HsaINT0035220 @ hg19
Intron Retention
Gene
ENSG00000170175 | CHRNB1
Description
cholinergic receptor, nicotinic, beta 1 (muscle) [Source:HGNC Symbol;Acc:1961]
Coordinates
chr17:7350822-7352107:+
Coord C1 exon
chr17:7350822-7350969
Coord A exon
chr17:7350970-7351897
Coord C2 exon
chr17:7351898-7352107
Length
928 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
CTCCTTCTGCTCATCCCCAGAGA
3' ss Score
8.9
Exon sequences
Seq C1 exon
GTCACCTACTTCCCCTTCGACTGGCAGAATTGCACTATGGTGTTCAGCTCCTACAGCTACGACAGCTCGGAGGTCAGCCTGCAGACAGGCCTGGGTCCTGACGGGCAAGGGCATCAGGAAATCCACATTCATGAAGGGACTTTCATTG
Seq A exon
GTGAGTAGGCATGGCTCCTACATCCATGGGCTCTATCATTTCCAGCTTCTAACAGACTCATAAATATACTGTCAGTGATGCCCAATATAGCCCTGTGGGGTCAGCAGGATGGGTATGGCTATCTACATTTTAAAAGTATGGAAATTGCCGGGGGCAGTGGTTCATGCCTGCAATCCCAGTACTTTGGGAAGCCGAGGCGGGCGGATCATTTGAGGTCTGGAGTTCGTGACCAGCCTAACGTGGTGAAACCCCGTCTCTACTAAAAATGCAAAAAATTAGCCAGTCATGGTGGCAGATGCCTGTAATCCCAGCTACTTGGGAGGTTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTGGAGGTTGCGGTGAGCCGAGATGGCGCCACTGCACTCCAGCTTCGGTAACAGAGTGAAAGTTCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGCCTGGCGCAGTGGCTCACGACTTAATCTCAGTATTTTGGGAGGTGGAGGCGGGCAAATCACCTGAGGTCAGGAGTTCGAGACCACCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCAGGTGTGGTGGTGGACACCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATCACGCCACTGCACTCCAACCTGGGCAACAAGAGCAAAACTCTGTCTCAAAATAAATAAATAAAAATATGGAAATTGAGACTTGCCCAAGTTTATTAGAGATGGGCTACTCAGCCCAGTTTTCACAGCTAGTTTCATCAAGTCAGCCCTCTCAGGTCTAGGCTGTGGCAGAGCAAGCCATACCTGGCACTAACCAGGACAGCTCTCACATCTGTGTTCCCCTCCTTCTGCTCATCCCCAG
Seq C2 exon
AGAATGGCCAGTGGGAGATTATCCACAAGCCCTCTCGGCTAATCCAGCCTCCAGGCGATCCTAGGGGAGGGAGGGAAGGACAGCGCCAGGAAGTCATCTTCTACCTCATCATCCGCCGCAAGCCTCTCTTCTACCTGGTCAACGTCATTGCCCCATGCATCCTCATCACTCTTCTGGCCATCTTCGTCTTCTACCTGCCACCAGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170175-CHRNB1:NM_000747:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.085
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(29.5=100),PF0293211=Neur_chan_memb=PU(0.1=0.0)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(23.7=57.7),PF0293211=Neur_chan_memb=PU(91.7=31.0),PF0293211=Neur_chan_memb=PU(0.6=1.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTACTTCCCCTTCGACTGG
R:
TGGTGGCAGGTAGAAGACGAA
Band lengths:
348-1276
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)