HsaINT0035246 @ hg38
Intron Retention
Gene
ENSG00000135902 | CHRND
Description
cholinergic receptor nicotinic delta subunit [Source:HGNC Symbol;Acc:HGNC:1965]
Coordinates
chr2:232528862-232530139:+
Coord C1 exon
chr2:232528862-232528971
Coord A exon
chr2:232528972-232529938
Coord C2 exon
chr2:232529939-232530139
Length
967 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
TGTCCATGTGCCGCCCTCAGAGA
3' ss Score
8.72
Exon sequences
Seq C1 exon
TTCCCTCAAGTATACGGCCAAAGAGATCACCCTGAGCCTGAAACAGGATGCCAAGGAGAACCGCACCTACCCCGTGGAGTGGATCATCATTGATCCTGAAGGCTTCACAG
Seq A exon
GTGCTGGGAACAGCCGCCAGTGGGTGGGCAGGTCCCTCAGACACACACAGACACACTGGCCCTGTCCACCCCAGAGACACACACGTGCACACACACACACACTTAGGACACCAATACACAGCTCCTCACACACGCAGCTAGACACAGAAGGGCAGACACATATCCGCCCACAGAGGAGCACACAGACACTCACACTTCCTGAATGCAAAGCTATCCCAAAGGCAGAGAGAGAAGGTGCCAGGGCCCTCCCCATGCCTCTGCCCAGGCCCGGAAGTCATGCTTCTCCCACATGAGATGCCTGTGGCTGACAGGGGTTTAGTCTTTCCTGTGCCTGGTGAGCCCAGGGGTGTGGTTGGCATGAGGGCTGTGTTATCCTGATGGGGGTGTCTGCCACCCCTCCTGACATCCTCATCCCCGATCTGTACCCAGGCTCGGATCCTCCATGGGGCCTACCACTTGCCCTGTCCATCAGAAGGGACCCTGTCTCACTGTCTCAGGCTGGCACATCATGGCAGGGATAGTTTTACTGTCACTGGCTCATTATCCCCAAGGCCCAGGCCGAGGAGTGGCTCAATTAATGTCCAGGAGGCTTTTCTTTGTTACTCAGGAAGACAGGCTCAATGTCTGAGAGCATTTGTTTGACTTGGTGTCTTAATCTGCAATACCTGTTTTTGGCTCGTGTATCTTTTGAGCCAAAAGATACTCCTTATTTGAGTCCTGTATGGCCTCAGCTTCTATTTTTTCCGAAAAGATAAAAAAGAAATCAGTCACAGAGGAAGATTTCCCCTCACAGATGGAAACTTCCATCCCGACCCCCCAGGGAACGACACCCACCAACGGGACCCCGTAGACAGCCCATCTGCGTCTCTGGACTGGCTTGCCCTGCCCAGCCCCTCATTCTGTCCCCAGGCCCTGCCTAGCCCCCTTGGCCTGGCCTGACCCTAAGATGTCCATGTGCCGCCCTCAG
Seq C2 exon
AGAACGGGGAGTGGGAGATAGTCCACCGGCCGGCCAGGGTCAACGTGGACCCCAGAGCCCCTCTGGACAGCCCCAGCCGCCAGGACATCACCTTCTACCTCATCATCCGCCGCAAGCCCCTCTTCTACATCATCAACATCCTGGTGCCCTGCGTGCTCATCTCCTTCATGGTCAACCTGGTCTTCTACCTACCGGCTGACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135902:ENST00000258385:6
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=0.243
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(16.7=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(17.6=57.4),PF0293211=Neur_chan_memb=PU(8.9=30.9)
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:
TCCCTCAAGTATACGGCCAAAGA
R:
TGTCAGCCGGTAGGTAGAAGA
Band lengths:
310-1277
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