HsaINT0035182 @ hg19
Intron Retention
Gene
ENSG00000080644 | CHRNA3
Description
cholinergic receptor, nicotinic, alpha 3 (neuronal) [Source:HGNC Symbol;Acc:1957]
Coordinates
chr15:78887647-78894606:-
Coord C1 exon
chr15:78893595-78894606
Coord A exon
chr15:78889075-78893594
Coord C2 exon
chr15:78887647-78889074
Length
4520 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
TTTATCATTTTGTTTTGCAGATT
3' ss Score
11.62
Exon sequences
Seq C1 exon
TGCTGTTGGGGATTTCCAGGTGGACGACAAGACCAAAGCCTTACTCAAGTACACTGGGGAGGTGACTTGGATACCTCCGGCCATCTTTAAGAGCTCCTGTAAAATCGACGTGACCTACTTCCCGTTTGATTACCAAAACTGTACCATGAAGTTCGGTTCCTGGTCCTACGATAAGGCGAAAATCGATCTGGTCCTGATCGGCTCTTCCATGAACCTCAAGGACTATTGGGAGAGCGGCGAGTGGGCCATCATCAAAGCCCCAGGCTACAAACACGACATCAAGTACAACTGCTGCGAGGAGATCTACCCCGACATCACATACTCGCTGTACATCCGGCGCCTGCCCTTGTTCTACACCATCAACCTCATCATCCCCTGCCTGCTCATCTCCTTCCTCACTGTGCTCGTCTTCTACCTGCCCTCCGACTGCGGTGAGAAGGTGACCCTGTGCATTTCTGTCCTCCTCTCCCTGACGGTGTTTCTCCTGGTGATCACTGAGACCATCCCTTCCACCTCGCTGGTCATCCCCCTGATTGGAGAGTACCTCCTGTTCACCATGATTTTTGTAACCTTGTCCATCGTCATCACCGTCTTCGTGCTCAACGTGCACTACAGAACCCCGACGACACACACAATGCCCTCATGGGTGAAGACTGTATTCTTGAACCTGCTCCCCAGGGTCATGTTCATGACCAGGCCAACAAGCAACGAGGGCAACGCTCAGAAGCCGAGGCCCCTCTACGGTGCCGAGCTCTCAAATCTGAATTGCTTCAGCCGCGCAGAGTCCAAAGGCTGCAAGGAGGGCTACCCCTGCCAGGACGGGATGTGTGGTTACTGCCACCACCGCAGGATAAAAATCTCCAATTTCAGTGCTAACCTCACGAGAAGCTCTAGTTCTGAATCTGTTGATGCTGTGCTGTCCCTCTCTGCTTTGTCACCAGAAATCAAAGAAGCCATCCAAAGTGTCAAGTATATTGCTGAAAATATGAAAGCACAAAATGAAGCCAAAGAG
Seq A exon
GTAAGGATATGGCTTTTATTACATTGGTCATTCATTCATTCAACAAATATTTATGGGTTCCTCGTGGGGCAAGGCATAGGGTAGGGGGTTAAGAAATTGCCCTCTGGAGTCAGTGGCCTGTGTTAAGACCAGTTATATGTCCTTGGGTATGTTACCTCACCTCTCTGAGCCTGTTTTCTCTTCTGTAAAATGGGATGATAAAGCTTGGTATGTGGTACCCTGAAGCTAGCCACCAGGCTGCCAGCAGGCTGGCAGGCTGGACCATGAAAACACCTGATGCCAATAGACTAGATTAGGATGTAGGCTGGAAAAGGGCATGGGGCCAGATGATCTCCAGTTAGTATTGGTTAATTGAGGTTATATTTTTATTTTTATTTATTTTTTTGAGACAGGGTCCTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCGCAATCTTGGCTCACTGCAACTTCCGCCTCCCAGCTCAAGCGATTCTCCCACCTCAGTTTCCCGAGTAGCTTGAACTACAGATGCCCCGCCACCATACCCTAATTTTTTTGTACCGATGGGGTTTTGCCATGTTGCCCAGGTTGGTCTCAGACTCCTCGACTCAATCTGCTCACCTCAGTCTCCCAAAATGCTGGGACTACAGGCATGAGCCACCGCACCTGGCCTTTATTTTTACTTTCTAATTGTATATGTGTTCTCACTGAGGAAGAATTTACGTGGAGTAAAGTGCACACCTCTTCAGTGTACATCTCAATGAGTTTTTACATCATGTATACAACCATGTAACCAAGACCCAGGTAAAGATATAGAACACTCCCAGGGCCCCTAGAAAGTTCCCCAATGCCCTTGCCAGTCAGTGTCTCCCTCCCTGCTTGGTACCCACCATCCTGGCTTAGGCGCAGTGGCTCACGCCTGTAATCCTAGCACTTTAGGAGGCTGAGGCAGGTGGATGGCTTGAGATCAGGAGTTTGAGACCAGCCTGGGAAACATAGCGAAACCCCGTCTCTAACAGAAATACAAAAATTAGCCAGGCGTGGTGGCACGTGCCTGTAGTTCCAGCTACTCAGGAGGCTGAGGTGAGAGGATCACTGGAGCTCAGGAAGTCTAGTGAGCTGTGATCATGCCACTGCACTCCAGCCTGGGTAACAGAGTGAAGTCCTTTCTTTAATTAATTAATTAATTTTTTAAAAAACCATTATACTGACTTATTTGATAATTGATTAGTTTTACCTATTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTCACCCAGAATGGAGTGCAGTAGTACAATCTCTGCCTACTGCAACCTCTGCTTCCCAGGTTCAAGTGATTCACATGCCTCAGCCTCCCAAGTGTCTGGGACTACAGGTACCCGCCCGCTACCATGCCTAATTTTTTGTATTTTTAATAGAGAGGGGATTTTGCCATGTTTGTCAGGCTGGTCTTGAACTCCCGACCTCAGGTGATCTGCCCGCCTTGGCCTCCCAAAGTGCTAGGATTAAAGGTGTGATCCACCACACCTGGCCTTTTGAGCCCTCAGAAGAACATTTATCCATAAACATTCTTGAGAAGGCATGCCAATAAGAAGAGAAATAAATCCAGGGGGCTACAAAGGAGAGGAGGAAAGCCTCAGGCTCCACCAGTCAATGGGCAGCTCAGTTCTCTGCACTTCCCTTTAGCCAGGCTCTGCTGGGCTTGTGAGGGACCCCCTGAACCTGCATCTCTGGGCTGGGAGTGGCAGGCTAAAGAGGCAAAGTGGCAGGGGAACAAAGATCTCCCTAGCTCTCCCCTCCACCAAGCCCCTCCCCCTGCCAGCCCCAGTCTCTGGCCACACCTTCCCAGTTTCTGGGTCTTTAAAGTAGTCTTCTCATGCTTCTGGGCCAGCTCTCAATTTGGGCTAGTTCACCACTTTGCCTAACATCTGTGACTCATCAGAAAATGGCCAATATCATTGTGCTTTAAAGACTTTAGGAGCTAGATATAAGCCAGGCACAGTGGCTTACACCTGTAATCCAACACTTTGGGAGGCCAAGGCAGGAGGATCACTTGAGCCCAGGAGTTCAAAACCATCCTGGGCCACGTAGGGAAACCCTTTCTCTACAAAAAAAATTTAAAAATCAGGCCAGGTGCAGTGGCTCACGCCTGTAATCCCAACACTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGGTTGGGAGTTCAAGACCAGCCTGGCCAACAATGGTGAACCTCCATCTCTACTAAAAATACAATAAATTAACCGGGGGGTGGTGGTGGCATGAGCCTGTAATCTTAGCTACTCGGGAGTCTGAGGCACAAGAATTGCTTGAACTCGGGAGACAGAGGTTGCAGTGAGCCAAGATCACACCACTGGACTCCAGCCTAGGTGACAGAGTGAGACTCCGTTTCAAAAAAAAAAAAAAAATGCCGGGTGCAGTGGCTGACGCCTGCAATCCCAGCACTTTGGGAGGCTGGGGCAGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATAAAACCCCATCTCTACTAAATACAAAAATTAGCTGGGCATGGTGCTAGGCACCTGTAATCCCAGCTACTCAAGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGTGGAGCTTGCAGTGAGGCGAGGTCATGCCACTGCACTCCAGCCTGGGCGTCTCAAAAAACAAAAAATTGCCCAAGTGTAGTGACACACACCTGTAGTTCCAGCTACTCAGGAAGCTGAGTGGGGAAGATTACTTGAGCCCGGGAGGTCAAGGCTGCAGCAAGCCATGATTGCACCCCTGCACTCCAGCTTGAGCAACAAAGCAAGACCCTGTCTCAAAAAAAAAAAAAAGATATAAAATTTCTGTCCAGCCAGCTCTTTTTGCACCACTATTTCTATTCATGTATAAAACCCAAGTGTCATCTTTCTTCATGAGGCTTGAGTAAGGGTCATTTTATAAATCAACATTAGTATCACTAGGCTCTATTCATTAAGGACTCTGTTCTGAAACAAGCTTCTGAGGGAAGTACTGTTCTTATCCCCATTTTACAGATAAGGAAATTGAGGCTAAGAGCGGTCATGGAATTTACCCAGATTCTCACAACTCAAAAGGAGCAGAGCTGGGATTCTAATCAGTTTGTCTCCAAGTCTCTGCTTTTCCACACCTCTGCCTCCTAGAGCCTTAGGAGGTGGCTGGTAGGGGGTGGGTAGGAATCTCACATCTCAAGGTGTATCTGAAGCACACACAAACCAGTCTTAGGAATTCAAATGAAGTACCTCATGGCAAATATGGCATCATAATTCTAATTTTACCTATGACAGTAGTGTCACCAAGAGAACACATTTACTCAGGCTCACAATGGTGATGTAAAATCTTCATCTCCCAGCGCCATTTCAGTATACTTATAATAAAGAGGCAGCATGTAATTTATTAATTTCATTATTGCTTCAAAATCAGCTGACTCATGGGTTCTCTCAATTCAATTATGGCTTCTTTGCTTTCTGAATTGTCTAGGAGTATAATTACAATTTTCCTTCCTATTTCAAGCCCAAATTGAAGCTGTATTATATACAATTGGTCTTGCTTTTTCTCCCATCTTTTACTTTATTGTCAGCAATTATTTCTGATGTTCAACCTGCTCTCCAACTGCACAGTATCCCATGATACTTTGGTCTTATGAGTAAAAATGACTTTTGATCAGCTGGGCATCGTGGAGAGGGCAGTGGGGAGGGAAAGAGTGATGAGGATGGACTTGCCCTGATAACGCTTATCTCATTTTTGGAACAGATGTTAAAAGGAAATTTATTTTGTTGTTTTTGAGACAGGGTCTCGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCTGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGAAATTCTCATGCCTCAGCCTCCCAAGTAGCTGGGGATTACAGGCATGTGCCACCACTCCTGGCCAATTTTTGTATTTTTGGTAGAGACAGGGTTTCAACAGGGTTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGCCAAATTTATATCTAAAACTGGATAGAGTACTTTGAAACAATGGTAGATTATATTGGACTATATTAGCCATTCTAACCAAGGCCCAGAATCCTGCCATGGAAGCCTAAGTAACTGGTTTCACTAACTTTATAAAATTGGAATTCAGTTTAGAAAAACTAGGTTATGCATTTTTAGGAAACTTCTGATTTGAAACAGATCTAACATGACAGATCTTTTATACCTGTTTCTCTCCTGCATAAACAGAAACTTGAGAATGGTGGATTTCCTCAGACCACATCAATTAGGAAAAAAAGGGCTTCTTACATATTAGAGACAAAATGGCTTCTACTGCAACGTGTTGATTACATCTTCAGTATTGAAAATGTATTCATTTGCCTTTCCCTCCATGTTTTTTTTCTTTTATCATTTTGTTTTGCAG
