HsaINT0035215 @ hg19
Intron Retention
Gene
ENSG00000170175 | CHRNB1
Description
cholinergic receptor, nicotinic, beta 1 (muscle) [Source:HGNC Symbol;Acc:1961]
Coordinates
chr17:7359113-7360932:+
Coord C1 exon
chr17:7359113-7359260
Coord A exon
chr17:7359261-7359901
Coord C2 exon
chr17:7359902-7360932
Length
641 bp
Sequences
Splice sites
5' ss Seq
GCGGTATGT
5' ss Score
9.45
3' ss Seq
TTTCCTTTGCCTACCCACAGCTG
3' ss Score
11
Exon sequences
Seq C1 exon
GTTCCAGCCTGAACTGTCTGCCCCTGATCTGCGGCGATTTATCGATGGTCCAAACCGGGCTGTGGCCCTGCTTCCGGAGCTACGGGAGGTCGTCTCCTCTATCAGCTACATCGCTCGACAGCTGCAGGAACAGGAGGACCACGATGCG
Seq A exon
GTATGTCCAACGGGGGTGGAACAAGGCCAGGTCTAGGCGACCTTGGCCCCACCCCCAAATTCCGCACCAGCACTCGCTTTCGTTTTTTTTGTGTGGTTTTTTTTTGGCTTTTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCTCGATCTCGGCTCACTGCAACCTCCGCCTACGGGTTCAAGCGATTGTCCTGCCTCAGCCTGCCGAGTAGCTGGGACGACAGGGGCGCGCCACCACGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGTGGCTTCACCATGTTGGCCAGGCTGGTCTGAAACTCCTGACCTCAGGTGATCCGCTCGCTTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTCGCTTTCGTTTCTGATTGGACCTCTCCCTCATTTGGTCCCACCCCCTGCTTACCTACTGGTTCTTTATGCCCATGCATTGCCTGCAGTCTCGCTCTCCTGTTGGCGCTGCCGGCTGTTGCCTCAAACCAGTGGTAGGAGGACTCAAGCGGGTAGCGGGCGGGGAAATGGGGGGGTTTCCCTGGGGGTCTGGGCCCAGAGCTCAGGAAGTTTCCTTTGCCTACCCACAG
Seq C2 exon
CTGAAGGAGGACTGGCAGTTTGTGGCCATGGTAGTGGACCGCCTCTTCCTGTGGACTTTCATCATCTTCACCAGCGTTGGGACCCTAGTCATCTTCCTGGACGCCACGTACCACTTGCCCCCTCCAGACCCCTTTCCTTGAAGACTGGAGGGTTGAGACCCAGGCCCCCTGCCAGTTGAAGTGAGAGTTTGGTGATACTGTCAAGCCCTATCCTTCTCTGCCTCTTAACTCCTTCACGAGGAATCTGGGCCTCTTATTTCGTTTCTGGGGACTGCATTGGACTGAGGGCTGGGTAGGCAGGTGTCTTGGACCCACCTGAAATGCAGTATCATCTGATTTACTCTTTGGGATCTTGAAGAAGCTCTTTTGGGTATCAACACCTAGGTCGCCAGTGAAATAGAACACAGAACAGGAACTAGATTATAAGCCTTATGAGGTCAAGAAATGTGACTTGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCGGGCGGATCACCTGAGGTCGGGAGTTTGAGACCAGCCCGACCAACATGGAGAAACCCTGTCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGTACATGCCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGAGAATCACTCGAACCCGGGAGGCAGAGGTTGCAGTGAGTCAAGATCACGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCATCTCAAAAAAAAAAAAGTGTCTTGTTCACTGCAGCATGCCCAGTGCCACGCACAGGTGCTGACCTATAGTAAGTGCTTAACATTTGTTGAATAGGGGAAAGAAATTTCCGGAAGTAAATACAGCAATTAATAATGTTTATAAGCTGGGCATGGTCGCTCAGGCCAGTAATCCCAGTGACTTAGGAGGCTGAGGTGGGAGGATTACTTGAAACCCACAGTTTGAGACCAGCCTGGGCAACATAGTGAGACCCTGTCTCTAAAAAAATAAAAATAGAAATAAAGTAGTGCTTATTGTTTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170175-CHRNB1:NM_000747:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(20.8=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.1=66.0)
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:
CCCTGATCTGCGGCGATTTAT
R:
GAGGCAGAGAAGGATAGGGCT
Band lengths:
351-992
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)