MmuINT0036220 @ mm9
Intron Retention
Gene
ENSMUSG00000022041 | Chrna2
Description
cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal) [Source:MGI Symbol;Acc:MGI:87886]
Coordinates
chr14:66767624-66771785:+
Coord C1 exon
chr14:66767624-66768656
Coord A exon
chr14:66768657-66769787
Coord C2 exon
chr14:66769788-66771785
Length
1131 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
AAGCCCAATTCTAACTCCAGGTG
3' ss Score
4.59
Exon sequences
Seq C1 exon
TGCAGACGGGGAGTTTGCGGTGACCCACATGACCAAGGCCCACCTCTTCTTCACGGGCACTGTGCACTGGGTGCCCCCAGCCATCTACAAGAGCTCCTGCAGCATCGACGTGACTTTCTTCCCCTTCGACCAGCAGAACTGCAAGATGAAGTTTGGCTCCTGGACATACGACAAGGCCAAGATCGACCTGGAGCAGATGGAGCGGACGGTGGACCTGAAGGACTACTGGGAGAGCGGCGAGTGGGCCATTATCAACGCCACCGGAACCTATAACAGCAAGAAGTACGACTGCTGCGCGGAGATCTACCCCGACGTCACCTACTACTTCGTTATCCGCCGGCTGCCGCTGTTCTACACCATCAACCTCATTATCCCGTGCCTGCTCATCTCCTGCCTCACCGTGCTCGTGTTCTACTTGCCCTCTGAGTGTGGAGAGAAGATCACGCTGTGCATCTCGGTGCTGCTCTCCCTCACTGTCTTCCTGCTGCTCATCACAGAAATTATCCCATCCACCTCACTGGTCATCCCACTCATCGGCGAGTACCTGCTCTTCACCATGATCTTCGTCACCCTCTCTATTGTGATCACAGTCTTCGTGCTCAATGTCCACCACCGTTCCCCTAGCACGCACAACATGCCCAACTGGGTGAGGGTGGCCCTGCTAGGCCGGGTGCCCCGGTGGCTGATGATGAATCGGCCCCTGCCGCCCATGGAGCTCCATGGCTCTCCAGGTCTGAAGCTCAGCCCCACTTATCATTGGCTGGAGACCAACATGGATGCTGAAGAAAGGGAGGAGACAGAGGAAGAGGAGGAGGAGGAAGAAGATGAAAACATATGTATGTGTGCAGGCCTCCCAGACTCTTCCATGGGTGTCCTCTATGGCCATGGCAGCCTGCATCTGAGGGCCATGGGGCCTGAGGCCAAGACTCCATCCCAGGCTAGTGAGATCCTGCTGTCACCTCAAATACAGAAAGCACTAGAAGGTGTACACTACATTGCTGACCACCTGAGGTCTGAGGATGCTGACTCTTCG
Seq A exon
GTGAGTTGGGATGAGGAAAGCCCCTCCCCACCCCGTGGGTGACTCTGCCAGCTTAGCAGGGAAAAATCCAAGCCCAGGGCATGCCCTTGGGCAACCCTTTCCCTTCTTCTTGTAAGGACCAGTCACCCTCAGTCATGTCCAAAGAGTCTGGACTTGATCATGAAAGGGAAACACTAGCTAGAAGTCCTCTGGTTACTTCCTGGCCGATGGCAGAATACCACAGGGTCCATCCCCCTCTCTTCAACCTAAGTGGGGGAGAGTGAGGAAATTGGGGAGCTCAGATGCTGGTCTCCATCTGCTTTGTCTTTGTCTGGGCAGTCCCTCTATGAGAGGGGCGGGGTGGGGCGGGGCAGGGCAGGGAGATAGACTGCTCTGAGAAGGTACAGAAACCAAATACAAACGCATCCACTCAGTGCATGGCTGGCCGCTGCACTACCCTGTGGTAGAGGGTCTCCTCCATCTGGGCTCTGGGCAGTCTGTGACGTTCCCTAGTCACTCTCAAACCCTGCAGATTCTCAGCTGAACCAGGGTAGGCTCCCCTCCCCCAGGGCTGCATATAGTAAGTACTTAGTGTTCAGAACCTGGCTGTCCCCTTACCAACCAAAGGAGGAGTGAAAGGTTACTATGGGACAATCTTATTGAGTAGATAAGAACATTGATCATTAATTTGGAAATTTCTAAGAATGTAGATCCTCTGGCTTGGCCTGTGAGCTGAAGAGCTACAAAGCTCCAGCTCTTCCACACTGGCTTGCCCTGGGCTACAACCTGCCTCTTTCTGTCCCCTTCAGGTGTGTGGGGAAGTAGCATGGGACAGCACATTATTGGGGACTACTATGAGCTACATTTAAAATTTCCTGATTTTGATGGCCTGTGCCTAGTGTCTCCTCATGTCCCTCTGGACTCCTGAGCCTAGCAGTATGTGGAAATGGGAAAAGATAAAATGGGATTCCCAGGGATGTATCAGCCCTGAGCTAAGCCTGTTTCTCTCTCCACCCATCTCTATGTGTGGGATAACCTTGGCTTTGCAAGCCTTCGGTGGCCTGGTGACTACTGCCTCCATGAGGCTGGATGTGGGAGGGACATCTTCTCAAAGCCTGGCTCTTGTCACTGTAAGCCCAATTCTAACTCCAG
