HsaINT0035187 @ hg38
Intron Retention
Gene
ENSG00000101204 | CHRNA4
Description
cholinergic receptor nicotinic alpha 4 subunit [Source:HGNC Symbol;Acc:HGNC:1958]
Coordinates
chr20:63359548-63361343:-
Coord C1 exon
chr20:63361090-63361343
Coord A exon
chr20:63359700-63361089
Coord C2 exon
chr20:63359548-63359699
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:ENST00000370263:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.011 A=NA C2=0.015
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