BtaALTD0005287-2/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000011390 | CHRND
Description
Bos taurus cholinergic receptor, nicotinic, delta (CHRND), mRNA. [Source:RefSeq mRNA;Acc:NM_174271]
Coordinates
chr2:120976508-120976870:+
Coord C1 exon
chr2:120976508-120976585
Coord A exon
chr2:120976586-120976617
Coord C2 exon
chr2:120976715-120976870
Length
32 bp
Sequences
Splice sites
5' ss Seq
CAAGTTGAG
5' ss Score
-10.48
3' ss Seq
CCCTTGTCCGTGTCCCCCAGCAA
3' ss Score
7.97
Exon sequences
Seq C1 exon
GGCTGGACAGACAGCCGGCTGCAGTGGGATGCAGAAGACTTTGGGAACATCAGCGTCCTGCGTCTGCCCGCTGACATG
Seq A exon
GTGTGGCTCCCAGAGATTGTGCTGGAGAACAA
Seq C2 exon
CAATGACGGCTCCTTCCAGATCTCCTATTCCTGCAACGTGCTCATCTACCCCTCGGGCTCCGTCTACTGGCTGCCACCCGCCATCTTCCGTTCTTCCTGCCCCATCTCTGTCACCTACTTCCCCTTCGACTGGCAGAACTGCTCCCTCAAGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011390-4-5,5-5-2/2
Average complexity
Alt5
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=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(16.3=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(23.5=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGTGGGATGCAGAAGACTT
R:
GAGGGGTAGATGAGCACGTTG
Band lengths:
112-144
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development