HsaINT1007680 @ hg38
Intron Retention
Gene
ENSG00000129749 | CHRNA10
Description
cholinergic receptor nicotinic alpha 10 subunit [Source:HGNC Symbol;Acc:HGNC:13800]
Coordinates
chr11:3669796-3671384:-
Coord C1 exon
chr11:3671252-3671384
Coord A exon
chr11:3669942-3671251
Coord C2 exon
chr11:3669796-3669941
Length
1310 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
CCTCCTTACTGACCCTCCAGAGT
3' ss Score
7.65
Exon sequences
Seq C1 exon
TAATTTTGCCCTAGGTCTGGCCAGGAGGCCTCACATCCAGAGACCTGCCCCCGCTCTTGCAGTGCCAGGGCCATGGGGCTCCGGAGCCACCACCTCAGCCTGGGCCTTCTGCTTCTGTTTCTACTCCCTGCAG
Seq A exon
GTATGAAGCTCAGTACACCAGCCCTGGCCTCTCCTGGTGGTGCTACTATTCCTGTTCTCCCAAAATCCCTTTCCATGTAGTCTCTCTTGTGTTTCTCCTCAGTACCTGTTCTGAGAACAAGCTCTCTATTTGGGGAGTGTGGAGGAGAGGGGTGCTGAAGTGCGTGAGAGGAGACTTGCCTGGCTAGGGTGGAAACAGTGAGCGGGGAGCTTCCAGAGACAGGGCTGGGAAAATCAGAGGGGCCAGATGTTGAAGGGCCTGCCGGCCAGGCCAGGTCTTTCTCCTGCAGATGACGGGGAGCACTGAAAGGTTTCAGCAGCATACTAGCCTGGTCAGATGTGCATGCTTAAAAGCGTGGTCCTGGGGCATGGGAGGGGTAGAAGAAGGTGAGCCTTTGGGGAAAGGGAGACAGTGAAGGGAGGGCCCTGACCTGGAGGGGAGAGGGTAGACTCAAGACGATGTTTCGCAAAATCTGGAGGATTTGAATGATCTGACAGGATCTGGAGATTAACTGGATTCCCCGAGGAGGAGGCAGCAGAGGGAGAAGGGAGGGATAATTCCCAGATTTCCAACTAAGGTCACTGTTGAAGCTGAGGGCATGCTATTTGCTGAGATAGGGAACATGGGATAGGAAGCAGGTTTCAGAGCATGGAGGGAGGAAGCGAGTTCATATTTTGGACCCTCAGAGTTGAAGGTGCCTGTGGGAAACTCAGGAGTGGACTGTACTCTATTGGGGTCTGGAGCTCAGGAGAAAAATCTGGGATGAAGAAAAAGATGGGAGCCAAGGACAGGATTCATGGGAACAATGTTTAGGTCAGGGATTGAGGAAAATTTGTGTCAGTAAAGCCTGGGGAAGTGTGTTTTCAGAGTGAGGGAGTGTTCCATCGCATCAGAAGTTTTGAAGAAACCAGCTCGAGATGGAGAAGTGGAAACAGGTTTGAGAGATACTGGAGGGGGCAGAGCAGTGGGGTTTAGAATCCCTGGGTGAAAGTCTGGACTCTTGTGGCTTATTTGGGCCCCTCTAGCATTTGTGGAGAGGCAGGCAGACTCCAGGTCCTTGAAAAGGGGAGGGTGGAGGAGAAATTTGTCAGCCTGGCGCCAGAAGATAGTACCAGTTCACTCCATGGCCTTTACCTCATGTGTCCCTGCAGGCAGGCCAGGGAGGAACTAGAGCCACAGCTAGAGCAAGAGAAGGCAGACACCAGGAGGACACTCATAAGGACAGGGCCCCAGCCCTGGGAGTGGAGGGTGTGAGCAGAGGCCCTGGGACTAGGGCCTGGGATGGACAACCCTCCTTACTGACCCTCCAG
Seq C2 exon
AGTGCCTGGGAGCTGAGGGCCGGCTGGCTCTCAAGCTGTTCCGTGACCTCTTTGCCAACTACACAAGTGCCCTGAGACCTGTGGCAGACACAGACCAGACTCTGAATGTGACCCTGGAGGTGACACTGTCCCAGATCATCGACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000129749:ENST00000250699:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=79.6)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTAGGTCTGGCCAGGAGG
R:
CATGTCGATGATCTGGGACA
Band lengths:
270-1580
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains