HsaINT0035251 @ hg38
Intron Retention
Gene
ENSG00000108556 | CHRNE
Description
cholinergic receptor nicotinic epsilon subunit [Source:HGNC Symbol;Acc:HGNC:1966]
Coordinates
chr17:4897774-4899107:-
Coord C1 exon
chr17:4899001-4899107
Coord A exon
chr17:4898892-4899000
Coord C2 exon
chr17:4897774-4898891
Length
109 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGA
5' ss Score
4.3
3' ss Seq
CTGTGCCGACCCTTCCCCAGGAA
3' ss Score
9.13
Exon sequences
Seq C1 exon
CTGCCTTCTGCCAGAGCCTGGGCGCCGCCGCCCCCGAGGTCCGCTGCTGTGTGGATGCCGTGAACTTCGTGGCCGAGAGCACGAGAGATCAGGAGGCCACCGGCGAG
Seq A exon
GTGGGACAGGAGCCAGAGGCGGGTGGAGCGAGGCAGAGGCCCACCACTGTCTCCCATGCCGCTGGCTCCTGCAGCTGCCTCTTTACTGACTGTGCCGACCCTTCCCCAG
Seq C2 exon
GAAGTGTCCGACTGGGTGCGCATGGGGAATGCCCTTGACAACATCTGCTTCTGGGCCGCTCTGGTGCTCTTCAGCGTGGGCTCCAGCCTCATCTTCCTCGGGGCCTACTTCAACCGAGTGCCTGATCTCCCCTACGCGCCGTGTATCCAGCCTTAGCTCGCACCGACTTCAATTTCCCACCCATCTCCAGTAGGAAATTGATTTTGAAAAAGTAGGCTGCCGCCACCACGGCATTATGATCCCTTCCCCCTGCTGATCAATCTGCAGTTTGTGAACTTCACAAGAATGGTGTGTGCCCGTTCCCTGGCGTGTGTAGGCCTGGCCGCAGTCCAGGGGTCAGCAGGAGGAAAGGGTTCACATAGGCTCTCAGGTGCCAGTCTTCCAGAAAGCAAGGACTGCCCTTCATTCAGCCTTGCTGACCTCCCAGCCTTTCTAAGGCTCAGCCCCACGGGACTCTGGTGGCTGCCAGCTTGTGAGCTATCTATCTATATTCATTTCATAGCCAAACAGGAGACCCCTTTGCAGGACTTGCACACAGGGAGGCTGTAGCCAGGAAACCCTCTTCTTCCCTGGTCTGGCTCTGCTGGAGCGGGTGGGAACCAAACACCTTCAGTGCTGGTGGCCCTCAGGCCCACAGGTTTAAGGCTGAGGCTGCCCTGACCCTTCCACAGTCATTTCTTCTAGGTTTTCTTGGCCCAGCACTGCCCATCCCACCCCATGAGGCTCACTCATTGCAGATCCCAGCCCACCCTGCCCCTTTCTTCCCCACCCTGGAGGCTCTCTCTGCCTAGTCTACAGTACTGACAGAAAGCAAGGACATGCGGCCTGCATGGTGGGAGCTGGTTGAATTGTCTTTATTAACAAACAGGATATCCAAGGCCACTACATTGAGGAGGGGTGGGGGGGGAGGGAGAAGGGTTACTTGCTGCTCACACTATATACAGATGCAAGCAAGGGGCGTGGAGAGTGAGGGCTCCCTGCTCCCTCCCTCCACCGGGGAAGGGCATGGGCTAGAAGAGGAGAGGGGGGTCGGGAATGGGGGGAATGTTTTGGCTGGCGGGGTCCCCCCTCCATTCCCTGGAGTTTGGGGGAAGGGGAATCATTAAAGTGCTTTCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108556:ENST00000293780:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.056 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(15.4=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.6=59.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGTGGATGCCGTGAACTTC
R:
CCTACTGGAGATGGGTGGGAA
Band lengths:
254-363
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