HsaINT0035200 @ hg38
Intron Retention
Gene
ENSG00000147434 | CHRNA6
Description
cholinergic receptor nicotinic alpha 6 subunit [Source:HGNC Symbol;Acc:HGNC:15963]
Coordinates
chr8:42752620-42756824:-
Coord C1 exon
chr8:42755846-42756824
Coord A exon
chr8:42753311-42755845
Coord C2 exon
chr8:42752620-42753310
Length
2535 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
AATTTTTGTTTGCATTTCAGGTA
3' ss Score
9.63
Exon sequences
Seq C1 exon
TGCTGTTGGTGACTTCCAAGTAGAAGGCAAAACAAAAGCTCTTCTTAAATACAATGGCATGATAACCTGGACTCCACCAGCTATTTTTAAGAGTTCCTGCCCTATGGATATCACCTTTTTCCCTTTTGATCATCAAAACTGTTCCCTAAAATTTGGTTCCTGGACGTATGACAAAGCTGAAATTGATCTTCTAATCATTGGATCAAAAGTGGATATGAATGATTTTTGGGAAAACAGTGAATGGGAAATCATTGATGCCTCTGGCTACAAACATGACATCAAATACAACTGTTGTGAAGAGATATACACAGATATAACCTATTCTTTCTACATTAGAAGATTGCCGATGTTTTACACGATTAATCTGATCATCCCTTGTCTCTTTATTTCATTTCTAACCGTGTTGGTCTTTTACCTTCCTTCGGACTGTGGTGAAAAAGTGACGCTTTGTATTTCAGTCCTGCTTTCTCTGACTGTGTTTTTGCTGGTCATCACAGAAACCATCCCATCCACATCTCTGGTGGTCCCACTGGTGGGTGAGTACCTGCTGTTCACCATGATCTTTGTCACACTGTCCATCGTGGTGACTGTGTTTGTGTTGAACATACACTACCGCACCCCAACCACGCACACAATGCCCAGGTGGGTGAAGACAGTTTTCCTGAAGCTGCTGCCCCAGGTCCTGCTGATGAGGTGGCCTCTGGACAAGACAAGGGGCACAGGCTCTGATGCAGTGCCCAGAGGCCTTGCCAGGAGGCCTGCCAAAGGCAAGCTTGCAAGCCATGGGGAACCCAGACATCTTAAAGAATGCTTCCATTGTCACAAATCAAATGAGCTTGCCACAAGCAAGAGAAGATTAAGTCATCAGCCATTACAGTGGGTGGTGGAAAATTCGGAGCACTCGCCTGAAGTTGAAGATGTGATTAACAGTGTTCAGTTCATAGCAGAAAACATGAAGAGCCACAATGAAACCAAGGAG
Seq A exon
GTAAATGTGTGTTCCCTCCACCCAGCCAGCTTGCACCCTTTGCAGCCTATGGGCACTCTGGATGCACAGTCAGACCTTCAGTGTGACTTTTGTTCCTGAGAGGGTCAGGCGGCCTTGCTCTGAGACCTGGCTCTGTTATTATGTGGTTATGGGTGGACTGACAGGGTCAGACCTGCCAGTGGAGCGGGGTCAGGTGCAATAGCCCCAGAGCAAATCTCCACCTCCAGAAATGTGAACTCAAGTAAAATTTGCTTAAAATGAACATTCAGGGCCGGGCGTGGTGGCTCACGCCTGTAATCCTAGCACTTTGGGAGGCCAAGGCAGGCGGATCACCTGAAGTCAGGAGTTTGAGACCAGCATGGCCAACATGGGGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCAGGCATAGTGGCACAGGCCTGTAATCCCAACTACTTGGGAGGTTGAGGCAGGAGAATCGCTTGAACCCAGGAGGTGGAGGTTACAGTGAGCTGACATGGCGCCCCTGCACTCCAGCCTGGGTGACAGAGAGAGACTCCATCTCAAAAATAAAAACAAACAAACAAACATTCAGGGCAACCTCAGTTAATGAAACTAAGAGCCTCAGCCTGGGCAACATAGTGAGACCCTGAACTACCAAAAAAAAAAAAAAAATTAGCAGGCGTGTTGGTGCATACCTGTAGTCCCAGCCACTCAAGGGGCTGAGGTGGGAGGATTGCTTGAGCCCAGGAGGTTGAGGCTACAGCCTGGGAGATAGACGACAGATCAGGGCCCTGTCTCAGGAAAAAAAAAAAAAAGCCCCTGCACAAGAAACAGCAGCAAATAAAAAGGTAGAAAGAGAAAAGCTGCCCCAGAGGGAAGGAGAAATGAGTTCGGAGCAGCGTGCAGCCTGGGGGTGCTGGGAGATGTGGGAGAGGGCGAGAGTGCATTCGTTCCGGCAGCTCTGGCCCCACTTGTCCTACTTGAGGGATTTAGGTGCTGGTGAAATGAGCCCCAGGGATATTTTTAGCGTTCACGTACTCTGTTCCTGCTGTCCAGAGTCTAACTATAGCAGCATGTACCTCCCTCAGCTTCCAAAGACAGAGCTCAAGAGAATCATGCCAATTTCCCACACCATGTGGGTGACTAGCGGAAGGCATCTGAAACTCAGGCCTGGTGTCTAGGTTTGACCTCGGACTGCAGCTGCTGGCAGCCATCGCTCCTAGTGAAAGGATACTGTGAAACCGAAAGTCCGCCCTGTTGGTGTAGAAGGAAGATGCTGTGAATGGCTGTCATGCAGATGTGTCACCGGACAAGAGAGCCCAGAAAAATTCACCTTCATAAAATTTAAAAGAAGACCCTCTCTCTACAAAAAAAACAAAAATTAGTAGGGCATGGTGGCACATGGCTGTAATTGCAGCACTTTCGGAGGCCAAGACGGGAGAATTGTTTAAGTAAGGCCAGGAGTTTGAGACCAGCCTGGGCAACATATTGAGACCTTATTTCTAAAAAACAAATTTAAAAAAATTTGCCAAGCCTGTTGTCCCAGCTATGTGGGAGGCTAAGGCGGGAGGATTGCTTGAGCTCAGGAGTTCCAAGTTCCAGTGAGCCACAATCGCACCACTGCACTTCAGCCTGGGCAACACAGCAAAATCCTGTCCCTAACATTTTTTTTTTAATCGAAGAAACAGCTGCTGTTGACTTAATCACTACCAGTTAGGGCTCTCAAGACACAAGTACAGATACAGTGGCAGAAGGCTGGAGGGTCAGGAACTGGGAGAAACACAACCAGCTCTCCATGGCCAGCATCCCTTTGAGGGCTGGAGGGCTGCCTATTCCTGATAAAGTGGTTCTCAATCATACCCCTCCATGTCCTCCGCCCCCAGTGGCACCCCCTGCCTCAAACTCATTCCCCAGACTTGCCATGGAGCCAGACTACCCACCGTTGCAAAGAATGAGTCTAGCTCTCTGAGCAGTTGCTTCTCTGGAGCGTTTCTTGCAGTTGGGAAAGTCCCTGGTGACCCACGGAGTCAGGGCTTTGCCGCAGACTCTGCTGTCTGAGGCACTCACAGAGGCTGTGCATCTGCCCTCTGCAAACGAAACAAAATTTCTTATGTGTCCTGTACAGGAGACCTGGATTCACCAAATACCAATATTTGCTTTATTTTCATTTTTATTTATTTTTCGAAATGGAGTCTTACTCTGTCACCCAGGCTGGAGTGCAGTGGTGTGATCGTGGCTCACTGCAACCTCCACCTCCCAGGTTTAAGCGATTCTCTTGCCTCAGACTCCTGAGTAGCTAGGACTACAGGCACATGCCACCATTCCTGGCTATCTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGCCCAGGCTGGTCTTGAACTCCAGACCTCAGATGATCCTCCCACCCAGCTGATATTTGCTTTAAAACGTGCCGGAGAAATCTTCTTCAAAAAAGAAGCAGCTTATTGATGAAACAAGGCATGTTTCTTATGGTTTTGGTTTTTTAAAACAGCTCTTAATTTTTGTTTGCATTTCAG
Seq C2 exon
GTAGAAGATGACTGGAAATACGTGGCCATGGTGGTGGACAGAGTATTTCTTTGGGTATTTATAATTGTCTGTGTATTTGGAACTGCAGGGCTATTTCTACAGCCACTACTTGGGAACACAGGAAAATCTTAAAATGTATTTTCTTTTATGTTCAGAAATTTACAGACACCATATTTGTTCTGCATTCCCTGCCACAAGGAAAGGAAAGCAAAGGCTTCCCACCCAAGTCCCCCATCTGCTAAAACTGATGGCTACATGGAAAAAGAGGACTTTCTTGCACATTAGGAAGCAGAATATCCTCCAGTGTAGCACAGGGGGAGAAGTGAGAAGTGTTATGACATTAGTGCCCTGATTGGGCAGCACCCACGGCTACAGTATCAGGTCAGGTTTCTCGTGTCTGTGTGTTTGGCTTCTAAAGACAAGAATGACTTACAATACAGCCTAATTATGTAATTAACATCAAGCCACACTAAAAAGTTCTGCTGTACCTCCAGTGGATGCTGTTTCTCAGTATTATGACATGTGACAGGTGAACTCTGGGAATTGGACCATGCAACATTTGTGAACTGTTTGCAACACTTTGTGAACTATTGCATCCTTGATTTCTTGTGCATGTCTCTGTAATGTAACTCACCCTCCTCAGCATTATTTGATACACTGATTGTTAGTTTTAAAAAAAAAAAAAAAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000147434:ENST00000276410:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=35.2),PF0293211=Neur_chan_memb=PU(86.1=62.4)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.1=70.5)
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:
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]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development