HsaINT0035181 @ hg19
Intron Retention
Gene
ENSG00000120903 | CHRNA2
Description
cholinergic receptor, nicotinic, alpha 2 (neuronal) [Source:HGNC Symbol;Acc:1956]
Coordinates
chr8:27317278-27321510:-
Coord C1 exon
chr8:27320496-27321510
Coord A exon
chr8:27319272-27320495
Coord C2 exon
chr8:27317278-27319271
Length
1224 bp
Sequences
Splice sites
5' ss Seq
TCGGTGCGT
5' ss Score
8.67
3' ss Seq
GTGTGCTGTCTTCCCCACAGGTG
3' ss Score
13.89
Exon sequences
Seq C1 exon
TGCAGATGGGGAGTTTGCAGTGACCCACATGACCAAGGCCCACCTCTTCTCCACGGGCACTGTGCACTGGGTGCCCCCGGCCATCTACAAGAGCTCCTGCAGCATCGACGTCACCTTCTTCCCCTTCGACCAGCAGAACTGCAAGATGAAGTTTGGCTCCTGGACTTATGACAAGGCCAAGATCGACCTGGAGCAGATGGAGCAGACTGTGGACCTGAAGGACTACTGGGAGAGCGGCGAGTGGGCCATCGTCAATGCCACGGGCACCTACAACAGCAAGAAGTACGACTGCTGCGCCGAGATCTACCCCGACGTCACCTACGCCTTCGTCATCCGGCGGCTGCCGCTCTTCTACACCATCAACCTCATCATCCCCTGCCTGCTCATCTCCTGCCTCACTGTGCTGGTCTTCTACCTGCCCTCCGACTGCGGCGAGAAGATCACGCTGTGCATTTCGGTGCTGCTGTCACTCACCGTCTTCCTGCTGCTCATCACTGAGATCATCCCGTCCACCTCGCTGGTCATCCCGCTCATCGGCGAGTACCTGCTGTTCACCATGATCTTCGTCACCCTGTCCATCGTCATCACCGTCTTCGTGCTCAATGTGCACCACCGCTCCCCCAGCACCCACACCATGCCCCACTGGGTGCGGGGGGCCCTTCTGGGCTGTGTGCCCCGGTGGCTTCTGATGAACCGGCCCCCACCACCCGTGGAGCTCTGCCACCCCCTACGCCTGAAGCTCAGCCCCTCTTATCACTGGCTGGAGAGCAACGTGGATGCCGAGGAGAGGGAGGTGGTGGTGGAGGAGGAGGACAGATGGGCATGTGCAGGTCATGTGGCCCCCTCTGTGGGCACCCTCTGCAGCCACGGCCACCTGCACTCTGGGGCCTCAGGTCCCAAGGCTGAGGCTCTGCTGCAGGAGGGTGAGCTGCTGCTATCACCCCACATGCAGAAGGCACTGGAAGGTGTGCACTACATTGCCGACCACCTGCGGTCTGAGGATGCTGACTCTTCG
Seq A exon
GTGCGTTGGGGTTGGGAGAGGCGCCAGCCTGGGTGGCCCCACCAACTTAGCGGGGAACCACCTTACCGCAGAGTGTGAGCTTGGGCAGCCCAGGCCCCTCTCGTGAAGGCCCACTTTCCTCAGTCATGGTCCTTAGATGGAATAAATAGCAAGAGAGCACATGTAGCTGGCCGCTTTGAGGACGTTTATTGGCACGTGGCATGTTACACACCACGGAGTCAGGCATGAGCAGCTCAGCCTAACAGGGATCCTGAGAGCCGGAGAGGGAGGATCCCAGATGCTGAACCCCGTGCCTCCCTCACGCCGCCAGCTCCCACCATTGCCTTGGAGGTGGCGGCAGGCAGGGGGAGCATTTCAGGAGAGACCCAGAAAGTCAGCTGCTGCAGTGTCAGCCTTTGTCTTTTGTCTTGGATGGTCTCTTCCTCCGCCTCCTTGTTCATGGGCTCCTGAGGATCTTGCAAACTTCACTCTTCAACCATAAACCCTGCAGATTCTTGGTTGTGCCAGGTGGACTCCGCTCCCCCGCCCCTGCCATGGCATTGGCCCCACCCTGACCCCTGCCCCAGCTCCTGTCTGCCATTGAGCAGGCCGCTACTCTAGCACAAAATTCTACTAAGCCTAGGGAAGGATGAAAGGCCGGGAGGTTATTACTGAGTGGCCTTGATGAACAGACAAGAAAATTAATCATGATGTCATCCAGGAGCAGTGGAGAATCCAGGCTCCCTTGTCTGGGCTGTGAGCCCAAGTTCTACAAAGCCCCCGCCCCACCCCCAGCCTGCCTGGGGTCCCAACCACCTTCGCCTGTTTCCCTCTCCCCAGCTCCAGCAGGTGGGTGAGGAGGCAACCTGTGAGCAGCAAAGTCTGGTGTTGCATTGAAGTCACTGCAGGCCCCCTAGAAGGGCCCATGCCCCTGGGTGGTCGTGCCGCCTCCTTGCGTCCCTCTAGCCTCCTTTACCTATAGTCTAGGAGCATAATATGGACAGGTCTGGGCATGTGGAGGGGCTGGGATGGGAGGGGAATCATCAGTGGAGCTTACTGGAGCCTTGAAACAGCCCGTCCCTCCCTTCCACTCACCCCGCTCCCTGTGCTGACCTTTGCTCCCCAAGGTCTCTGTGGGGCAGTTGCTGCTGCCCCCAGTGGCCGCCTGTGCAGGGGCTGTGAATGGGGGGAACACATCCCTTTCCCAGGCCTGGCCCCTGTCACTGTGTGCTGTCTTCCCCACAG
