BtaINT0038343 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002252 | CHRNA2
Description
cholinergic receptor, nicotinic, alpha 2 (neuronal) [Source:HGNC Symbol;Acc:HGNC:1956]
Coordinates
chr8:75872774-75875070:-
Coord C1 exon
chr8:75874056-75875070
Coord A exon
chr8:75872900-75874055
Coord C2 exon
chr8:75872774-75872899
Length
1156 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
GCACCCATCTCCCCCTGCAGGTG
3' ss Score
11.1
Exon sequences
Seq C1 exon
TGCAGATGGGGAGTTTGTGGTGACCCACATGACCAAGGCCCACCTCTTCTCCTCGGGCCTGCTGCACTGGGCACCGCCTGCCATCTACAAGAGCTCCTGCAGCATCGACGTCACCTTCTTCCCCTTCGACCAGCAGAACTGCAAGATGAAGTTTGGCTCCTGGTCGTACGACAAGGCCAAGATCGACCTGGTGCAGATGGAGCAGACGGTGGACCTGAAGGACTACTGGGAGAGCGGCGAGTGGGCCATCGTCAACGCCACGGGCACCTACAACACCAAGAAGTACGACTGCTGCGCCGAGGTCTACGCCGACGTCACCTACTACTTCGTCATCCGGCGCCTGCCCCTGTTCTACACCATCAACCTCATCATCCCTTGCCTGCTCATCTCCTGCCTCACCGTGCTCGTCTTCTACCTGCCCTCCGACTGCGGCGAGAAGATCACCCTGTGCATCTCTGTGCTGCTCTCACTCACCGTCTTCCTGCTGCTCATCACCGAGATCATCCCGTCCACCTCGCTGGTCATCCCGCTCATCAGCGAGTACCTGCTCTTCACCATGATCTTCGTCACCCTGTCCATTGTCATCACCGTCTTCGTGCTCAATGTCCACCACCGCTCCGCCAGCACCCACAACATGCCCCACTGGGTGCGGGTGGCCTTTCTGGGCTGTGTGTCTCGGTGGCTTCTGATAAGCCGGCCCTTGCCACCCTTGGAGCTCCGAGACACTCCGGATCTGAAGCCCTGCCCCTCCTATCACTGGCTGGAGACCAACGTGGATGTGGAGGAGAGAGAGGAGGAGGAGGAGGAGGAGGAAGGCAGATGGGTGTGTGTGGGTCCTTCGTCCCCCTCCGTGGGCGTCTACACCCGTGGCAGTCTGCACCCAGTGGCCTCGGGTCCCAGGGCAGAGGCTCAGGTGCCGGAGGGCGGGCTCCTGCTGTCCCCTCGTGTACAGAAGGCCCTGGAGGGTGTGCACTATATTGCTGATCACCTGCGGGCTGAGGATGCTGATTCCTCG
Seq A exon
GTGAGTGGGGGCTGGGGGAGGGTCCCTCCCCTGGGTGACTCTGCCAGCCTAGAATGGAACCACTCCCCCTCCCCCAAGGGTGTTAGCTGGCACCATCCCAGTCTCCTCCATAAGGACCAACTCCCTTAGTCATGGCTTTGGAATCTGGAATACATTGTGATGGAGAACAGCTGGCTGGCCACTCTTATGACATTTATTGGCAGCCCAGCAGTAAAGGCTGTCCCAGCTCAGCTTAACTGGGAGGCAGCAGGACAGAGGAGGAGGGGTCCCCCACGCCATCCTCACGCCAGCCACTTCCCACCAGTGACCCTAGGTGGGTGGACGGGGATGAGCGGAGGCGGACGGAGGGAATTCATCAGGAGATCCTCCAAAACCGGCCTGCTCCTTTGTCCTGGTGGGCTCCCCTTCCTCGTCCTTGTCCTGGGCTCTGGTCACTTTGTCAACTTCACTATTCACCCACAAACCCTGAGGAGCTTGGGTGGGCCAAGTGGGTTCCCATTCACCCCACCCCTGCTGTGTTCTGCATATTAGGTGACAAGGCCACTGCCCAGGGTCACAGAATTCTTCTCACCAACCTTGGTAAGGATGAAAGGCCAGGAGGTTATGACTGGGTGGCCTTGTTGAGTAGATAAGAAAAATTAATTATTATCTAATCTGGAGGCACCTGGCTGGGCTGTGAGCCCCAATCCCACGAAACCCTCAACCCTCTCTGCATATACCCCCTGCTAGCCTTCTCTGGGCCATACCCTCACCTACCTTCCCAGTGGCTGGGTGAGTGGTTGGGGAGGCAACTGTGGGGGAAACCAAGTCTTCACCGTTTTGCAACTTCTGAGTGTCGTGCTGAAAATCACTCTCCTCCAGGGAGGGTTCATGCCCCTGGGTGATTCTAGAACCTTCTGTGTCCCTCTAACTCCCATAACCTGGAACTTGAGAGCCCATGGAAAGGCTCTGGGCTATTGTCATAGGGGTGGGATAGGGTGGAAATCACTAAGTGAGGGTTATTTGAGTCTTGAGACATCTTTGTCGTCCCTGCCCCCTCCACTGCCTTAGCGTCCCAAGGTCTCAGTGGGGTTGCCACTGCCCCCAGCACCAGCCTCACAGGGGCTGCGTGGATGGGTCACTTCCCCTTTCACTGTGCACCCATCTCCCCCTGCAG
Seq C2 exon
GTGAAGGAAGACTGGAGGTACGTGGCCATGGTCATTGATAGGATATTCCTCTGGTTATTTATCCTCGTTTGCTTCCTGGGGACCGTCGGACTCTTCCTCCCTCCCTTCCTGGCTGGAATGATCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002252:ENSBTAT00000002910:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=33.9),PF0293211=Neur_chan_memb=PU(86.7=63.7)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.4=73.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAGAGAGAGGAGGAGGAGG
R:
CAGGAAGGGAGGGAGGAAGAG
Band lengths:
344-1500
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]