BtaINT0038348 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017198 | CHRNA4
Description
cholinergic receptor, nicotinic, alpha 4 (neuronal) [Source:HGNC Symbol;Acc:HGNC:1958]
Coordinates
chr13:54714619-54716277:+
Coord C1 exon
chr13:54714619-54714694
Coord A exon
chr13:54714695-54716125
Coord C2 exon
chr13:54716126-54716277
Length
1431 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
GCACCCGCGTGTCCCCCCAGTGA
3' ss Score
7.48
Exon sequences
Seq C1 exon
ATGGAGCTCGGGGGCCCGGGGACGTCGCCGCTGCCGCCGCTGCTGCTGCTGCTTCTAGGGGCCGGCCTCCTGCCTG
Seq A exon
GTAAGTTTCGGGGCGCTGGAAGGACCCCCTTTCGCCCGGTTCAGGGCAGCCTCGGACCTCCGGAGCCAGAGGGAGGGAGGCTCCTGGCTGCGGTCCCAAGCCGCGGGTGCTCGCAACGGGGCAGCTGCGGAGGCTCCCCCAACCCCGCATCCCCCAGACGCAAAAGACTGTCCTGCGGGCGCGGGCGGAGCCAGGCGAAGAAAGAGTTAACCTGTTCGGCAATTCGAAGAAAAGGATTGGGGTGGGTGTGGGGGAGATGCTGTTTCAAGAGCTAGACCCAGAAGCTTCAACTTGAATGGAGATAGGTGCGGCCCACCCCCGTTTATCCATTCTGCCCAATTTCCTTGCAGGCTGCACCATGCCTGCCCACCCCCCACCCCTGGGGGCTGGGGAATCAGAGGGCTGGTCTCTGCCCTTGGCAGGGCCCCACCCAAACCCCTTCTGCTCCCCCAGGCTCACTAGGACTGTCGAGGTTCCAGCCCCCTGCTCCTCCCCATTCCCTGGGAAGCCACCTTGCTATTTCAGGGGTGCATGGAGGGAATTTAATCCTCTGGCCTCCCCAGTGAGGAAGGAGAGATACTGTACTGTCAGAGGGACCAGGCTGGGGCTCTGGGCTGGGAGTGAAGGTCCTGCGGGTCTAGGACTGATCCCAGACGTACTTGTGAATGCCCTCATGGGTCCAGCTGTAACTCCCAGGTGAGCAGGACTGAGCTGAGAGGAGCAGGTAAGCAAGGGTCTCCTGTCCTGCCCTCAGATGCCCTCCACGATGCAGTGGTCGAAGCACAGGTGCCCAAGAGTGGCAGGGAAGCTCTCAGACCACAGATTGGCCACTGGGCTGGGCTGAATGAGGAAGCCCCTCCCCAGGTTCACTCCAGACCTGGTCATTGAGGAGAGACCATCCAGGAATGCAGCGTGCCAGTCTGGGGGTGCCAGGTCACTCATGCATCCAGGATGGTCTTCCAGGATGATCACTTGCGGTTGCTGCAGCCACAGGAAACCCTCAGGGGTGGAGCCCTCACTCCCCGTCCTTCTCTCCCTGCCTGGGCCTGCCCCGTCTTGTCCTGCGGTTACCCCCGCCTTGTGCTTTGAGACAAGGTGCTCAGGACTGTGCTAGTAGCTCTAGATAGAGCCCTTCTCTCCCGCAGTCACAGTCTGATGGGGAGTTGTCCAGTCAGCACTCATCACATCAGTGATACCTTCTCACAGTGATGGACCCAGTGCTCAGAAGGCTTCCCTTCCCTGGGGTAGAGGAGAAACTGCGAACGGAAGTATGGCAGCAGGTGCAAAGGTCCTGAGATAGGAGGGAGGAATGTGCTTTGAGGGGCTGGAAGGGAGCCCAAGTGCTGAATGAGGCCTGGCAGGAGGCCCAAGGGTGCAGCCTGGATGGCCACTGTCCCCTCCCCTGAGCCACGCACCCGCGTGTCCCCCCAG
Seq C2 exon
TGAGCAGCCATGCAGAGACCCGGGCTCATGCGGAGGAGCGGCTGCTGAAGAAGCTCTTCTCTGGCTATAATAAGTGGTCCCGGCCTGTGGCTAACATCTCGGATGCGGTTCTTGTCCACTTCGGCCTATCCATCGCGCAGCTCATTGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017198:ENSBTAT00000022855:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.154 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=76.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCTGCTGCTGCTTCTAGG
R:
AATGAGCTGCGCGATGGATAG
Band lengths:
183-1614
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development