Seq C2 exon
ATTCAAGATGATTGGAAGTATGTTGCCATGGTGATTGATCGTATTTTTCTGTGGGTTTTCACCCTGGTGTGCATTCTAGGGACAGCAGGATTGTTTCTGCAACCCCTGATGGCCAGGGAAGATGCATAAGCACTAAGCTGTGTGCCTGCCTGGGAGACTTCCTTGTGTCAGGGCAGGAGGAGGCTGCTTCCTAGTAAGAACGTACTTTCTGTTATCAAGCTACCAGCTTTGTTTTTGGCATTTCGAGGTTTACTTATTTTCCACTTATCTTGGAATCATGCAAAAAAAAAAATGTCAAGAGTATTTATTACCGATAAATGAACATTTAACTAGCCTTTTTGGTATGGTAAAGAGATGTCAAAATGTGATTCTATGTGATTAGTATGCTATGCTATGGAATATACATGTAAAAATGTTTCCTTTTAGTTGTTGAAACAAAACTGGATAGAAAAATGCTGTTCAGAAATATGAAAAGTCATTCAGTTATCACTACAGATCTCCCAGTAATTTTTCTTATTTAGCCCATAATCTCTTTGAAGGTTTATACTAATTCAGCAATCCCCCATCGTTACCCATTTCTTACCATGCATTTCTCGTTCTTTACTGGGTCTAAAGGGCTATGCCTCCATTTCAGAGAGCTTCAACTACTTCTCTTGCATACTTCTAAATTATACCATGAGAAATCATGCCTAGTTATTCATTGTTAATATAACTGTCTTAGTACACCATAAACTGGGTGGATTATAAACAACAGAAACTTCTCAGTTTTGGAGGTTGGGAGGTCCAAGGTCAAGGCACCAGCAAATTTGGTGTCTGGTGAGGGTCCTCTTCCTCAAAGGGTGCCTTCTAGCTGTGTCCTCACATGACTGAAGGGACTAGCTATCTCTGTGGGGTCTATTTTATAAGGGCACTAACCCCATTCATGAGAGCAGAGCCCCCATGGCCTAATCACCTTTCCAAGGCCCCACCTTCTATCTAAGACAATCACGCTGGGAATAGGTTTCAACATATGAATTGGGGGAGGACACATTTGGACCACAGCATGAACCTTTAGAACAGGGTTTCTCAGCCTTAGCACTATGGACATTTTGGGCTGGATAAATATGTGTTGGTACAGAATGGGGGTATCCTGTGCATTGTAGGATCTTTAGCAGTACCCTAGCCTCAACTCACTAGATGCCAATGACATACCTTGCTTCTTCACCAGTTATGATAACCAAGAATGTCTCCATTGTTAAATGTTCCCTTAGGAGCAAAATTGCCCCTGGTTGAGAAACATTGCTTTAGACAAATTGTTAAGAGTATCATGTACTACACTTCTGAAACTTAACGTGATCATCACCACTGACAGATGATTCACAGAGACTGTTTGAATCTTGTCTCACTAGTTTTTCCTGTGCAAAAATAAAATGGACAGAATTGCAGCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080644-CHRNA3:NM_000743:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=34.0),PF0293211=Neur_chan_memb=PU(86.7=63.6)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.5=72.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]
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)