAGTCACCCACCTAACCAAAGCCCACCTGTTCTATGATGGGCGTGTGCAGTGGACACCCCCGGCCATCTATAAGAGCTCCTGCAGCATCGACGTCACCTTCTTCCCCTTCGACCAGCAGAACTGTACCATGAAGTTTGGGTCCTGGACCTACGACAAGGCCAAGATTGACTTGGTGAGCATGCACAGCCGTGTGGACCAACTGGACTTCTGGGAAAGTGGGGAGTGGGTCATTGTGGATGCCGTGGGCACCTACAACACCAGGAAGTATGAATGCTGTGCCGAGATCTATCCTGACATCACCTACGCCTTCATCATCCGCCGACTGCCACTGTTCTACACCATCAACCTTATCATCCCGTGCCTGCTCATCTCCTGCCTCACCGTGCTGGTCTTCTATCTGCCCTCGGAGTGCGGCGAGAAGGTCACGCTGTGCATCTCGGTGCTGCTTTCTCTCACCGTCTTCCTGCTGCTCATCACCGAGATCATCCCGTCCACCTCGCTGGTCATCCCGCTCATCGGCGAGTACCTGCTCTTCACCATGATCTTCGTCACCCTCTCCATTGTCATCACGGTCTTCGTGCTCAATGTACACCACCGCTCACCACGCACACACACCATGCCCGCCTGGGTGCGCAGAGTCTTCCTGGACATTGTGCCCCGTCTCCTCTTCATGAAGCGCCCATCTGTGGTCAAAGACAACTGCCGGAGACTTATCGAATCCATGCACAAGATGGCCAACGCCCCTCGTTTCTGGCCAGAGCCTGAGAGTGAGCCCGGCATCTTGGGTGACATCTGCAACCAAGGCCTGTCACCTGCCCCAACTTTCTGCAACCGCATGGACACAGCAGTCGAGACCCAGCCTACATGCAGGTCACCCTCCCACAAGGTCCCTGACTTGAAGACATCAGAGGTTGAGAAGGCCAGTCCCTGTCCATCACCTGGCTCTTGTCACCCACCCAATAGCAGTGGGGCCCCAGTGCTCATCAAAGCCAGGTCCCTGAGCGTCCAGCATGTGCCCAGCTCCCAGGAAGCAGCCGAGGGCAGCATCCGCTGCCGGTCTCGGAGTATCCAGTACTGTGTTTCCCAAGATGGAGCTGCTTCCCTGACTGAGAGCAAGCCCACTGGCTCCCCAGCCTCCCTGAAGACCCGTCCATCCCAGCTTCCAGTGTCAGACCAGACCTCTCCATGCAAATGCACATGCAAGGAACCATCTCCTGTGTCCCCCATCACTGTGCTCAAGGCTGGAGGCACCAAAGCACCTCCCCAACACCTGCCCCTGTCACCAGCCCTGACACGGGCAGTAGAAGGCGTCCAGTACATTGCAGACCACCTCAAGGCAGAAGACACAGACTTCTCG
Seq A exon
GTAAGTCTGTGCATGGGAATCACCCCGACCCAGATAGGACCAGATGTCTTGTGTTTCCCACACATGATCCAGAAACCAAGGCCCCAGAGAAGCTGCACACATTGAGGGTACATAGTGTAGTCTCTGCCTGGCATGCCTCACAGTCCCTAGGCCACGCTGGGGTTAACATGGCACAGTATAGCTGGTGGACAGTAAACTGAGATGCTGCACCTTCATCCAGGTTTCCCAAACAGCAGGTAGAGAAACTGTTTCTAGCCCTATGATTCTAACACCTGCAAGGTCTTCCTTTGAAGTGTTCAGGCTGTTTAATGGCTGGCTACCCATGCCTGGGTGACAGGCAAGGTCCCATGTTGGCCTTCCTCAAAATGTAGTGGGGCTGCTGCTTCTGCTGCTGCTGGCCTGTAACCCCAAGAACAGCTTTCCCCTGGGCTTCCACCTAGTGAAGTGTGGTCCTTTGCACCCAAGAAAGGTTGAGAGGTTATAGGAAAGAGAGTGGAGCTGCAGAAGCTGTGCTGCTCGCCCCCCCACCCCCCACCCGTCATCATTCCTTTTGAAGGGTTGTAGGGTGCGGACATAATGCTGCCCCACTGCAAGGCTCTCAGGAACCTGGTGACAGAACGCAGGTGCTTAGCAAATGCTACCTGCATTTGTTCTTCATGCTTCAAGCTTTGACTCTACAGAGGCCTGAAAAAGAATGTCCATGTTCCTCTGTTTCTCCTGCACTTTTCCCAGATCGCAGCTCTGGTGAATAGCTAGGCTGGGCAGCAGTTGTAGCTCTGTCTGACCATCTTCTCTTTCACATTTGTCTGGCTGTCACAGTAAGGGTCTCCAGGACTGGGGTCTGGGATCAGATGACGCTGAGTGCAGGACTCCTGATGCTAGATAAGCTGTTTGCCGAATCTGGGTCTGCCTGTGACAGGGCACAGTTTGGGGTGTAGAATAGGAGTCTCAGAGAGAGGTCAGATGAAGAAGGCATTAAGAGAAGTCCTACCCTGGCCTACCTTTCTCTCTGCTGTGCCAACTGAAATGTCTGTGGCATCTTTACATTGACCTTGTCTGGGCCTGGCATTTGTCATTGTCCCTCCTGACACCTTGGCTTTGCTGGTTTCTGTTCATCTTCCTACCCAGCCTGAGGTTTGCCTGTTGACATTACTGGCTTGTCTCCTAGAGCTGCTAAGCCCTGCAAAGAAAGGAGGCTGATGCTCCCATATTCCCAGGAGTGGGTCTTGGCTCCCAGAGTCATCCCATTGAGTCCCTGGAATGTGTGAAGCCATTCTGGGGACTCCAGAGACATGTCTGCAGAGAAATTTTGGTTCTGGGACTGTCTTGCTGCAGCTCTGGGGTGGAGGGAGAGCTCCAGGCACTGGAGTGAGGCCACTGAGGGAGGATGGATATGACAAGTTTAACTGAAATCCTTCTGAAACCAGTGCATCTGCAGCATAGTCCCATGGCTGGGGCTTGTGACCTCTTCCATCTCTGCTGGCCTGCTGCAGCTGCCTGACCTGGTTCTGGCCCTGGGAATCTCTCTGACTTAATAGAGACAGGACAGCAGGGCTTTGGTCCATGACTGTGGTGTTTCATCTTCGAAGTCTTGGTCCCAGGTACAGGGAAAGGAAGAGGAACACCAAGCAGCCGTTTGCTCTGAGGAGCCCTTGAGGGGCTTTTTATCTAGCAGAGATCTATTCATCCTGAAGTTTTCTAAGTGAGCATGGCTACTTACGTTGGCTTAAACCAACAGGACACCTATGATTTCTTTGAAAACTCAGGGTAGAAGCCCTTGCAACTGGGACAACCCAGACCAAGTGTTTCTCTGCTGGGTTGAGTTCTATTTACCACATCTTACTCCCTGCTGCTCACATATATGCACAGACTGGCTCAGGAACCCCCTCATGCCCTGTCCCCGGTGCAGCTCTGATCAAGCTTGGGGTAATTACAGGCCCTTCTAGACAAATGATGTGCTCACAGGACAGTGATGAGGAAAAAGCAACAGTGTGTGACAGCCACCCTGCCTGAAGTACAAGGGCAGATCTGCATGCAGAAACTGCCTTCAACACATTGCTAATTCTCAGGCCTAGTCAGACCTGGCATTAATCTCCCTCCCGAGTCTTTGCTTCTGAGAACTGCTTGAGGAAGTAGCTACTTTGCATCAGGCCCTGGAAGAAGCTAGAGTCCACACTGTGGGATCCAGAAGTGTGTGTAGAAGGAGCCATTAGTCATTTGGACGTCATCGTCACCATGTGCTATATAGCACGGTCCAATGAGGATTGACTGGGTAGTCACAAACGGTGGATATATATATATCATTCTTTTGTGTGCATCTTGCCACCATTCACCCTCTGTCTCTGACCATCCTCCCTTCTTGGAACATCTCCTGGCACCACTGCCTCCCCACCAGTGCCTGCTCAGGCTGGCTATGCTGCCCATGTAAGAAGTAGGTGTGCATGGTCAGAAGCAGACCAGGGGGCAGTTGGGCACTTAGGCCTTGCTTTTGGGATGGCCTTAGTGATCAATCCATTACCCAGCATGTCCTGGCTCTTACCCTCTGGACTAGGACACGTGGCTGACATCTTTCTGAGATCCACTTTTTCTTAATTTGATTTTATGCTATGTGTATGGATGTTTTGATTACATGTATGTCTGTGTGTCACATGCATGCCTGCTGCCAGCAGAAGCCAGAGAGTGTGTCAAATCCCTTGAAAAGGGAGTTATGGATGGTTGTGTCCACCATGTAGGAGTTGGGAATTGAACCCAGGATCTCTTGAAGAGCAGCCAGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCCTGGGATCCACTTCTGACATCTGCACTGTGAGAAGATAGACTCAGCCTCTGTGCTGCTACCAGCTTTAGAAAACATAAGACATACTTCATCCCGAAGTCATGGGCCCTTTGTCTGGCCAAAGTAGGCCCAATGAGCTACATTTTGAGCTTAGGCAGCCTGCCAAGCAGGTAAGACCAGCTAGTGTACAACATGATCCCCAAGCCTTCTGTGGCGGTGTGGACTACCAGAAAGCACTCAGATGTGTCTGAATTCAAAGACCCCACACATGCAGCCTTAGATATGGGTTCTATAGATGCCCAGTCCACCTCATATGTTACCTCCCTCTGTTCTACCTAGCAGCAGCCTCTCTGACCCTGCAGATTCTCTGGCCATGCTCTGTCTCACCACATCAGTGTACAGATGTGTATCTGATGGGAAATACAGAAACTGTGGCTCATAGTGCCAGGTTCCAGAAGATTCTATGGTTGCCCATGGTATCTGAGAGCTAGAATGACCCATGTCTGTGTTTGCAG
Seq C2 exon
GTGAAGGAGGACTGGAAATACGTGGCCATGGTCATTGACCGAATCTTCCTCTGGATGTTCATCATTGTCTGCCTTCTGGGCACTGTGGGACTCTTCCTGCCTCCATGGTTGGCTGGTATGATCTAGGGAATAGCGGCACCTAGCTCCCAGGTCTCTACAGGGCCATGCGACTCGTCAGTCACCCACATCTTCCAAACCGGCCATGAGACACCTAGGAGAGAGAGATGCTGCCCTGGTTGACCCTGGTTCTAGTCAGGCCACAGGCCTGGTTGGAGCTAGTTGAGGACTGATATAGTTACAGGCTGAGTCCCTCATTAAAGTTTCTCCAGAGCAAGTGACAGTCACTCCCTGGCTTACAGACAGCACACACCCATCTGTGTCACAGAGAATGATCCAGTGTTGATCTCAGTTGTCCTTTGAGGCCAAAACAATTCATCCCCCTTCAGGAACCAGAGCCCCTCGTGCTGTGGGATTCCTACGGCCCAGGAAATTCCCATGGTGCTCTGCTGGCCACACCCTCTCCCTCCCCATAATGTGGTTCCCTCAACCCTCCAGGCTGGGCTGCTCTCTGACTCAAAGGTGTCAGATGTAAGCCCCGGCAGGTTTTTATTTTGTTTAGGTTGAAGCGAATTGGTAAGAAATAGAGCAGTGAGATATGTGGATGAGTCCCACTCACAGGTGAATGAGTGCAGGGTCTCACAGGAAGAGTGAGGCACCACAGGACTCCTGCTTCCATCTCAGGGTCACAGGCATCAATCATGAGCATTTCCTAGGGTCCATAAACCCGAGGAGGGCAAGGGCATAGAGGGTCTCAGGGTTGTGATGGAGCCAAATCCTGTCCAGGGCCTGGGCCGTTCATCCCCTCATGGATCTTCCTTGATATCCCTGTATGTTTCTGCCTCTCTGGAATTAGAAGACTGAAAGTAAGATTTCTCATCACGGTCCTGTGGTGTGGCCACAGTTCACCTGAGCACATCTCTCTAGACCAGTAGGAGTGGTGCGAAGCCCCTTCAATGTTGTAGAATAGCGTGAGCTGCCAAGAGACTTCTAAGCAAAACAGGCTCTGTGACTCATTTTTCGAGGGCCATCGACCAAGTCTTAGGGGTGCCTCACCCTGTCTGCCTTGCACTTAGGGAAGACCCGAGAGGTTCCTCTTCCCCTTCCCAAGATGGCACCAGGCAACCTAGAGAACCCACCGTGGTGGGATGGGAGAACGAACATGCTGTGCACATCTCTATGAGATTCCACTGAGTGAAGCCCAGAACATGGGAGGCATGCAAGAAATCACCCTGTGTCGTGGTCCCAGTTGACCCTCCGCTGTCTCCACCAGCCAGGTGGGTTTCACAGAGCTGGGCCCTGCACCCTCAGCCAAGCTGTTCTAGGCCCTGAAGCTGAGGTCCCTGTTTGGATAGTCCTGGGGACTGCAGAATGAAAGAAGAACTTAATGAACGCACCAAGCCTCCAGTAGGTACGGCTGCCACCTCCGTGGTATGACTTGCCCATCCCAGCTGAATGAGGATGTCAGGAAGGAGGTATGCCAGAGGGCCAGCATTGCCTTTACCTGACTACCTACAGGCAAATCCACCTTTAAACACAGAGCTGCTGGACATCCAGGGTGCTGGTGGGAAAGGAACTCCACACTGGGAGCCCCAGGCCATTCCTATGAACAGGAAGGGGATGCAGAGGCCTGGTCTCTGAACTCTGGATATTGTTCCAGGTCTTCCCTAGAGTCCTAAGGGCATCGAGGATCCCATCTGCCATGTTTCAGTCTGCCCTCCACTGACTGACTAGATCTCTAGCCCCTATATTGGAACTGTCGGGATGCTGCAAGATGACCCTGGTGGGGAAATTCATGCCAGAATCTGGGGACCAAGGGGAACACAAGCCCCAGTGATGAAGACAGCAGGTAACACCTGACAGATGTGTGTTCTACCATTATGGTGCATACGTGGCTCCAACCACAAGAAATGCAGACAACAGTGGAGATCAGGGCAAGGCCATTGTGACATGGAACAGGACCGCTGTGCTGGTCTCTTCAGGGTTAGGAAAACTGAACTGCTGGGATGCTCCTGACAGGCTACCCACTTCCCCCTACCCCCCAACACACATTCACAAGCCAGAAAAGGAAAATAAAACACCGTGTTCTCCCCATTCCCACTCAGCCGGCCTTTTGTCTGCCTGCTTCCAGTGTTGATATGTGTTCAAGATAAAGTTCAGTTAGGGCAGAATGCTTGATTTAAGACTTTTGAACCAGTGAGCTTTAAAGAACAGAGACTGTGTGGCCCCAGCCCCTCTGATACGTAGACATTATCTCCCCAAAGCTCCCAGTCCTCCCAGTCTACCCCATCCCATTAGACAGCATCAACTCAAATGTGAGTCTTGGAGACCAGTTCGGCTAGCCATCATATGTCTGGGAATCCCATATTGGACTCTGCAATGTCTGGCTTCTTTCGCTTGTGTGGCCAAGGCTCATCTGCGGTGTTGTGTGTGATAGACTCATTGCTGTTGTGTGCTTGTTGGATCTTAGTTGTTTCTGTCTGAATAAACCGAGTCGTGGTGTCTTCCCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027577-Chrna4:NM_015730:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.192 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=25.1),PF0293211=Neur_chan_memb=PU(91.1=73.2),PF113173=DUF3119=WD(100=20.0)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(8.4=73.8)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: