HsaINT0035177 @ hg38
Intron Retention
Gene
ENSG00000120903 | CHRNA2
Description
cholinergic receptor nicotinic alpha 2 subunit [Source:HGNC Symbol;Acc:HGNC:1956]
Coordinates
chr8:27469761-27471194:-
Coord C1 exon
chr8:27470986-27471194
Coord A exon
chr8:27469982-27470985
Coord C2 exon
chr8:27469761-27469981
Length
1004 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGGCTCTGATTTGATGGCAGGTG
3' ss Score
5.64
Exon sequences
Seq C1 exon
GTTCGGTGGTGAGAGGAAGCCTCGCAGAATCCAGCAGAATCCTCACAGAATCCAGCAGCAGCTCTGCTGGGGACATGGTCCATGGTGCAACCCACAGCAAAGCCCTGACCTGACCTCCTGATGCTCAGGAGAAGCCATGGGCCCCTCCTGTCCTGTGTTCCTGTCCTTCACAAAGCTCAGCCTGTGGTGGCTCCTTCTGACCCCAGCAG
Seq A exon
GTGAGTGTTTGTCACCTGTCATTGTAAGACTTCATCTCATGCCTGTGGGCTCACAAATTGTAGGAAGGAGTCTGCAGGTGGATGTGTTGCAACCGTCAAAGCTGCAGGGGACTTCAGAGGCCATCAGCCAGGTGGCTGTTTCCACTGGCAGAGGTGGAGGGGCAGTCACAGCTCTGACGTTAGCATCTGTGTCACCTTAAATGTCCCCAAGCTTCAATGTCCTCAGCTGCAAAACGCAAATAGTGTTGTGTACCTCCCAGGCCTATTGTGAGGATTAAACGCAAGTTTGTGACCAGAATCTGGGATACAGGAGGCACTCGGGACACAGCGCTTTCTGTCCCAGATGGTGCTGACACGTTTTTCTGGGATTTGGAGCTGTAGTTCTCGACTCGCTCGGACAGCAGAGCCCTGAAGGGGTGAAGCTGTTTGCTGAACACAGTGAAAACTGACATGAGCGATGCCATAGAAACATTTTGAAAAGTTTTGTTTATCTGATAGGAAGTGGCAAATGCCCATGGTTTAAGAAAAAATTGGGGAGGTTCCCAAAGCGGTCCATTTCCCTGTTAGCATTAATGGTTCATCGGACAAGTGGGTGGGAACGGGAGACTGCTTACCCTGGCCAGGCTTACTGCAATGCCAGAGCCCTTCTCCCTGCAGCCCCGCCACGTAGACCAGGCGTCTCTTCCACTTCCCTGTCCACCTGGCACTCCTCCATATGGGGCTGAATCTTGTCTCTAGATTCGTTTCCCCTCTTCCCTGCCTCTGCCCCTGCCCCTCGCCACCTGCAGCACTAGTTCTCACTCTTTTCTTCTCTAACATCACAAAACAGCTGACCTTTCCTGAGCTCCGACCCCGCAGCCTGCTCATGCTGTGCTCAGCTCTGATAGACATTATCATCTGCCATCTTCAACAATGTTTTGAGATAGGTTCTGGATAAGCATCTCCATTTTACAGATGAGCAAACTGAGGCTCAGTGAGGCTGAGTGGCTCTGATTTGATGGCAG
Seq C2 exon
GTGGAGAGGAAGCTAAGCGCCCACCTCCCAGGGCTCCTGGAGACCCACTCTCCTCTCCCAGTCCCACGGCATTGCCGCAGGGAGGCTCGCATACCGAGACTGAGGACCGGCTCTTCAAACACCTCTTCCGGGGCTACAACCGCTGGGCGCGCCCGGTGCCCAACACTTCAGACGTGGTGATTGTGCGCTTTGGACTGTCCATCGCTCAGCTCATCGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120903:ENST00000407991:2
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=0.449
Domain overlap (PFAM):
C1:
PF0315410=Atrophin-1=PU(5.4=12.0)
A:
NA
C2:
PF0315410=Atrophin-1=PD(93.4=77.0),PF0293118=Neur_chan_LBD=PU(40.6=52.7)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCACAGAATCCAGCAGCAG
R:
CACCACGTCTGAAGTGTTGGG
Band lengths:
348-1352
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