HsaINT0035187 @ hg19
Intron Retention
Gene
ENSG00000101204 | CHRNA4
Description
cholinergic receptor, nicotinic, alpha 4 (neuronal) [Source:HGNC Symbol;Acc:1958]
Coordinates
chr20:61990900-61992695:-
Coord C1 exon
chr20:61992442-61992695
Coord A exon
chr20:61991052-61992441
Coord C2 exon
chr20:61990900-61991051
Length
1390 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGT
5' ss Score
11.37
3' ss Seq
TGGCCTGCCTCTCCCCGCAGCCA
3' ss Score
11.58
Exon sequences
Seq C1 exon
AGCCCGGCGCTCCCTGCCGCGCCGCCGCCGCACCGCGCCCCACAGGAGAAGACGAACCGGGCCCGGCGGCCGAAGCGGCCCGCGAGGCGCGGGAGGCATGAAGTTGGGCGCGCACGGGCCTCGAAGCGGCGGGGAGCCGGGAGCCGCCCGCATCTAGAGCCCGCGAGGTGCGTGCGCCATGGAGCTAGGGGGCCCCGGAGCGCCGCGGCTGCTGCCGCCGCTGCTGCTGCTTCTGGGGACCGGCCTCCTGCGCG
Seq A exon
GTAAGTTACGGGGCGCGGGATGGGCCCCCTTTCGCCCGCGTTCGGATGGCCTGGGACCCCCAGAGCCAGAGGGAGGCAGGCTCCTGACTGCGGTCCCAAGCCGCGGGTGCGCGCGACTGGGCGACCGCGAGGCTCCCCATCCCCAGCCGCACAGGCTGCGCTCGCACCCGGGCTGAGCCAGGCGAGGAGGGAGTTGACCGCCGGCGAATGCGGAGGGCTGGGAAAGGGGCTTTCCGCGGGGTGTGGGGGGTTCCGCTGCTATTTCAGGGCTGGCCCCAAAAGCTCGAACTTGAGCAGAGGTGGGGCCACCTTCGCCCTTCCCCCATCCATCCAGCTAAATTTCCCTGAAGACCCCCATGCCTGCTTCCTCCGGTTTAGGGGATCAGAGGGGTGGCCTCTGCCCTTGGCGGCCGCCACCCACCTTTTCTGCAGGAAGGACAAGGTCGCGGGTGGGGACTCTGGGCTGGGAGTCAAGGCTCCCAGGGGTGTAGAACTGACCCCTCCCCCTCCCCGAGTCCTGTCTGCGCTCTCAGGCCAGCGGGACCCACCAGGGAGGTGGAGGTCTCCCCCTCCGCCCAGACCCGCCCCTTATGGCAGCGCCCAGGACAGGCGGGGAATGCCTCAGATCCTGGGGCCCCGGACCTGGAGCACAGATGGACCTAGGGCTGTGCTCCTCCAGAGCGACTCATCAGGGGCGTTCTGGGTCTGCCCAACAGCACGGGCAGGCTGGGGTGCGGAGGGGGCTGGCACCTCGTTGGGGTCTGCATCTGAAACACTCCTCGGGCATCAGGGGATTGATGAACCAGGGGAGGTTCCGTAGGAAGCGGGCGCTTGTGGGGGCCCGATCCTCCTTCCCCTTCCTCCCTCTTCCTGCCTGGGCTGGCCCCGCTGCCCTGTACTCCCTCCTTTGCTGCTGTTACCCCCGAGTGTCCTCTGACTCGCCAGCTGCTAGAGACACAGCCCTTCCCTGGAAGTCAGTGTGACAGGAGACCCAAAGCAGTCCTCGGCCCATCCGCCGCCTGGTTTTGTGGTGCGGTCAAGGTGCTGGGAAGGCCTCCGTGGGCTGAGGGGCCTGGGAAGCTTCCCCGAGGAAATCACAATTACACCCAGGGGTGGGAGAGAGCCGGAGGCCAAGAGAGGTCAGCGCACGCCACGCCCGGCACACACACACACACACACACACACACACACAGCACACGCCCGGCACACACACACACACAGAGCGCACGCCCGGCACACACACAGGTCCTGGGGTGGGAAGGGCTCATGTGAGGAGCTGAAAGGAAGTGGACGTGCTGGGCAGGGGGCTGGGGCAGCCTGGAGAGCTCCTGGACAGCTCCCGGCTCCTGTCCCGCCTGCACCTGAGCCACTGGCCTGCCTCTCCCCGCAG
Seq C2 exon
CCAGCAGCCATGTGGAGACCCGGGCCCACGCCGAGGAGCGGCTCCTGAAGAAACTCTTCTCCGGTTACAACAAGTGGTCCCGACCCGTGGCCAACATCTCGGACGTGGTCCTCGTCCGCTTCGGCCTGTCCATCGCTCAGCTCATTGACGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101204-CHRNA4:NM_000744:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.029
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=76.5)
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:
ACAGGAGAAGACGAACCGGG
R:
ATGAGCTGAGCGATGGACAGG
Band lengths:
358-1748
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)