HsaINT0035235 @ hg19
Intron Retention
Gene
ENSG00000117971 | CHRNB4
Description
cholinergic receptor, nicotinic, beta 4 (neuronal) [Source:HGNC Symbol;Acc:1964]
Coordinates
chr15:78923630-78927929:-
Coord C1 exon
chr15:78927781-78927929
Coord A exon
chr15:78923675-78927780
Coord C2 exon
chr15:78923630-78923674
Length
4106 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
3' ss Seq
AGCCCCGTTTCCCTCCCCAGAAT
3' ss Score
9.46
Exon sequences
Seq C1 exon
GGAACTGCCGCGTGGCCAATGCGGAGGAAAAGCTGATGGACGACCTTCTGAACAAAACCCGTTACAATAACCTGATCCGCCCAGCCACCAGCTCCTCACAGCTCATCTCCATCAAGCTGCAGCTCTCCCTGGCCCAGCTTATCAGCGTG
Seq A exon
GTAGGTGCAGAGGGCAGCTGTGGCTCAGGCTCAGGTGGAGAGGCCGCTCATGCCCAAGCCCCAGGCGATCATTGGTCAAAGGAATGAAACTACTATAGTTGACTTAGACTTACCAGTACGTGTCAGGGAGGCTGCAGAAGGGTCCATGAAGTTCATAGGTGTCCAATATTTAATGAAGTCATGATTTTGTTCTAACAAAGAAGAAATGAGGGTAGGAGCAGGATGACCATTGGGTAGGCAGCCAATGGGCCTGCTGTAGACTCTGCTCAGCTGGGTCTCCAGCATGACCATAAGCTTCTCCTCCTTGTCTTTACAGCCCCACCCTATTCTCTCCCCTAGACTGCTCAGATAACCTTACATGCTTCTTACTTGTTGGGAGAAGTAAAAACCAGACTGGGGGAACTGATAGGTACAGAGAGGCCCAGGTGTAGGGGCAGGACCAGAGGCAGTGCAGCACCTATTGAGCCAGGCTGGTGAGGGATGGACAGTGGGCGTGGCTGCTGCAGGCATGGAAAGGAGGAGTGGATGGCAGCATTCACAGGTACCATTGTCAGGTTGTCCATATGTGGATGTGGGGCAGAGGTGGGGGTGCTGAGGGAGGAGGTGCCTGGGAATTTCTCTTCTCTTTGCTGCCTCTGAGTTGGAGATGTCAGAGGGAACCATGGCCTATTGTAAACCTTCCCATGTCCCCATCCACAGGGTTAGAACTCCGTCCCTGGAAGAAGCTCTGGGGGAACATTCACAAGGGGAGAGTGCAGGGCGCTGTGTCCAGCCAGGGGAAAGAGACCACCAAGGGGGCTGACCCTCCTCTGGCCAGGTAGCTGCCTTCTGAAATGCCAGACTCTCTCTCTAGCACGGTTGGCCCACACACACCCAGCCTGTCAAACCTACAGCCCTCAGGAAGGCTTTGGCCAAATTAATGACTGGCTCCATCTCCTGGGAGGACGCACAGCCCCAGGATGGGGAGGGCTGGAGAGCTGTGTACTCTCTGCCCCTCTCCCTCCGTAGTCGGACCAGAAGGAAGGAGGGCTTTCAGCCAGGCTTGCTCAGGCTGGTGTCTGAGTGTTATTGTCCAGCCCAGGGCTTCTTGCTTAATGAGTTGAACCCAGCTGCTGCGGTGCAGCTGCTGCCCTAGTGAGGGTGAACGAGCAGGAGGCTCTGCCGCACTTCCAGACTCAGGCTACCTGGTCAGATCTGCTCTGCCGGCCCTATAGGGTGATAGCGGCTACCAGAAGGAGGAGGGGATGCGGCCACCAGCCCCCACCCATGCAAGTTATATTTCCGAAAGCTTGTGTATACAGTAAATATTAGGTTGTGGGTTGCCAGGGTTTGTTTATTTATTTGAGGAGGGAGGGTTATAGGTACAACCAGTTTAAAGATGGAAATTTTTAGAGAGCAGGTAGGGATTTAGGGCTGGGTAAGGAAAGCAGGCTTGTCAAAGCAGCTGTTTTGTCATTGACTCCAGAGTCTGGTGAGCCAGGCACTCCCTCGCCAGCATCCCCACCCCCACCTCTCCAGCCCCCCTTATTCCCTGACCCTTCCACCTGCTCCCCTGCCCCAGCACTGTTTCCTCTGCTGACTCTCATCTCTTTTCCTGCTCCTGGGCTTGCCTGTTTTGATGTCCTTGACTCTCCTCTGAGTCTTCCTCTTTCCAAGCCATCTCCCCTGTACTTGACACATTCTCCTGGAAGACACCAGAGTACACAAGCTCAAGTCCCTGAACCTCGTCTTTACTCCCAGACATGTGAGGAAAATGACATAAAGACCCAAATGCCACTTGGCAAGAGATCGGGGGTATGCAGGGGGGCAGATCTGATGCTGTGGAAGCTCAGGGGGTAAGTTTGAGCCCAAATATATCAGTAACTACATTAAATGTAAATGGCCTAAATATTCTAATCAAAATGAGACAAATTGCCATGCATTCTTCTTCTCCCTCCTCCCTTCCCACCAACAGCCTGGAATGTGGAATTTGTGGTTAGAGCTCCAACAGTTATTTTGATCCATTCTTATGAGGGCCACACTCTAGGTATGGTGGAGAAGAAAGTTGGAAAGAATCTGGGTACCTATCAGAACTTTGTAGAGCAGAACTGCCATATATGTCTAAAGTGTTAACATGAGAGGGACATGAATTTCTACTTTATTTAAGCCTGTGTTACTCTGGATCACTGTTACTGGCAGCCAAACCTTATCTTACTGATAATCTTATCTAGTTGTAGGTTCCTTGAGGAAATGACTCCCAAAGTGAGATCAGTATGCTGGAAGTTATCTTGATAAAGGAGAGGCACCAAAATTGTACAGACTGAGAACACAAGACTTATCCAAAGTACTAAAGAAGGCCAGGGGGCTGGAGGACAGAACAGAGGGACATAGGGAGGTGAAGTGAGGCTGGGAAACCTGGCAAGGCCCCGTAGACCCTGCGAAGGAGCAAGATTTTTATTCTGTAGGTGAAGGAAGCCAAGGAATTAATCTAAACAGGGATAAAATTGAGGGAGGAAATGACAGGAACTTTGGAAGGTTTATTTGGGCTGCGTACGAAGAAGAGATGTATGTGTGTGTATGGTGGCGGTGGTGGTGGTGTACAGAATGAACATAGGCCAGTTAGGAGGGTCTTACATGGTCCAGGTGAGACATGGATTATGGTGGCCTGGATTATTATGGTAGGATTCCTGTATATTCAAAAAATATTTATGGAGTATCCAACATGTTACATACTCTTCTATCTGCCTTATTTTCTCATAGCCATTAGATTCTAGTGGGAGGTGGCAGACAATACACAGATAGATAGATGGTGTTTAGGGGTGAGAAATGCTACGAAAAAAAAATAAGGAGACTGGGTGAGGTGGCTTGTACCTGTAATGCCAGCACTTTGGGAGGCTGAGATGCATGGATCACTTTAGCTCAGGAATTTGAGACCAGCCTGGGCATCATGATGAATCCCCATCTCCACAAAAAATTTTTTAAAATTTAGCCAGGTATGGTGGCCTGTGCCTGTAGTCCCAGCTACTCAGGAGCCTGAGGTGGGAGGATCGCTTGAGCCTGGGAGGTGGAGGTTGCAGTGAGCAAAGATCACACCACTGCCCTCCAGCCTGGGTGACAGAGTGAGACCCTGTCTCAAGAAATACACACACACACACACACGAAAGAAAAGAAAGAAAGGGAGAAAGAAAGAAAGAAAGAAAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAGAAAAGAAAAGAAAGACAGAAAGAAAGAAAGAAAAAGAGAAGGCAGGGCAGGGACCGAGGTGCTATTTTATGTAGGTCAGGGAAGATTTCTCAGATAGGATGACATTTCTGATAACAGAATAAAGTGTGGAAGCATCCCAGGGGGTTTCCAGGAAAAGGGAACAGTGTGTGCAGGAGCAAAGAGGCAGTGCAGGGGAAGTGGAATGAGCAAATGGCGGAGTGTTGAGATAAGAGGTCATAGAGCTAATGGGATGAGGGGTGGTGGGGAGGCAGATCACTAGGGCCTTGTGGACTCTAAGCAGAACTTTGGCTTTTACTTTGGATGAGATGTGGCAGCAGAACAATTAGTAGAAGGGATTGAGATTGTAAAGGGATCACCCTGGCTACCATGTAGAGAATAGACTAAAGGCAGGCCAGGACAGAGCAGGAAGACCAGTTAGGGGGCTCCTGCGGTAGTCTAAGTGACAGATGATGGTGGCGGTGGAGAGAAGCAGACAAATATGAGTTGCTTTAGAAGATATAGCTTACAAGACTTATTGATGGATCAGAGAGCAAAGTGTCAGAGACAGTGTCCACGCTTCTGGCTTGTGGAACTGGATGGCTAGGGGTGCCATTCACTGAGACAATGAAGCCAAAGGAGGACCAGGTTCTGGGGAAGATCATGAGCTTTGTGTCAAACATGCTGAGTGTGACATGCCTTTGGGCCATCCAAGAGATGTTGGGGTGGCAGTTGGTCACGTGGGCCTGGAGCTCACAGCCTTTTGCACAATAAAGTGCAATCCATTTGTGAGGCTCCTCCTTCCTGGTGAACTGATAGCCCCGTTTCCCTCCCCAG
Seq C2 exon
AATGAGCGAGAGCAGATCATGACCACCAATGTCTGGCTGAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000117971-CHRNB4:NM_000750:2
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:
PF0293118=Neur_chan_LBD=PU(19.9=82.0)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(13.9=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
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)