HsaINT0035241 @ hg38
Intron Retention
Gene
ENSG00000135902 | CHRND
Description
cholinergic receptor nicotinic delta subunit [Source:HGNC Symbol;Acc:HGNC:1965]
Coordinates
chr2:232534224-232535838:+
Coord C1 exon
chr2:232534224-232534342
Coord A exon
chr2:232534343-232535129
Coord C2 exon
chr2:232535130-232535838
Length
787 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
CTCTCTGCCCCTACCCACAGGAG
3' ss Score
11.87
Exon sequences
Seq C1 exon
GCCGGCCCCCAGCAAGCTCTGAGCAGGCCCAGCAGGAACTCTTCAATGAGCTGAAGCCAGCTGTGGATGGGGCAAACTTCATTGTTAACCACATGAGGGACCAGAACAATTACAATGAG
Seq A exon
GTAAGGGACCACAGGATTGCCATGTACAGGTGTTCAAGTAGGGCACTGATTAAGTGTATTCTATCTTAAGAGGGCAGGGTTCCCCTTAGAGGCACACACCAACTTAGATGAGGGAGTTAATGTGACACAGATTCCAGGCCCCCCCGCCAGGGAGAGAGAACTCCTGCCTGGCACCCTATAGCAGCACTGGGGCCAGGCACACACACATAGGCACACAGCTCCACCCTGTCCAGGCCACACTCTGAGCATCCCTTAGGATCCCTTCTTTCTCCCAGCTGCCAATCATTTTCTGTCCCTACTCAGTTCCAAGCCTGATACTCCAGACAGAACCAGACATTTTAAAGGTAGCCATATATGGTTATTCAACATTATACAACTTCTAAAAACTATCTCTTGAGAAAGGGCACCTTTTCCCAGTTCACATATGGGCTGGCAGCAGCCCTGACTTGCTGAGATGGGGGAGAAGAAGAGAGGGGTCTATCCACCTTCCTCAGCCCCTAGGAGAGACCCCTGGGCCTCAGTTCCTCTCTAGCCCCAGAGCCCTGTGCTACAGCAGAGAGGGAGGCTATGGTCTGTTCCCGCCTCCTCAACAGAGTGATCAGCCCTGCCTGTGGCCAGAGGGGCCTGGGACCTTGCTGGGGACAAGCCAGCATTATCCTGCAAGCCCGAGGCAGCCTCTGCAGGCACACTGAGCCGCCCTCTGCCTCCATGGCTGGGCCCCAGCTTGGGGGTGGGGCTTTGTGGCCTGAGGCCCTTCTCACCCCACTCTCTCTGCCCCTACCCACAG
Seq C2 exon
GAGAAAGACAGCTGGAACCGAGTGGCCCGCACAGTGGACCGCCTCTGCCTGTTTGTGGTGACGCCTGTCATGGTGGTGGGCACAGCCTGGATCTTCCTGCAGGGCGTTTACAACCAGCCACCACCCCAGCCTTTTCCTGGGGACCCCTACTCCTACAACGTGCAGGACAAGCGCTTCATCTAGGGTGGGCCTGTTGGGGAGCCAGGAGACAGCAGGGTCTGAGAGAGGAGCCACAGTCCCTAATGACACCCACTCCTAGCCCTGAGGCTCGTGCCCCTCAGACTGGGGAAGAGTCCAAGGAAGGGAGGGAGCAGCCACTCCTCAATGCTCAATGGCTCCCCTGAAATCAAGACAGGGGCCACCCGAGATGGTCTGAGGGTGGACATCGGCTACAGTGGGTGGGCAGGACGATTTGGGGGGAGGCCCGAGGCTGGCTCAGGGGCCAGGGAGGAGGCCACTCAGGGTGGCCTCAGGGGGAGAGCTCTGATAGGGGTGAGACAGATAGGGCCCCTTCTCTGCTTCTCCTCCCCCAAGGTGTGGGGTAGAGCAGGCAGGAATCTGCGCCTTCACTCTCTGGCCCCTCCAGCCTCCCTCTTCCTACCTACCCTTCAACCTCAGGCTTCTGAGGCCTCACCTGGGACTGAGGTTGAGGACACCTCCCTCCCTCCAGACCCCAGAGTATCCTTTCCTAGCTCTTTCTGCCTTGACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135902:ENST00000258385:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.475 A=NA C2=0.183
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(16.5=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.1=50.8)
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:
ACCACATGAGGGACCAGAACA
R:
CTCCCTCCCTTCCTTGGACTC
Band lengths:
343-1130
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