HsaINT0035247 @ hg38
Intron Retention
Gene
ENSG00000135902 | CHRND
Description
cholinergic receptor nicotinic delta subunit [Source:HGNC Symbol;Acc:HGNC:1965]
Coordinates
chr2:232529939-232531463:+
Coord C1 exon
chr2:232529939-232530139
Coord A exon
chr2:232530140-232531351
Coord C2 exon
chr2:232531352-232531463
Length
1212 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGC
5' ss Score
4.69
3' ss Seq
GCTAAGTCTGGCTTCCCCAGGTG
3' ss Score
5.57
Exon sequences
Seq C1 exon
AGAACGGGGAGTGGGAGATAGTCCACCGGCCGGCCAGGGTCAACGTGGACCCCAGAGCCCCTCTGGACAGCCCCAGCCGCCAGGACATCACCTTCTACCTCATCATCCGCCGCAAGCCCCTCTTCTACATCATCAACATCCTGGTGCCCTGCGTGCTCATCTCCTTCATGGTCAACCTGGTCTTCTACCTACCGGCTGACA
Seq A exon
GTGAGCCTCCAGGCCCCGTCCCCTGCTCCCCCTCCCCAAGCCCACCTGAGCACAGCCAGCCCCAGCCCTGCCCCCTCACTTCCTCCTGGGAGCCACCTGGGGTCTCCATTCCTGGAGCTCCCTGCCTGGATCCAGGTGTGAGGGCCAGGTGGCCACCCAGAGGGAGGGCTGTATGATTCTGGGCAACATCCCCAAATGGACAGGGCAGGGCATCTCCAAGATGCTACTTCCCACGGACTCTCAGAAGAACTGCTAAACTGTCCCTCTGTCAGGGCAGAGACCAAGTCCCTCACGGTCACCAGTGTGTGACCGTGGGCCTGGCACACAGGAGGCCCTCAACTGTTGAACCAGTGGGTGAATAACAGGGTCTCTAGGACAGTAGGGTGTGAGGCAGAAAACCCATCTATGCTCACCTGACTCTATGAGGCAGTGGTTTACAAGTTCAGAGTATTTACTATGAGCAGGGCATAGTGAGTCCCAGGGTCAAAGGCCACCCAGCCCCTGCCCCCGGCAGGACTTGAGGAGGGAGAAGTGGGGCACCTTCCATCTGCAGTGGGGTTGGGAGGGCTTCTAGAGGAGGTGGAGTTTGAATGGACTTGAGCAGGATTGGGTGGGGCTACCACAGGCAGGAGGAGCAATGCCAATAAGGAGGGGGCCAGGCAGGGGCTGAAGGGACCTCAGCAGGGGAGCCCCCCTTCCCGCCCTTGCCATCACGTGCAGGAGCTCAGGTGGGAAGAGCAAGACAGCACTGGGCTGGGGTCTCTGAGTGAGGGGCTGGGAGTTGAGGTGTTATCCTGGTTCTACAAGGACAACCTGGCACTTTCTAAGCGGGGAGTAACGCACGCAGGTCTGTGCTCCAGGAGGGTTCAGTGGCGTGGGTGGGTTGTGACAGCTGATTTTCATGAGCACTTACCCAGTGCCAGGCAGAGTGATGCGTGTTAAACACACTCTGTCACCACATTTAACAGTTGAGAAAACTGATGCACAGAGAGGTTGGGCTACTTGCCCAAGGTCACCCAGCTAGTAAGTGGCAGAGCTGATATTTGCACCCAGGCACTCTAGCTCCATAACCCGTAATTTTCATCAGGGTATGATGGTACTACAGAGGTGCCAGGGGCCACAGCGGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCTGGACCCTCTAGGACCGGTGCCCCAAGGTCACAGCTAAGTCTGGCTTCCCCAG
Seq C2 exon
GTGGTGAGAAGACATCAGTGGCCATCTCGGTGCTCCTGGCTCAGTCTGTCTTCCTGCTGCTCATCTCCAAGCGTCTGCCTGCCACATCCATGGCCATCCCCCTTATCGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135902:ENST00000258385:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.243 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(17.6=57.4),PF0293211=Neur_chan_memb=PU(8.9=30.9)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(15.6=100)
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:
AGAACGGGGAGTGGGAGATAG
R:
CCGATAAGGGGGATGGCCAT
Band lengths:
310-1522
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