HsaINT0035174 @ hg19
Intron Retention
Gene
ENSG00000129749 | CHRNA10
Description
cholinergic receptor, nicotinic, alpha 10 (neuronal) [Source:HGNC Symbol;Acc:13800]
Coordinates
chr11:3688462-3690580:-
Coord C1 exon
chr11:3690426-3690580
Coord A exon
chr11:3688995-3690425
Coord C2 exon
chr11:3688462-3688994
Length
1431 bp
Sequences
Splice sites
5' ss Seq
CAAGTACTG
5' ss Score
0.23
3' ss Seq
CCTGCCCCGCCTGCCCCCAGAGC
3' ss Score
10.34
Exon sequences
Seq C1 exon
GATGAACGGAACCAGGTGCTGACCCTGTATCTGTGGATACGGCAGGAGTGGACAGATGCCTACCTACGATGGGACCCCAATGCCTATGGTGGCCTGGATGCCATCCGCATCCCCAGCAGTCTTGTGTGGCGGCCAGACATCGTACTCTATAACAA
Seq A exon
GTACTGCCTATCTGGGCCCCTCCTCTCTCTTACCCCTCTCTAGACTTGCCCTTAGCTGTGGGGGTGTAGTGATCCCCTCTCCCTACCACATAACCTGGTTGCCACGCTGCCCTGGAAGCTTTTCCCCAGGACCCTTCTAAGCTGCCAGGCACTCAGCCCCTCCATGGCACCCCCACTTTAGGCTATCCCAGGCCAGCCCAGGCTGAACGTCTCCTCGGAACCTACTGTGTGGTCCAGGGCAGTTGTCTGAATCACAAGGGCCTCTCTAGGGCACACTTTTAGCTCTAAGTCTCTCAGGGCTCCCCGAAGAGCCTGTGTAAGGGTCTCTTTCCTCCAGGACATAGCCCTCTGGAACACTGCTTTATGTCTCCTTGACCAGTTCCGTGTCTCCCAGCCAGCACATAGCTCTGCATATTTTCTCTGGGGCCCTTCTACAAGTTTTGCAGATGTCCCCCAAGGGAAGTCACTGTGTGTCCCGGAGCTACCTCTGGGTTCTGCAGAGGCCTTTTTATACATCCTCTGGCTACGTCTGTGTCCCTTCTGGGCCCTTCAGGCACCACCCCTTCCAGGCCTCGAAAGGCAGCGGGTCTCTCTAGGTGCACTCCACCCTCTGTGTTGCTTTGTTCTGAAAACAAGAATCAAATTAACGAAAAAAAAACAAGCACAAGTTTATTTATTTATTTGAGACACAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCTATCTCGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCAATTCTCCTGCCTCAACCTCCCAAATAACTGGGACTGCAGGCACCCGCCACCACGCCCAGCTAGTTTTTTGTATTTTTAGTACAGACGAGGTTTCACCGTGTTAGCCAGGGTGGTCTCGATCTCCTGACCTCGTGATCCGCCCACCTCGGCCTCCCAAAGTGCTGGGATCACAGGCGTGAGCCACCGCACCCAGCCACAAGCAGAAGTTTATTAATCTGCTGTACCCATCATGGGAGAGGCCTTAGTTCAAAAGTATTTCTCTCTGAAGGCAGTGACTTAGGGGCCTTGCTTAAATAGAAATTCAAGAAAGAGCCAGTAAGTTATAAATAGTGGCAAGACAAAGGACAGCCACCTTTAAAAGGCGGGAAAACGTGGAAAGAGGGTAAAATCTGTTTCCAGATTCCTCTGGCACCTACTGGTGCCCTTTGGATAAGCAAGTGCTGACTCCAGCAAGGAAGGGCTGATGTCCTGCCATCAGGCCAGCAGACGCTGGGGCCAGGTGCTCCCCTGCGTCGTGAGTGTCTCGAACTTAACGAGCCTCAATATTCTGGGGAGAAGTTTTGGTTTCTTTCAGCCCCTGGGGGTCTGCCCTGGGCTCCCGGCCTCCGGGGCTGCTCCTCAGGCTGGACAGCCTAGGTGAGCCCTGCCCCGCCTGCCCCCAG
Seq C2 exon
AGCCGACGCGCAGCCTCCAGGTTCCGCCAGCACCAACGTGGTCCTGCGCCACGATGGCGCCGTGCGCTGGGACGCGCCGGCCATCACGCGCAGCTCGTGCCGCGTGGATGTAGCAGCCTTCCCGTTCGACGCCCAGCACTGCGGCCTGACGTTCGGCTCCTGGACTCACGGCGGGCACCAACTGGATGTGCGGCCGCGCGGCGCTGCAGCCAGCCTGGCGGACTTCGTGGAGAACGTGGAGTGGCGCGTGCTGGGCATGCCGGCGCGGCGGCGCGTGCTCACCTACGGCTGCTGCTCCGAGCCCTACCCCGACGTCACCTTCACGCTGCTGCTGCGCCGCCGCGCCGCCGCCTACGTGTGCAACCTGCTGCTGCCCTGCGTGCTCATCTCGCTGCTTGCGCCGCTCGCCTTCCACCTGCCTGCCGACTCAGGCGAGAAGGTGTCGCTGGGCGTCACCGTGCTGCTGGCGCTCACCGTCTTCCAGTTGCTGCTGGCCGAGAGCATGCCACCGGCCGAGAGCGTGCCGCTCATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000129749-CHRNA10:NM_020402:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.011
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(24.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(36.8=31.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGGCCAGACATCGTACTCTA
R:
TGAAGGTGACGTCGGGGTAG
Band lengths:
350-1781
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)