HsaINT0035188 @ hg38
Intron Retention
Gene
ENSG00000101204 | CHRNA4
Description
cholinergic receptor nicotinic alpha 4 subunit [Source:HGNC Symbol;Acc:HGNC:1958]
Coordinates
chr20:63356371-63359699:-
Coord C1 exon
chr20:63359548-63359699
Coord A exon
chr20:63356416-63359547
Coord C2 exon
chr20:63356371-63356415
Length
3132 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
3' ss Seq
TTCCTCTCTCGGTGCCCTAGGAT
3' ss Score
9.61
Exon sequences
Seq C1 exon
CCAGCAGCCATGTGGAGACCCGGGCCCACGCCGAGGAGCGGCTCCTGAAGAAACTCTTCTCCGGTTACAACAAGTGGTCCCGACCCGTGGCCAACATCTCGGACGTGGTCCTCGTCCGCTTCGGCCTGTCCATCGCTCAGCTCATTGACGTG
Seq A exon
GTAGGTGAGGGCGTGGCCATCGTGCACTGTGACTGAGGTCGCCCTGCAAGGAGCACAGGGGTCTGGGTGGGCAGAGGGGACACAGCCATCAACACTCCCCGTGGCTGTGAGTGTCCGGCCCGGGCTGGTACGTCAGAACGACAGCCACCAGCTCTGCCCCGCCTGAGCCCCAGCCAAGGGTTGATTCAGAGCGTCCCAGCCAGGCCCTGCCCTTTCCTCCCCCTTGACGTGGGAACACTCCAAGTGGCCAGGTTCTCAGTACAGAGCCCAGGCACCTTCGGAAGCAAAGAACAGCAAAGGCCTTGCTTGGGGGTGGCGGGGCACGCTGTGACCTCGGAGCAACAGGGACAACCGGCCGGGGCAGGGGCCGGGGCAGGAGCAGGCACTGTGGTGTCCCGGCAGCACCCCAACCTTAGCTGGCCCCAGAGGCCCCTCACCCACAGATCTGGAATGTGGGGTTTGGGGGAGTCTTGGGCGAAGTCTGTTTGTCTGAAGATATGTTCTTTCTGGTGGGGGGCCCAAGAAGGCTGCTGGGAGGAAGCCTACTGGTCCAGCCAGGCCCCTGCAGCGTGGGCCAGTGCACATGGAGCCCCAAGGCAGGATAGGAACCAGGAGGCTTCGAGGCTGAGAGAACTGAGCTGCGGGAGGCTCGGCCTTGTGCTCGGTTGAGATGCTTGGTTACCTACCCAGGCCTGAGCCAGACTGTCTGGGGGTCTCGGCGGCCCTGGAGGGGCCGGGTAAGGGGCAGCAGAGACATTTCCACGTTTCCCAGCCAGGCTCAGCCACTCCAAATGGGGTGAGACCATCCCTCAGGGTACCTGGCTGGGTGGGGGTGCATAGCCTGGGGGCTGCCACCATGGAGGAGGGCAGGTTGGGCAGGCCATGGTCTCTGGGAGCTGGCCCACTTGCGAGTGGGCAGCCAATGGCCAGCTGAGCTGCAGGGGCTCGTCTTCCACACTGAAGTCCGCCAGCTCCAGCCCTGCTGCCAAATCCCAGCTCGCTGGTCCAGGGAGGGCACCCCCACATGGGGAGGCATTTGTATGCTGTAGAGGCCCAGCCCACACCTTGCCAGGATGCCAAGCCTGGGTCTGCCGCTGAGGGAGGAGCCACCGGGTTGCGGGAGAATTTCCTCTCTTTGGGAGGCTGGTGCCGTGCGTGTTGGGTAACCCTGGGCCTGGGGCCTGTGAAACGGGGTGAGAGCTGCTTCACTATCCCAGGCTGAGTGGGCCACACCCCAGGGGCTTTTGGGAGGTGTGGGGAGCTGCAGCCACATTCCCGCGGACAGGCTGCTCAGTGGTGGCAGTTGCCCATGCAGGGCAGCGCATGGAGACTCCAGTCAGCCAGCCCCGTCCAGGGTTGGCCACCCAGACCTCCAGCCTCAGTGTCCTGGAGCTGCCCTTGAGTGGCTCCTGTGGAGTGTCCCTGGCGGAGGCCCAGCCAGAAGACAATGCGGGTTGCACAGGCTTGGCAAGCCTGCTGAGGTTTGCAAACACGGCTGCAAAGTGATAGCTGGCAGAGGCGGCCGCTGGCAGCTGCCCAAGGCTCTGGGTCTGCCACCCCCCACCTGGCTGCCTACCTGAGCTTCTCAGGGCTCAATCCATGGCTCCCTACGCCACCACAGAGTCCCCAGTTTGCCCAGGAGACATTGAGGCCTGGAGCACACCCAGAACCAAGACTCCCAGAGCTGCCCACCCCTCTCTCCACCCTGCAGCCGACTAAGGACTTACACGAACATGCACACGTGGGTGCTGACGCTCCTGGGTGCCCAAGGCCGAGGGCCACGTGTGCACGGAAGGGGCTGCCTGATGCTCCTGGGTGCTGGCCTAAGGCTGAGGACCACGTGTATGTGGAAGGGGCTGCCTTGTGTCTGGCCCACTCTGCCCGTCCCACCAGGGGCTGGGGATTCACCTGTGCCCCCTTTGCGGGCTCGGATACTTGTTATAGGTGCCATCACCAGGGTCTGTCCTGGAGGGGAGGGCTTGTGAGCTGCACGTGTGAGCTCAGGCCCCAGGACTGGCTGCAGAGGAGGGTCTGGAAGACCCAGTGCTTTTCCAACCAGCCCAGGCCAGTGCTGAGTGGTGGTGAAATGTGCAGTGTTGACCTGCCCTCCAGCTTCAAGGGCGACTGAGAATGACGGCTGCAAGGGGGTAGGGCACGACACTGGGCAGGAGGGCCAGGCCTGGCCACGTGAAGCTGGTTCTGAGGACCCTGGAGCTTCCTCAGACACACGGGATGAGGTCCTGAGGGGATGAGGTCCTGTGGGGAGATATGGCCCTGCACGGAGACATGGTCTGTGGGGACGTGGTCTGTGGGACGTGGTCCTGTGGGGACATGGTCAGTGGAGATGTGGTCCTGTGGGTTGTGGTCCTGTGGGAATGTGGTCCTGTGGAGACGTGGTCCTGTGGGGACACGGTCCGTGGAGACGTGGTCCTGTGGGAATGTGGTCCTGTGGGGATGTGGTTCTGTGGGGACGTGGTCCGTGGAGATGTGGTCCTGTGGGTTGTGGTCCTGTGGGGACGTGGTTCTGTGGGGATGTGGTCCATGGAGATGTGGTCGGTGGGGACGTGGTCCTGTGGGGATGTGGAAGGAGGTGGGTGGGGTGGGTCGGAAGGGGCTGGGGTGAGTGGCCCAGCTGCACACAGTGACCTTGAGTGACAGGTCCCACCTGCTCAGGTCATGAGGCACAGTCCTGGAGGGGCCACCCTGGCCAGCAGTGGAACCCACTTATGTGCCAGGGGCAGCTTTGCTGGCTGTGTGTGCCCACATGGGGGCCTTGTCTGCAGAGGGGCTGCCCCCAAGGGCCGGGAGGGAGCAAGGCAGGTGGGCAGAAGGAGGCTCCCCATGCCCGCCACACCTGTCCTTAGCTGGGGAAGCCTGTGAGGCCGCCGACTCCTCTCCAGTTTCCTGCTGGAGATGTTTGTGGCCTTGTCCCCACATCCCTAGGTCCCCTCAGAGTCCCCATCCTGGGCTCGGCTGCCTCCAGGGACGGGGCACTCACCCCCTCCACAGGTCGCCCGTCCACCATATCTTGCCCTGGCCGTGTCCTTGTGCCAGTGGCTGTAGATGAGGAAACCTAGGGCCAGAGAAAGACACCAAGGGGTCACTGGCCCCCTTCCTCTCTCGGTGCCCTAG
Seq C2 exon
GATGAGAAGAACCAGATGATGACCACGAACGTATGGGTGAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101204:ENST00000370263:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.131
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(18.8=76.5)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(14.1=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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