HsaINT0035195 @ hg19
Intron Retention
Gene
ENSG00000169684 | CHRNA5
Description
cholinergic receptor, nicotinic, alpha 5 (neuronal) [Source:HGNC Symbol;Acc:1959]
Coordinates
chr15:78880656-78882978:+
Coord C1 exon
chr15:78880656-78880765
Coord A exon
chr15:78880766-78882146
Coord C2 exon
chr15:78882147-78882978
Length
1381 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
TTTATATGTGTGTATTTTAGTGC
3' ss Score
9.73
Exon sequences
Seq C1 exon
GAATGGATAGATGTAAAATTAAGATGGAACCCTGATGACTATGGTGGAATAAAAGTTATACGTGTTCCTTCAGACTCTGTCTGGACACCAGACATCGTTTTGTTTGATAA
Seq A exon
GTAAGTTATATTCTAAATATAGTTTTATATTTTCAAAAGAAAACATTTGTATTTCTATTAGGCACTAATAATTTTTCTCCCTTTTGAAATTGTTTAGGTATAAAAATCAAATGACATGACCGCATGTGCCTGGGTATGATTACATGTTTTATAGATGAGGAAACAGAGGCTTAGGGTGGTTGTTCTTTTCCAAGATCACAGAGCTAGCACATGGCAGAGTAGGGGGGTCACACCAAGGGGACTGATACCTCCATTTACTCTTTGTTTTACTAGACTACATATTTGGCAGACTTCTAGATTTTTTTGTATGTTTTTTACGTCGTTGAGGTCATATTTTATGTTGAATTGTGCATCCTTCTAGTTGTGTTTAAATACTGTATCGTCATTTTCCCACAATGAGGAATGCTGGGTTAATTATCAATTCATCTTTAGAGGCATCCTACCTAGGTGTGTTTTGAGGATTTTTTTTTTTTTAACTTAGGGGAGAGGAAAATTCTGGGTACCAGTTTTATTTTTTTCTAAGACCACTCCTGGGCAAATCTGGGAATTTGTGCTTATCTTAAAGCACTTTGTCTGATTCGAAAGAAGGCCATTTGGCATGAGGACAGAGCAACTGCTATGCAAAAATATCTTTAATCTTTTGACACTTTTTACCTCCATGCTTCTTAAGAAGTGAACAAAGCTTGTAAGGACACATGATGCAGCTTCCTGGAGCATCATTTTATTTTCAGTAATTGAAAACATTTTTATATTAAACATGGATATATTACAGAATAGTGTGCAAAAGCCACATGAATTTGAAGACAGCAACATTTTAAAGAAATCTTATGTTGGTGGTGTGCTTTCCTAGTATATGGATTCTATACTAGACTTTTCTCATATATGAATTCACTTGGTGGGAGAGCTTGAGAGGCATAGCTGCTTTTCAGGGTCATGCCCAGCTTGGTGTTCATGGTCTTTCCCCATCAAAGTAAAAAACGGCCAGTATTTGCGATGAAGGAAGAAGAGCACTGTGGAGGGAGTCTAGGAGTGTGGATTCAGGTTCTGGCTGTATGCGTGCCCATTGTGTCAATAGCCTGAGTCTATTCTGTGTGTAAGGTGAGGTCTTTTCAATCATTAGAATCTCAGGCTTCTGTGAAAATTTGTCAGTTCTGGAGTAGATGCAGAAGAAGGGGTTCAGTTCTAGTAGAGTTAGATATTTAAGGAAGATATTCCTGGAGCAGGGTCCCTATGTAGCACGTATATCTTATCTGAAGTATAGTAATTTAAAAATTATTTCATGCAATCAATGATAGGCCTGCTTTTATATTAGGCTTATATTAATACAATTCATGTGCATTGTTTAATTTCTGCATTGTTATTTTATATGTGTGTATTTTAG
Seq C2 exon
TGCAGATGGACGTTTTGAAGGGACCAGTACGAAAACAGTCATCAGGTACAATGGCACTGTCACCTGGACTCCACCGGCAAACTACAAAAGTTCCTGTACCATAGATGTCACGTTTTTCCCATTTGACCTTCAGAACTGTTCCATGAAATTTGGTTCTTGGACTTATGATGGATCACAGGTTGATATAATTCTAGAGGACCAAGATGTAGACAAGAGAGATTTTTTTGATAATGGAGAATGGGAGATTGTGAGTGCAACAGGGAGCAAAGGAAACAGAACCGACAGCTGTTGCTGGTATCCGTATGTCACTTACTCATTTGTAATCAAGCGCCTGCCTCTCTTTTATACCTTGTTCCTTATAATACCCTGTATTGGGCTCTCATTTTTAACTGTACTTGTCTTCTATCTTCCTTCAAATGAAGGTGAAAAGATTTGTCTCTGCACTTCAGTACTTGTGTCTTTGACTGTCTTCCTTCTGGTTATTGAAGAGATCATACCATCATCTTCAAAAGTCATACCTCTAATTGGAGAGTATCTGGTATTTACCATGATTTTTGTGACACTGTCAATTATGGTAACCGTCTTCGCTATCAACATTCATCATCGTTCTTCCTCAACACATAATGCCATGGCGCCTTTGGTCCGCAAGATATTTCTTCACACGCTTCCCAAACTGCTTTGCATGAGAAGTCATGTAGACAGGTACTTCACTCAGAAAGAGGAAACTGAGAGTGGTAGTGGACCAAAATCTTCTAGAAACACATTGGAAGCTGCGCTCGATTCTATTCGCTACATTACAAGACACATCATGAAGGAAAATGATGTCCGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169684-CHRNA5:NM_000745:4
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=0.016
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(54.9=40.3),PF0293211=Neur_chan_memb=WD(100=46.0),PF0293211=Neur_chan_memb=PU(58.2=16.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAACCCTGATGACTATGGTGG
R:
CTTTGCTCCCTGTTGCACTCA
Band lengths:
354-1735
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)