HsaINT0035211 @ hg19
Intron Retention
Gene
ENSG00000174343 | CHRNA9
Description
cholinergic receptor, nicotinic, alpha 9 (neuronal) [Source:HGNC Symbol;Acc:14079]
Coordinates
chr4:40337844-40339381:+
Coord C1 exon
chr4:40337844-40337989
Coord A exon
chr4:40337990-40339226
Coord C2 exon
chr4:40339227-40339381
Length
1237 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
CATCTGGATTCATTGTGTAGGAT
3' ss Score
6.05
Exon sequences
Seq C1 exon
CTGCAGAGACGGCAGATGGAAAATATGCTCAGAAGTTGTTTAATGACCTTTTTGAAGATTATTCTAATGCTCTTCGTCCAGTGGAAGATACAGATAAAGTCCTGAATGTGACCCTGCAGATTACGCTCTCTCAGATTAAGGATATG
Seq A exon
GTGAGTAACACATGGTGCTGACTCTGTGGAATGATTCTTAGAGGATAAACAACCATGCTTTCTGAAGAGAATGTCTTAACTGGGAATTTGAGAGGGAATGATAGCTCCTTAAGCAAGCTGGTGGGAGAAGAGAATGTCGGGAAAAGGAAGCTTTCTACAAAACTAATTAATTTCAAGAAACGTTACCTAATCCTGGTCATTAACTGTAACAGTCTTAGATAATCTAAAGAAAGATGGGGTTACATACTGTATGCAGCCATTTATATAAAATGTCCAAAAGAGGTAAATCCGTAGAGACAGAAAACGGCATAGAGGTTGCCGGGGTCTGTGGGGAGGACGGGGAAAACGGCCAGTGAGTTCTTAATGATTACGGCGTTTCTTTGCGGGGGGAAGAAATGATCTTGAATTAGGCAGTGGTGATGGTTGCACAACGTTGTGAATATATTGGAAGCCGGTGCATTGTTCCCTTCGAAAATGATTAAAATGGTGAGTTTTAATGTGAATTTGATCTTAATTTTTTTTTTGAGACGGAGTCTTGCTGTCACCCAGGCTGGAGTGCAGTGGCATGATCTCCGCTCACTGTAAGCTCTGCCTCCTGGGTTCACACCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGAGACTACAGGCACCCGCCACCACACCCGGCTAATTTTTTTTTTGTATTTTTAGTAGAGACAGGGTTTTACCGTGTTAGTCAGGATGGTCTCAATCTCCTGACCTCATGATTCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCGCCCGGCCAATCTCAATTTTTTAAAAAAGGTAGTGTTTTAAGATGGCATAGCTTATTAGTGCTTATCTATGTTTAATTACACAATGTTATGAAACTTGAAAGATTTTCCTTCTGCACATTGTTATTTCCTGACTTTTGCTTTCAAGTACATCATTCATTGATCAATTTTCAGGAAATATAGGCAGTTGATCTATGCAAAGATATCAATACTAAAATATTTGTCCACTTTACATTCTGAACACTAAATCTAGGAGGAAAAAAAATATGATCTTGGCAGTCAATCAAGGGGATAGAATAAATAAAGAATAAAGCTCTCACTTTACTTATTGAAATTTGATGAGTGTTTGTGAAATTCCTATTGTGAAGAACAAGTGTCCTATCAGTGGAAAACATTTCAAGTGTCTGCTAGGTAAAGCGACATCTGGATTCATTGTGTAG
Seq C2 exon
GATGAAAGAAACCAAATTCTGACTGCTTATTTGTGGATCCGCCAAATCTGGCACGATGCCTATCTCACGTGGGACCGAGATCAGTACGATGGCCTAGACTCCATCAGGATCCCCAGTGACCTCGTGTGGAGGCCAGACATCGTCTTATATAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000174343-CHRNA9:NM_017581:2
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=0.000
Domain overlap (PFAM):
C1:
PF039817=Ubiq_cyt_C_chap=FE(57.8=100),PF0293118=Neur_chan_LBD=PU(35.8=79.6)
A:
NA
C2:
PF039817=Ubiq_cyt_C_chap=PD(22.9=36.5),PF0293118=Neur_chan_LBD=FE(46.8=100)
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:
GCAGAGACGGCAGATGGAAAA
R:
ATATAAGACGATGTCTGGCCTCCA
Band lengths:
294-1531
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)