RnoALTA0008940-3/3 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000017424 | Chrna2
Description
cholinergic receptor nicotinic alpha 2 subunit [Source:RGD Symbol;Acc:621533]
Coordinates
chr15:42820331-42823817:+
Coord C1 exon
chr15:42820331-42820440
Coord A exon
chr15:42822788-42822923
Coord C2 exon
chr15:42822924-42823817
Length
136 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
AGCTTGTCTCCTCTTCCCAGTGC
3' ss Score
7.84
Exon sequences
Seq C1 exon
GAATGGAATGACTACAAGCTGCGCTGGGACCCGGCTGAGTTTGGCAATGTCACCTCCCTGCGCGTCCCTTCAGAGATGATCTGGATCCCAGACATTGTCCTCTACAACAA
Seq A exon
TGCAGATGGGGAGTTTGCGGTGACCCACATGACCAAGGCTCACCTCTTCTTCACGGGCACTGTGCACTGGGTGCCCCCAGCCATCTACAAGAGCTCCTGCAGCATCGATGTGACCTTCTTCCCCTTCGACCAGCAG
Seq C2 exon
AACTGCAAGATGAAGTTTGGCTCCTGGACATATGACAAGGCCAAGATCGATCTGGAGCAGATGGAGAGGACAGTGGACCTGAAGGACTACTGGGAGAGTGGCGAGTGGGCCATTATCAATGCCACCGGAACCTATAACAGTAAGAAGTACGACTGCTGCGCGGAGATCTACCCCGATGTCACCTACTACTTTGTGATCCGCCGGCTGCCGCTGTTCTATACCATCAACCTCATCATCCCATGCCTGCTCATCTCCTGCCTCACTGTGCTCGTGTTCTACCTGCCTTCCGAGTGTGGAGAGAAGATCACGCTGTGCATCTCGGTGCTGCTATCTCTCACTGTCTTCCTGCTGCTCATCACGGAGATCATCCCGTCCACCTCGCTGGTCATCCCACTCATCGGCGAGTACCTGCTCTTCACCATGATCTTTGTCACCCTCTCTATCGTTATCACAGTCTTCGTGCTCAATGTACACCACCGCTCCCCCAGCACCCACAACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017424-5-7,5-6,5-5-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.084
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=33.4),PF103294=DUF2417=WD(100=50.0),PF0293211=Neur_chan_memb=PU(87.0=64.2)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAATGACTACAAGCTGCGCT
R:
CTGTTATAGGTTCCGGTGGCA
Band lengths:
246-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]