HsaINT0035237 @ hg38
Intron Retention
Gene
ENSG00000117971 | CHRNB4
Description
cholinergic receptor nicotinic beta 4 subunit [Source:HGNC Symbol;Acc:HGNC:1964]
Coordinates
chr15:78628967-78631185:-
Coord C1 exon
chr15:78631076-78631185
Coord A exon
chr15:78629946-78631075
Coord C2 exon
chr15:78628967-78629945
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:ENST00000261751:4
Average complexity
IR
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),PF0293211=Neur_chan_memb=PU(86.2=63.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
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