Seq C2 exon
GTGAAGGAGGACTGGAAGTATGTTGCCATGGTCATCGACAGGATCTTCCTCTGGCTGTTTATCATCGTCTGCTTCCTGGGGACCATCGGCCTCTTTCTGCCTCCGTTCCTAGCTGGAATGATCTGACTGCACCTCCCTCGAGCTGGCTCCCAGGGCACCCCCGCTGACCATCTTTTGACCGTCTCTGCTACAGCTGCCTCTGGTGTCCCCTTTGGGATGAGCAGGTGCCTCTCCGCGGAGTCTGGACACTGACCCAGGGATTGCAGGCTTCCATCCAGCTTAACGTTATTGTACCAGGGCTGACAGCCTGCTGGGTGCAAAGCCCTGTTTTGGATACGGAGGAGCTGGGGAAGCTCTGCAGAAGGTCGCAATAGTGTGGTGACCAAGTGGGGCAGAGTAAGATTCTCCTGGAGGAGCAGTGCAGACCCTAAGTGACAGAAGGGTCAACCAGGGGGACAGTGGGGCCAGGGTGACGAGGAAGGGAATGCAGACCTCAAAGGAGGGGCCGTGGGGGCAAAGGGGAGGGTTCTTGGATGTGGAAGGGCTTTGAACAATGTTTAGATTTGGAGATGAGCCCAAAGTGCCAGGGAGAACAGCCAGGTGAGGTGGGAGGTTGGAGAGCCAGGTGAGGTCTCTGTAAGTCAGGCTGGGGTTGAAGTTTGGAGTCTGTCCGAGTTTGCAGGGTGCTGAGCTGTATGGTCCAGCAGGGGAGTAATAAGGGCTCTTCTGGAAGGGGAGGAAGCGGGAGGCAGGGCCTGCACCTGATGTGGAGGTACAGGGCAGATCTTCCCTACCGGGGAGGGATGGATGGTTGGATACAGGTGGCTGGGCTATTCCATCCATCTGGAAGCACATTTGAGCCTCCAGGCTTCTCCTTGACGTCATTCCTCTCCTTCCTTGCTGCAAAATGGCTCTGCACCAGCCGGCCCCCAGGAGGTCTGGCAGAGCTGAGAGCCATGGCCTGCAGGGGCTCCATATGTCCCTACGCGTGCAGCAGGCAAACAAGAAAGACCATCCTGAGCTGCTCCTGACCCACCTCAAACTCATCTCATTTGGCCTGTCCTCCCTCCCTTCACCCCTCCTTCCCTCCCCAGGAACCCTGTTCCCTGTGCCTGGCTCCATCAGGAGGAGGCCTCACTTGGGAGTTGAAGATCTTTGCCTTTAGTTCCTTTGATTCTGAACTTCTCAAAGGCAGGTACTCTGCCTGTTATTTTTCCCACCCCCAGCACCTAGCACAGCGCCGGGTGAGTGGGGTCAGCACTTAGGGCGTTTGTTCTGAGTGGTTGAGGGGAGCAAGCTGGATTGTTTGGGCCCCAGGACTGTTGTGTAGATGGCAAAGCTGTGGTCCCGTCCCTTATCAGCCTGCCTCGTCTCTCCCAGAGCCCCGAGGTGTGTTGACCTGCTCTGAACCCTTCAGAGCAGCCTGTGTGTGCACCTTGGAATGCAATGCACCACCCCACAGTCTGAGGCTGCACCCAGGATCCCAGGCCGAGCTGCTGCTCCTGGGATCGGGCAACAGACCTCCCCCCAACTCTGTCCAGACTGGAGGGTGGGACATTGGCAGCTAACAGATGTGGGCATCGGGTTCTCGGGACAGCATGGAGGCTCCAGGCAGGAAGCCGAGCAGGGCGAGCTTCCAGTTTCCTTTTGGTCCTAGGGGTCCCCTCCTTCCAAACCCCAAAATGTCTCTCCCTGACACTCTCAGGGGAAACCAGCCTGGCTGTGACGCCCTGGCCCAGGCCCTGCCATGCCTCACTTCTCTCCCACAACCCCCCTGCTCATGGCACATCTGGTCTCTGGCTCCTGTCTACTCGTGTGCATGCAGCCCCCAGCGCCCCCTCTCCTCCCACTTGCTCTCCGGAGGCCTCAGAGCTCTCGGGTCCAGGCTCCCAGACCCACTCTCCTGAGACAGTGATGTTCACTTCTGTTATCCATGTCTCCCATCCATCTTGCATGTGAATAAAGAGATTAAATAAAGCTGCACCTACTGCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120903-CHRNA2:NM_000742:6
Average complexity
IR-S
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:
PF0293118=Neur_chan_LBD=PD(59.9=33.9),PF103294=DUF2417=WD(100=49.6),PF0293211=Neur_chan_memb=PU(86.7=63.7)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.4=73.8)
Main Inclusion Isoform:
NA
Other Inclusion 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:
CAGAAGGCACTGGAAGGTGTG
R:
TTAAGCTGGATGGAAGCCTGC
Band lengths:
349-1573
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)