HsaALTD0001435-2/3 @ hg38
Alternative 5'ss
Gene
ENSG00000169684 | CHRNA5
Description
cholinergic receptor nicotinic alpha 5 subunit [Source:HGNC Symbol;Acc:HGNC:1959]
Coordinates
chr15:78589810-78595269:+
Coord C1 exon
chr15:78589810-78589849
Coord A exon
chr15:78589850-78590098
Coord C2 exon
chr15:78593092-78595269
Length
249 bp
Sequences
Splice sites
5' ss Seq
CTGGTATCC
5' ss Score
2.3
3' ss Seq
TTTTATTTTTTTCCTAACAGGTT
3' ss Score
12.17
Exon sequences
Seq C1 exon
ATGGACGTTTTGAAGGGACCAGTACGAAAACAGTCATCAG
Seq A exon
GTACAATGGCACTGTCACCTGGACTCCACCGGCAAACTACAAAAGTTCCTGTACCATAGATGTCACGTTTTTCCCATTTGACCTTCAGAACTGTTCCATGAAATTTGGTTCTTGGACTTATGATGGATCACAGGTTGATATAATTCTAGAGGACCAAGATGTAGACAAGAGAGATTTTTTTGATAATGGAGAATGGGAGATTGTGAGTGCAACAGGGAGCAAAGGAAACAGAACCGACAGCTGTTGCTG
Seq C2 exon
GTTGTTGAAGATTGGAAATTCATAGCCCAGGTTCTTGATCGGATGTTTCTGTGGACTTTTCTTTTCGTTTCAATTGTTGGATCTCTTGGGCTTTTTGTTCCTGTTATTTATAAATGGGCAAATATATTAATACCAGTTCATATTGGAAATGCAAATAAGTGAAGCCTCCCAAGGGACTGAAGTATACATTTAGTTAACACACATATATCTGATGGCACCTATAAAATTATGAAAATGTAAGTTATGTGTTAAATTTAGTGCAAGCTTTAACAGACTAAGTTGCTAACCTCAATTTATGTTAACAGATGATCCATTTGAACAGTTGGCTGTATGACTGAAGTAATAACTGATGAGATACATTTGATCTTGTAAAAATAGCAAAATATTATCTGAACTGGACTAGTGAAAAATCTAGTATTTGTATCCTGGCAAATAATACTAATTTATAATCCACAGTAAAGTTCATCCTTTGACTGTGCTGGAGAATTCCAGTTGTATTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169684-13-11,14-11,15-11-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(13.3=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(39.2=57.4)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGACCAGTACGAAAACAGTCA
R:
ACTTAGTCTGTTAAAGCTTGCACT
Band lengths:
306-555
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains