HsaINT0035237 @ hg19
Intron Retention
Gene
ENSG00000117971 | CHRNB4
Description
cholinergic receptor, nicotinic, beta 4 (neuronal) [Source:HGNC Symbol;Acc:1964]
Coordinates
chr15:78921309-78923527:-
Coord C1 exon
chr15:78923418-78923527
Coord A exon
chr15:78922288-78923417
Coord C2 exon
chr15:78921309-78922287
Length
1130 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
CATGCCCTGACCCTGCCCAGCGC
3' ss Score
5.12
Exon sequences
Seq C1 exon
GAATGGACTGATTACCGCCTGACCTGGAACAGCTCCCGCTACGAGGGTGTGAACATCCTGAGGATCCCTGCAAAGCGCATCTGGTTGCCTGACATCGTGCTTTACAACAA
Seq A exon
GTGAGTGGCAGGGTTGGTGGAGGCCTGGTGACAGCCAGGCCAGGGCAGCAGGCCCAGCCCTAAGAGTCATCCAGGCCTGAGTCCAACCCTGAGCCCCATCTCTGCTTTACCCAGCCTTCCAGGCCATCAAGCTAGAAGAGAAACAGAGGTGAGCAGAGCCAGAGCCCTCAGTTACAGATGGGGAGTTGGAGGCTGAGGGAGGGGAGGGACCTTGTCTGATTCACTGAAGCAGAGCTGGGACCACAGCAGTGTCCTGACCTTGAACCCAGCACCCTTTCTGTGTTCCATACTATCCTTTTGAGCCTCTGTTGCTTTGCCAGTGTTGGTGTTGGTACCACTGACTTACTGTGTGTAAATATCTTAGGCAGGTGGAGGAAGCCAAAGAGACTTTTCCTGAGTCGTGATTACACCAGCAGTAGCTTGAAATGGCTCAAAGTGTGTGGTCTGGGGACAGACAGACCTGAGTTCAAATCTCAGCTGTCCTGCTTACAAGTTTTCTGACCTTGAAGAAGTCACTTAACCTCTTTGGGCTTTGGCTTTCCCATCTGTAGAATGGGGATAATAATAAAACCTGCCTCACTGGACTACTGAGAGGCTTAAATGAGCTATTCCATGGGAAGCCTTAAGAGTGCTTGATGGGCCGGGTGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGATCAGGAGTTCGAGACCAGCCCGATCAACATGGAGAAACCCCGTCTCTACTAAAAATACAAAATTAGCCGGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAGGCCGAGACAGGAGAACTGCTTGAACCTGGGAGGCAGAGGTTGCAGTGAGCCGAGATTGCACCATTGCACTCAGCCTGGGCAACAGAGCAAGAGTCTGTCTCAAAAAAAAAAAAAAGGGGGGTGCTTTGATGTTAGGGCTCTCTCCACCACATAGTTGCTAACAAAAGCAGACCCCTCCTTTCAGTGAGGGCCTGGGGGATTGGAAGGGTGATTAGTGGGAAATAATCCCAAAGGGCTCTTCAGTGAGTTCTGAGAACAGGCCAGGTTTTGTGTATGGGTTTCACGATGTTCTCCATGCCCTGACCCTGCCCAG
Seq C2 exon
CGCCGACGGGACCTATGAGGTGTCTGTCTACACCAACTTGATAGTCCGGTCCAACGGCAGCGTCCTGTGGCTGCCCCCTGCCATCTACAAGAGCGCCTGCAAGATTGAGGTGAAGTACTTTCCCTTCGACCAGCAGAACTGCACCCTCAAGTTCCGCTCCTGGACCTATGACCACACGGAGATAGACATGGTCCTCATGACGCCCACAGCCAGCATGGATGACTTTACTCCCAGTGGTGAGTGGGACATAGTGGCCCTCCCAGGGAGAAGGACAGTGAACCCACAAGACCCCAGCTACGTGGACGTGACTTACGACTTCATCATCAAGCGCAAGCCTCTGTTCTACACCATCAACCTCATCATCCCCTGCGTGCTCACCACCTTGCTGGCCATCCTCGTCTTCTACCTGCCATCCGACTGCGGCGAGAAGATGACACTGTGCATCTCAGTGCTGCTGGCACTGACATTCTTCCTGCTGCTCATCTCCAAGATCGTGCCACCCACCTCCCTCGATGTGCCTCTCATCGGCAAGTACCTCATGTTCACCATGGTGCTGGTCACCTTCTCCATCGTCACCAGCGTCTGTGTGCTCAATGTGCACCACCGCTCGCCCAGCACCCACACCATGGCACCCTGGGTCAAGCGCTGCTTCCTGCACAAGCTGCCTACCTTCCTCTTCATGAAGCGCCCTGGCCCCGACAGCAGCCCGGCCAGAGCCTTCCCGCCCAGCAAGTCATGCGTGACCAAGCCCGAGGCCACCGCCACCTCCACCAGCCCCTCCAACTTCTATGGGAACTCCATGTACTTTGTGAACCCCGCCTCTGCAGCTTCCAAGTCTCCAGCCGGCTCTACCCCGGTGGCTATCCCCAGGGATTTCTGGCTGCGGTCCTCTGGGAGGTTCCGACAGGATGTGCAGGAGGCATTAGAAGGTGTCAGCTTCATCGCCCAGCACATGAAGAATGACGATGAAGACCAGAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000117971-CHRNB4:NM_000750:4
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=0.039
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.5=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(54.4=34.3),PF103294=DUF2417=WD(100=38.2),PF0293211=Neur_chan_memb=PU(86.2=63.3)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCTACGAGGGTGTGAACATC
R:
TTCACTGTCCTTCTCCCTGGG
Band lengths:
353-1483
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)