HsaINT0035199 @ hg19
Intron Retention
Gene
ENSG00000147434 | CHRNA6
Description
cholinergic receptor, nicotinic, alpha 6 (neuronal) [Source:HGNC Symbol;Acc:15963]
Coordinates
chr8:42610989-42612180:-
Coord C1 exon
chr8:42612071-42612180
Coord A exon
chr8:42611968-42612070
Coord C2 exon
chr8:42610989-42611967
Length
103 bp
Sequences
Splice sites
5' ss Seq
CAAGTATGG
5' ss Score
4.99
3' ss Seq
GTGTCTGACTTGCTTTGCAGTGC
3' ss Score
8.91
Exon sequences
Seq C1 exon
ATCTGGAATGATTATAAATTGCGCTGGGATCCAATGGAATATGATGGCATTGAGACTCTTCGCGTTCCTGCAGATAAGATTTGGAAGCCCGACATTGTTCTCTATAACAA
Seq A exon
GTATGGGTCTCTGACCACCGTAGCCTCTTTCCAAAGCTGCTGTTGGTGTATTCTGGCCTATAGCAAAGGGAGTGTTACTAATGGTGTCTGACTTGCTTTGCAG
Seq C2 exon
TGCTGTTGGTGACTTCCAAGTAGAAGGCAAAACAAAAGCTCTTCTTAAATACAATGGCATGATAACCTGGACTCCACCAGCTATTTTTAAGAGTTCCTGCCCTATGGATATCACCTTTTTCCCTTTTGATCATCAAAACTGTTCCCTAAAATTTGGTTCCTGGACGTATGACAAAGCTGAAATTGATCTTCTAATCATTGGATCAAAAGTGGATATGAATGATTTTTGGGAAAACAGTGAATGGGAAATCATTGATGCCTCTGGCTACAAACATGACATCAAATACAACTGTTGTGAAGAGATATACACAGATATAACCTATTCTTTCTACATTAGAAGATTGCCGATGTTTTACACGATTAATCTGATCATCCCTTGTCTCTTTATTTCATTTCTAACCGTGTTGGTCTTTTACCTTCCTTCGGACTGTGGTGAAAAAGTGACGCTTTGTATTTCAGTCCTGCTTTCTCTGACTGTGTTTTTGCTGGTCATCACAGAAACCATCCCATCCACATCTCTGGTGGTCCCACTGGTGGGTGAGTACCTGCTGTTCACCATGATCTTTGTCACACTGTCCATCGTGGTGACTGTGTTTGTGTTGAACATACACTACCGCACCCCAACCACGCACACAATGCCCAGGTGGGTGAAGACAGTTTTCCTGAAGCTGCTGCCCCAGGTCCTGCTGATGAGGTGGCCTCTGGACAAGACAAGGGGCACAGGCTCTGATGCAGTGCCCAGAGGCCTTGCCAGGAGGCCTGCCAAAGGCAAGCTTGCAAGCCATGGGGAACCCAGACATCTTAAAGAATGCTTCCATTGTCACAAATCAAATGAGCTTGCCACAAGCAAGAGAAGATTAAGTCATCAGCCATTACAGTGGGTGGTGGAAAATTCGGAGCACTCGCCTGAAGTTGAAGATGTGATTAACAGTGTTCAGTTCATAGCAGAAAACATGAAGAGCCACAATGAAACCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000147434-CHRNA6:NM_004198:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.015
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=35.2),PF0293211=Neur_chan_memb=PU(86.1=62.4)
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:
ATGGCATTGAGACTCTTCGCG
R:
CAGCTTTGTCATACGTCCAGGA
Band lengths:
246-349
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)