HsaINT0035238 @ hg19
Intron Retention
Gene
ENSG00000117971 | CHRNB4
Description
cholinergic receptor, nicotinic, beta 4 (neuronal) [Source:HGNC Symbol;Acc:1964]
Coordinates
chr15:78916636-78922287:-
Coord C1 exon
chr15:78921309-78922287
Coord A exon
chr15:78917634-78921308
Coord C2 exon
chr15:78916636-78917633
Length
3675 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
ACTCCTCTGTCTGCCTGCAGGTC
3' ss Score
13.32
Exon sequences
Seq C1 exon
CGCCGACGGGACCTATGAGGTGTCTGTCTACACCAACTTGATAGTCCGGTCCAACGGCAGCGTCCTGTGGCTGCCCCCTGCCATCTACAAGAGCGCCTGCAAGATTGAGGTGAAGTACTTTCCCTTCGACCAGCAGAACTGCACCCTCAAGTTCCGCTCCTGGACCTATGACCACACGGAGATAGACATGGTCCTCATGACGCCCACAGCCAGCATGGATGACTTTACTCCCAGTGGTGAGTGGGACATAGTGGCCCTCCCAGGGAGAAGGACAGTGAACCCACAAGACCCCAGCTACGTGGACGTGACTTACGACTTCATCATCAAGCGCAAGCCTCTGTTCTACACCATCAACCTCATCATCCCCTGCGTGCTCACCACCTTGCTGGCCATCCTCGTCTTCTACCTGCCATCCGACTGCGGCGAGAAGATGACACTGTGCATCTCAGTGCTGCTGGCACTGACATTCTTCCTGCTGCTCATCTCCAAGATCGTGCCACCCACCTCCCTCGATGTGCCTCTCATCGGCAAGTACCTCATGTTCACCATGGTGCTGGTCACCTTCTCCATCGTCACCAGCGTCTGTGTGCTCAATGTGCACCACCGCTCGCCCAGCACCCACACCATGGCACCCTGGGTCAAGCGCTGCTTCCTGCACAAGCTGCCTACCTTCCTCTTCATGAAGCGCCCTGGCCCCGACAGCAGCCCGGCCAGAGCCTTCCCGCCCAGCAAGTCATGCGTGACCAAGCCCGAGGCCACCGCCACCTCCACCAGCCCCTCCAACTTCTATGGGAACTCCATGTACTTTGTGAACCCCGCCTCTGCAGCTTCCAAGTCTCCAGCCGGCTCTACCCCGGTGGCTATCCCCAGGGATTTCTGGCTGCGGTCCTCTGGGAGGTTCCGACAGGATGTGCAGGAGGCATTAGAAGGTGTCAGCTTCATCGCCCAGCACATGAAGAATGACGATGAAGACCAGAGT
Seq A exon
GTAAGTTGCTAACCAGCCCCTGCCCACCTGCCCAACAGAAAGGGCTCAGATAGTAGCACCAGCTTCCCACTTCCTGCAGTTAATTCATAGGAGACAAGGACTCTCAAACTCTGAATAAGGAATCCAAAATTGAAATGAGTTTGTGTTAAATATTATAGCTTCATGCATCCGGGGAGAGGAAGGACGTGCCAGTGATTTAGTTTGTTTGTTTTAGGTGTCCCAGAAGCAAACGCCAAGATGGGGACTTGGGTGCAGGTGGTTTACTTGAGATGTGATCCTGGGAAGCACAGTGAGGAAGGAGGGAAAGTGAGACAGGGAAAGGAGAATGAATGAGCAGGATACTGCCGTGGGTACCCGGGACTCAGTACCCTTGCAGACCCGTGGGAACAAGCCTCAGGATCACCCCCCTGGAAGGAGGCTGAGGTATTTACCCACCAGCCCCCATTCCCTAAAGGATGAGGGTAGCCCCAGGACTTTAACTCTCCTGTGCTTCCAGGTAATGCCAGCCTGCCAGAACAAGCACCCTTGGTGCTGGAGAAAGCCCTGAGGCAGAGGAGAGAGGAAATGCGGGTGCCAGAAATGGAAGGCTGGGAAGTGACTCTGCAGGCTTTAGGGAACACAGGCGGGCTGGGGTACCAAGCGCATCTGCCCTATTCTGTTCAGACTTGCAAAGAAGCCATTCAAGCACTTATAGCTTCCAGGGCTATAGGAACATCAGTAAAAATACTATGATTACCAGGGTAATGAATTAATCGATTGTGCTAACTAGAATTACAGATTTTTATTTTATTTATTTATTTGAGATGGAGTTTTGCTCTTGTCGCCCAGGCTGGAGTGTGGTGGCACAATCTCGGCTCACTGCAACCTCCATCTCCCAGGTTCAAGTGACTCTTCTGCCTCAGCCTCCCAAGTAGCTGGAATTACAGGTGCCTGCCACCACACCTGGCTAATTTTTGTATTTTTAATAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAGCTCCTGACTTCAGGTGATCTGCCCACCTCAGCCTCCCACAGTGCTGGGATTACAGGCTTGAGCCACCGAACCTGACCTAGAATTACGGATTTTTTAAAAAGAGGTTTAATTTACTTTCACAGGATAAAGCAATGAGTGCTGGAGTCTGGGTATTTCACATGACTCCTTTGAATAAATAACACTTCTAAGGACAATGTCATAGTAACAACACAGAATGTGGTGGTGACAAATTTTCACACCCATTTCCATACCAGGAGGGAGAGCAAGTTTCATGCTCTTGTGAATGTTCTCATATTAACACCTTCAGATCAGATTCTTTGGACAGGTTTTTACTATGCAACATGGTGTCTGCCCCTGTGCAGCTGCATGGACAAAAGTGGACGTCTCATTCTTACCGTTTTGAGATTGCTTTCCACTCGCTGCATTCTCAAGGAGAAGCGCTGGCATTCCATTAGTTAGCCCACAGAGAAAAGAGCAGGAACAGCCCCAGAATCACACTGTGCCAAGAAAAGAAGAGAAATGCAAACAAATGGAATATAGGACATGAGATATTCTTCTGGTGTAGTTCTTGGACCAGCAGCACCGGCATCGCCTGCGAGCTTATCGGAAATGCAGAGTCTCAGGCCCCAATCCAGACCTGCTAGCTCCAAACCTGCATTTTAACCAGGTCCCCAGGAGATTCCCAGACCCATTGCAGTTTGAGAAGCACAGCTCTATAGGACTCTCAGATTTCACTTTCTAAAACGTTAATTCGATCACGCTATTACTTAGGTTAAATCATTCTGTAGGTCAGCATCACCTAATTCATTGGTTCCCAATCATTAATGTGCAGCCTGGGGCCCTGCTGGCTAAGTGAGAACCACGTGGGCAACACTGTGGGACCACCCTTTCTGACTGAGCCAGGATCTCTGGCGGAGACATATTGGAGCCTGCATTTTTAACCAATCCCTGGTGGTTCGTGTGCACATTCTAGATTGAGAAGTACTGGTCTCCTGCATCCCTGGCTGAGCCGGCACCCACCCTGAACTCTTCTGAAGACCTCACCACCCCCTTGGCACTCACGTGCCTTCTGCTCTTTCTAGCTCAATTAATTACAAGCCTCTTAAGGGAAGGAGCCAGGCAGGACCAGTTATTATAATCACCAGTGTTCATTAAGCTCCAATCACACATCAGGTGCTCTGCTGGGAGCTGACATACATTACTGCTAACCCTCCCTGGAATCCTGTGAAGTGGCTTTTAGTAGAACCCCCATTTACAATAAGGAGGCTTTCAAAGCGAAGCTCAGAGAGGTTCACTGACTTGGCCAGTGTCAAACAGCTGGCCCAGGCTCTGTACCCAGATCTGCCTGTCATCCTTAAACTTTCTTGCCCTTCCTAGTTTCTTGCCCTGCACTGAGCACATGGCCGGCTTATTGGTTGATTGACTTTCTTATGGATGGTTGGAGAAAAGAGGCTTTCTTCCCTTCTAGAGCATGCCTGCCCCTAAGCCAGCCCACGCCGCTTCTCATCTTCAGTACTTTTACCCACCCTGATTAACTGGTCACTATAAATAGCACAAAAATATTAAAAGGGGGAAACACACACACACACACACACACACACACACACACACACACACACCCCCGCTTGAAATTAGGGCTGTTAAAAAGAAACCCAGGAAAGCCAAGGAGTGCTCTGTGGAGAGAGCTGTGTGTGCCTGCTGAGTCTTGGGGACAGGTGCAGGCGTGCTTGGTTGCAGGTGTCGGGGTTGGCTTGACACAGGATTAGCCTGCACGTTAGGTACACCATTGACAGGGCCTTGACAAACTGGGTCACTGACGTCAGCATGCCCGTTGCTGCCCACATTTCCAACTCCAGAGCCTCTGCTGATCTCCGAAGCCTTCTGATCCAGCCCGTCTCTGCCAGGGAATGAATGCAGTGTGAGCCAGCCAGGCCTAGGGGTGTGAAAGCAGGCATCGGCGAGGGAGGCCAGGACCCTGGGCACACAGGCGTTTCTCTAGGTTCTCCCCCAGTGCAAAGGAGACAGGCCCATCTCTGGTGGCCCCTCTGGAGGCCAGCCAGGTCTCTGCCAACCTCACACCCCGCAGCAGGATCTAAGAAGACCAGAGAGACCTGAATGATGCAGCAGGAGGAGGCTGGGTCTTAATTACAGGAAACAGACACTGCTGTGAACAGACTTGAACAAATTAAACAGCAGGATTTCCAGGTGTTCTGTAAGCCCCGGTTTCTCTGCTCTCACTGAACTAGGTGGGAGCCACCTAGTTCTTTCTTTAGCTAGAACCAGCTCAGGCAGTGAGTTTGGGGTAAAAATGAGAAGTTGGGGCTTTGAGATCCTCAGGCCCTATCTCCTATGTATAACCAGATTTTGTTTTCAAATCATAATATGTAGTATTAACAAGCCCTCACATTCCTAGCTTTTCTGTACAGCCCAAGTTCCCAGTGCCCCTCCAACGCTGTGGGGGACAGGCAGGGGTGGAGGTGGAGAACAGCCAGAGAGGCTCAGAGCTGCCCAGCTGGGAGGCCAGCCTGGGACTCAGAACTTGCCCCCCTAGTATGCAGTTCCACGCCTGTGGCCTGTGGAGTCCCTGGCCAGAGAGTAAGGGCCTGACTCGGGGAAAGGAGGGACCCCAGTACTTGGCACCTGTGACCAACTCCTCTGTCTGCCTGCAG
Seq C2 exon
GTCGTTGAGGACTGGAAGTACGTGGCTATGGTGGTGGACCGGCTGTTCCTGTGGGTGTTCATGTTTGTGTGCGTCCTGGGCACTGTGGGGCTCTTCCTACCGCCCCTCTTCCAGACCCATGCAGCTTCTGAGGGGCCCTACGCTGCCCAGCGTGACTGAGGGCCCCCTGGGTTGTGGGGTGAGAGGATGTGAGTGGCCGGGTGGGCACTTTGCTGCTTCTTTCTGGGTTGTGGCTGATGAGGCCCTAAGTAAATATGTGAGCATTGGCCATCAACCCCATCAAACCAGCCACAGCCGTGGAACAGGCAAGGATGGGGGCCTGGGCTGTCCTCTCTGAATGCCTTGGAGGGATCCCAGGAAGCCCCAGTAGGAGGGAGCTTCAGACAGTTCAATTCTGGCCTGTCTTCCTTCCCTGCACCGGGCAATGGGGATAAAGATGACTTCGTAGCAGCACCTACTATGCTTCAGGCATGGTGCCGGCCTGCCTCTCCATCACCATCTCTCTCCACTTCCCCTTGTCCAGTTCCTCACACACTTCTAGATTCTTCCCAGCTCAGAGGCTTGGCATTTGCCATATCATCATCTTTTTTTTTTTCTTTTAAACGGAGTCTTGCTATATCGCCCAGGCTCAAGTGATTCTCCTGCCTCAACCTCCCAAGTAGCTGGGATTACAGAAAGCCGCCACCGTGCCCAGCTAATTTTTGTATTTTTGTTGGCCAGGCTGATTTCGAACTCCTGACCTCAAATGACCCACCTGCCTCGGCCTCCCAAAGTGCTAGGATTACAAGTGTGAGCCACTATGCCTGGCCTTCCCTATCTTCTACCTGAACCTTCTTCCTCTTCCCCCAGGGCTTCCCAAGCTCTTTCCACAGCCACATCAGTCAGGGCATGGCTCCAATCCATTCTTTGCTCCAATGTCACCTCCTCTGAGAGGCCTTCCCTAACCACCCAATCATTCTAAAGCAGCCTCCCTACAGTCACGTTACCCTGCCTCCTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000117971-CHRNB4:NM_000750:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.039 A=NA C2=0.031
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(54.4=34.3),PF103294=DUF2417=WD(100=38.2),PF0293211=Neur_chan_memb=PU(86.2=63.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.9=58.5)
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:
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
- Genotype-Tissue Expression Project (GTEx)
- 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)