Seq C2 exon
GTGAAGGAAGATTGGAAGTATGTGGCCATGGTGGTAGACCGGATCTTCCTCTGGCTGTTCATTATCGTCTGCTTCCTGGGGACCATCGGGCTCTTCCTCCCTCCGTTCCTGGCTGGAATGATCTGACTTGATGTCCCTCATGTTGGCTCCAAGGTGGCCTGGACAACCATCTTCTGCTCTTCTGTGACTGGAGCCATCTCTAGAATATTCTTTTGACTTAATGCCACCTGCCTGCGATGTTTCTACGAGGCCCCTGATCTAGCCTGGACTTCATATCCTCCTTGTCAACAGTTCATGGTGCCATTGCGGTGACAAGCACTGAGACCACTCAACATGACAACTATTTAGGGATGCTGAGGAACTAGAAGAGGTGAAGGCTGCTCTGTAGGTGATGACAACATGGTGGTGATATGGGGGGAGAGCAAGATAGTTCTGAAAGAGCATATAGGAGTTGTCTATGGCAAAAGGGTCAAACAAAGGGATGGAGGGGTCAGACCAGGACAAAGGGAAATAGAACACTGGCCCAAAGATGGGCACAAGGGGACAATGGGAGTGCCTGGTGTGGAAGAGTTCTGCACAACACTGTGGATTCAGAATGTCAGAGAGGACAGCCAGCTGGGGTGGGGAGGCTGGGAGGCAAGTTGGGATATTTTTGACCCAGGCCCAAGAAGAAGCTCAGAGTCTGCACTGAACCTGTCTCTATGCACTTTGCAGGAAATGTCAGAGGGACAGGGGTACTTCCCAAAGGAGTGGGGCACAAAGAAAGTTCTAGAGCAGTGGCTTTCAACCTGTGTCGTGGGTTGCAACCCTTCAGGGAGTCAAACGACCCTTTCACAGGGGTCACATATCAGATATCCTGCATATCAGATGTTTTACATGACAGTCCATAACAATATCAAAATTACTGTTATGAAGTTGAAATGAAAACAATTTTGTGGTTGGGGTCACAACATGAGGAACTGTAAAGGGTCATAGCATTAGGAAGGTTGAGAACCACTGATCTAGGTGCCCTGGTGGATGCTTGAGGCAGAATAGCAACATTGGGTATAAGTTGCTGGGCCATTATTCAACCAAAAGCACTTTGGAGCCTTCAAGTTCCCCTCAGTGTCATGTCTCACTGTTCTATGCTACAAAAAAAGAGGTATAGCAATTTCTACAAGGGATCAGGGCTACCTTCAAATCAAGAGGACAAAGTAAGAAGGCAGTCTCCAATGTTGGCACCCTTCTTGCTGTCCACAGGGACCTGGTCCTCAATTCCTGGCTCTGTCAGCATGCCTCACATAGGAACTGAGATCTTTGCATCAAGCTCTTTCAATTGTGTGCTCCTTCAGGGCAGAGTCTCTGCTCTTGTTGCTTTCACTCATCCTGAGCTGGGTGAGAGAGCTCAGTAGCTGGACCCTCCATCGTGAGTAGTGGAGAGAAACCAACCTGGTAGCTTTAGGCTCCAGAACTGCTACATAATACCAAAGCTTTGGGGGAGGACTCTTCCCCAGTCTTCCCAGGGCCCCATCAGGTGACTAACCTGCTCTGAACTGTCCTGTGTAGCTTGTTCTTTTACTTGTAATATTCCACGACCCTTCATTGCATAGAAGCCCAGCGGATTGGGCCTTTCAGAACATTCTGCAGTCCCCAAGGAATTAGGTCCCAGACGCTAACAGCAATGAGATTCAGGGTCACTAAGAGATATAGAGACCAAGTTTGTTCTCTGTCTTGGGGTGCTCTCCTTCCGAACCCCACACACAGCACCTCGACAGACCTAGGAGATCTGCTTGTCGGAGGCCTTACCCAGACTTCCTGTTACCAGTTCTAATGATACCCACTCAGTCTCAGGCCTTGGCTCCCCCTTTCTCCACTGAATGCAGCCGGCACCTCTTTTCTCTGTGTCAAACCCCAAGACATGATTTCCTGATGCAGAGATGCTTGTTGGATGATCCCTACCCCCCATCCTCCTTGCATGTGAGTGAAATGTCAAAATAAAGCTAAAATGTCTGCCGTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022041-Chrna2:NM_144803:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.081 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=33.3),PF103294=DUF2417=WD(100=50.4),PF0293211=Neur_chan_memb=PU(87.1=64.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.2=73.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGGCTAGTGAGATCCTGCT
R:
TCAGGGGCCTCGTAGAAACAT
Band lengths:
357-1488
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: