BtaINT0038339 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002252 | CHRNA2
Description
cholinergic receptor, nicotinic, alpha 2 (neuronal) [Source:HGNC Symbol;Acc:HGNC:1956]
Coordinates
chr8:75884421-75885860:-
Coord C1 exon
chr8:75885788-75885860
Coord A exon
chr8:75884573-75885787
Coord C2 exon
chr8:75884421-75884572
Length
1215 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCTCCCCTCCTGTCCAACAGTAT
3' ss Score
8.85
Exon sequences
Seq C1 exon
ATGGGTCCCTCCCGTCTTGTGCTCCCGTTCAAGACAAAGCTCGGGCTCTGGTGGCTTCTTCTGATCCCGGCAG
Seq A exon
GTGAGCGGGGGCGGTCCCCAGGGCATCCTGTCACACATGCGAGCGCACATGCCTCCGGTTGAAACTGCTGCAAGTGGGTTGGTGGTGACCCGCCAGAGCCTCAGGGTAGCTGTTCCATCGCGGGAAGGTAGGGGGCGCTCGCTGCGGCATCTGAACCTCCCAAGCCCAGTTCTCCCCATCTGCAAAATGCTAACTGTGCCGGTACCTTCCCAGGGCTCTTGGGCGTGTGACCTGGAATGAAGGCTAGTGACTAGCACCTGAGATACATACATGGCAGCTGCTATCGATGTTTTGAATTTTAGAGCGGGGGTTCTCGCCCTGCTCAGACAGGAGAACCCTGTAGAGGTGAAGCTGTTTGCAGAACAGGGTGAAACCAGACAAGGGGTGATTCCGTCAGACAATCTGGGGAGACTTTACCTAGCTGATGAGAAGGAGCAGATACCAGTGGTTTGAGGAAAAACAGGGGAGATTCTCCGAGTAGCAGAGAATTTCATGGTTAGCATTAGAGGTTCCTTATAAGAGGATGGGAGTGAAAGTTCCCGGGGCCAGCTCACCCCACACAATCAGGTGCCTCTCACAGTTTGCTGTCCCTTGGGTCTCCTCAGTTCCAGGCTTAATCTTTTCCCTTTGTCTGACTTCTTCCCACTGCTCTGCACGCCTCTGAGCACTTGTTTTCACCCCTTATCCATTGTTGTTGCTGTTCAGTTGCTAAGTTGTGTCCGACTCTTTGTGACCTCATGGACTTTGGCACGCCAGGCTTCCCCGTCCTTCACCATTTCCTGGAGTTTGCTCAAACTCATGTCCATTGAATCGATGATGCCATTCAATCATCTCATCCTCTGCTGCCCCCTTCTCCTCCTGCCCTCAATCTTTTCCAGCATCAGGGTCTTTTCCAATGAGTCAGCTCTTTGCATCAGGTGGCCAAAGTACTGGAGCTTCAGCTTCAGCATCAGTCCTTATCCAGTAGTCATAGAGTAACTGATATTGCTTGAGTGCCGACTATACACTGATCGGTTGCTTTGTAAGCTCGAACAGACGTTATTATATTTCATTCTCAGCAGTGTTTTGACATAGGTACTGGATTAGTGTGCTCATTTTGCAGATAAGGAAACTAAGGTTCAGTGAGGCTGAGTGGCTCTGGTTGGATGGGAGAGGGAGCCAAGCCCCCAGCACCACGGACTCCTGGAAACCCCCATCTCCCCTCCTGTCCAACAG
Seq C2 exon
TATCCTCGAAGAGGGCCCCCCACACCCAAGCTGAGGACCGCCTCTTCAAACACCTCTTTAGGGGCTACAACCGTTGGGCGAGACCGGTGCCCAACACCTCGGACGTGGTGATCGTGCGGTTTGGGCTGTCCATCGCCCAGCTCATCGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002252:ENSBTAT00000002910:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 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
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCCTCCCGTCTTGTGC
R:
CACATCGATGAGCTGGGCGAT
Band lengths:
222-1437
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]