HsaINT0035198 @ hg19
Intron Retention
Gene
ENSG00000147434 | CHRNA6
Description
cholinergic receptor, nicotinic, alpha 6 (neuronal) [Source:HGNC Symbol;Acc:15963]
Coordinates
chr8:42612071-42614256:-
Coord C1 exon
chr8:42614212-42614256
Coord A exon
chr8:42612181-42614211
Coord C2 exon
chr8:42612071-42612180
Length
2031 bp
Sequences
Splice sites
5' ss Seq
CACGTATGT
5' ss Score
7.26
3' ss Seq
CTGATTTCTATTTATTTTAGATC
3' ss Score
9.78
Exon sequences
Seq C1 exon
GATGAAGTAAACCAGATCATGGAAACCAATTTGTGGCTGCGTCAC
Seq A exon
GTATGTGCCTATATCATGTGTTGGCTTAATGATGTTGAATGGATAAAACCCACAAGCACTACCTTGTTCCATCTCCAACTGGTTATAGAATATAAAATATTATCCACTAGGTCATCTCCAAAGCCTAAAGTTCAGCTCTGGTAATAGCTGACTTGATGCATGCTTCACAGGTGCAGACACTTAGTGACAAAGGTCCCTCTGACATAGAGGTTTCCATCCTTCCTGGTTGCTGCTCTCAGATCTTCCACTTTTCTGTAACTTGAGCTCCAGGGTCTGATGCTTGCCTGCTCTTTGATCCCTGCTTGACCAGGCTTGGAGAAGTCAGTAGCTGAGCTTGGGAGCATGTACATGAGATTCCCAGCAGCTGGTTTTATCAGTTATACCTTTCTTCCTTAAGAAAGTCTTGGAGGGGTGCAGTGGCTCATGCCTGTAATCCCAGCACTTTGAGAGCCCAAGGTGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAACTTGGCCAACATGGTGAAATGAAACCCTGTCTCTAATAAAGATACAAAATTAGCCCGGCGTGGTGGTGGGTGCCCGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCAGTAGGCAGAGGTTGCAGTGAGCTGAGATTGCACCACTACATTCCAGCATGGGCAACAGAGCGAGACTCTGTCTTGAAAACAAAACAAAACAAAAAAAAAACAGAAAGGAAGTCTTAATCGTTTATACAGATTTTTTTTTAATTCAAAGCTTATCATCATACCCTTGAACTTTTTGATATTAGAGCTATACTCCAGTGTGAGTATAGCTCACGGAATATGGAAGTTGAGCCTAAAACTTTAACCAGCTAACTAATAATCAATACATAATTATCTAATGAAATATTTGCCTAAATCAGCTCAGCTATTTAGCTCCCTGTTCCCCATGGATATAATTGTCCAGATTTTGATAGCAACCAATGCATTCTTCAAATAAGAATGTATTATTTTTACTTTTTTTTTTTGTTTTTTGGTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTCCAGTGGCGCGATCTCGGCTCACTGCAAGCTCCGCCTCCCAGGTTCACACCATTCTCCTGCCTCAGTCTCCTGAGTAGCTGGGACTACAGGGGCCCGCCACCACGCCCGGCTAATTTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGGCAGGATGGTCTCGATCTCCTGACATCGTGATCTGCACGCCTCGGCCTCCCAACGTGCTGGGATTACAGGCGTGAGCCATCGCGCCGGGCCACTTTTTTTTTTTTTTTTTGAGACAGAGTCCCGGTCCGTCGCCTAGGCTGGAGTGCAGTGGCACGATCTCGGCTCACTGCAAGCTCCGCCTCCTGGGTTCATGCCATTCTCCTGCCTCAGCCTCCGGAGTAGCTGGGACTACAGGCAACCACCACCATGCCTGGCTAATTTTTTTTTTTTTTTGTATTTTTAGTAAAAATGGGGTTTCACCGTGTTAGCCAGGATGGTCTCAATCTTCTGACCTAGTGATCCGCTCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCTGGCCAAATGTATTCTTTTTTCAACAACAACTGTTGAACCATCATAAAGTTAACATTGGAAGAAAGTTATTAAGAAACACATTTTTTTTTTCCAGATAGAGTCACCCAGGCTGTAGTACAGTGACATGATCTCAGCTCACTGCAAACTCTGCCCCCCACGTTCAAGAGATTCTCCTGCCTCAGCCTCCCGAGTAGTTGGGACTACAGGCGCTGGCCACCACACCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACTATGCTGGCCAGGCTGGTCTCGACCTCCTGACCTCAAGTGACCTGCCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCATGCCTGGCCCGAAAGTTATTAAGAAATTTTAAAAGCTGATTTCTATTTATTTTAG
Seq C2 exon
ATCTGGAATGATTATAAATTGCGCTGGGATCCAATGGAATATGATGGCATTGAGACTCTTCGCGTTCCTGCAGATAAGATTTGGAAGCCCGACATTGTTCTCTATAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000147434-CHRNA6:NM_004198:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(7.2=88.9)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(17.4=100)
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)