HsaINT0035215 @ hg38
Intron Retention
Gene
ENSG00000170175 | CHRNB1
Description
cholinergic receptor nicotinic beta 1 subunit [Source:HGNC Symbol;Acc:HGNC:1961]
Coordinates
chr17:7455794-7457707:+
Coord C1 exon
chr17:7455794-7455941
Coord A exon
chr17:7455942-7456582
Coord C2 exon
chr17:7456583-7457707
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
CTGAAGGAGGACTGGCAGTTTGTGGCCATGGTAGTGGACCGCCTCTTCCTGTGGACTTTCATCATCTTCACCAGCGTTGGGACCCTAGTCATCTTCCTGGACGCCACGTACCACTTGCCCCCTCCAGACCCCTTTCCTTGAAGACTGGAGGGTTGAGACCCAGGCCCCCTGCCAGTTGAAGTGAGAGTTTGGTGATACTGTCAAGCCCTATCCTTCTCTGCCTCTTAACTCCTTCACGAGGAATCTGGGCCTCTTATTTCGTTTCTGGGGACTGCATTGGACTGAGGGCTGGGTAGGCAGGTGTCTTGGACCCACCTGAAATGCAGTATCATCTGATTTACTCTTTGGGATCTTGAAGAAGCTCTTTTGGGTATCAACACCTAGGTCGCCAGTGAAATAGAACACAGAACAGGAACTAGATTATAAGCCTTATGAGGTCAAGAAATGTGACTTGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCGGGCGGATCACCTGAGGTCGGGAGTTTGAGACCAGCCCGACCAACATGGAGAAACCCTGTCTCTACTAAAAATACAAAATTAGCCAGGTGTGGTGGTACATGCCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGAGAATCACTCGAACCCGGGAGGCAGAGGTTGCAGTGAGTCAAGATCACGCCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCATCTCAAAAAAAAAAAAGTGTCTTGTTCACTGCAGCATGCCCAGTGCCACGCACAGGTGCTGACCTATAGTAAGTGCTTAACATTTGTTGAATAGGGGAAAGAAATTTCCGGAAGTAAATACAGCAATTAATAATGTTTATAAGCTGGGCATGGTCGCTCAGGCCAGTAATCCCAGTGACTTAGGAGGCTGAGGTGGGAGGATTACTTGAAACCCACAGTTTGAGACCAGCCTGGGCAACATAGTGAGACCCTGTCTCTAAAAAAATAAAAATAGAAATAAAGTAGTGCTTATTGTTTGCATGTTGGGTCTTGTGGTCGTTTTCTTTTTACCTTTCTGTAATTTATTATGTTTTGTAATGTGTACTATCTCTGGGATTAAAAAAAGTTATTTCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170175:ENST00000306071:10
Average complexity
IR
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