BtaINT0038335 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018253 | CHRNA1
Description
Bos taurus cholinergic receptor, nicotinic, alpha 1 (muscle) (CHRNA1), mRNA. [Source:RefSeq mRNA;Acc:NM_176664]
Coordinates
chr2:22129883-22132799:+
Coord C1 exon
chr2:22129883-22130078
Coord A exon
chr2:22130079-22132561
Coord C2 exon
chr2:22132562-22132799
Length
2483 bp
Sequences
Splice sites
5' ss Seq
CCGGTATGT
5' ss Score
9.2
3' ss Seq
GTTTCACTCTGTCTTCTCAGGAG
3' ss Score
8.76
Exon sequences
Seq C1 exon
TGCAGATGGTGACTTTGCCATCGTCAAGTTCACCAAAGTGCTCCTGGACTACACTGGCCACATCACATGGACACCTCCTGCCATCTTTAAAAGCTACTGCGAGATCATCGTCACCCACTTTCCCTTTGACGAACAGAACTGCAGCATGAAGCTGGGCACCTGGACCTATGATGGCTCCGTGGTGGTCATCAACCCG
Seq A exon
GTATGTGATGACCCCTTGGGAGGAGTTTGGATGCAGGAAAAGCAAGACTTAGGTCTCCAACTCTGCCCCTACATTATCACAGGCTTGCTGCATCCATTAGCTCTTTGGGGATCATCTACTTTCATGCTTTTCAATGGCTTGGGCAAGTTCTTGACATGCTACATAAGAGAACCATCTGGGGCTTACATAATTTCCTATGCCCAGACTCAGGCCCAATAATTCTGATTGAATCAGCCTAGGGTGGAGCTAGGGCACCAATAGGTTTTAAAGCTCCCAGTTAAGTTCAGTCGCTCAGTTGTGTCCAACTCTTTGCAACCCCATGGACTGCAGCATGCCCTGCCTCCCTGTCCATCACCAACTCCCAGAGTTTACTCAAACCGATGTCATCCAACCATCTCATCCTCTGTCATCCCCTTCTCCTCCCACCGTCAATCTTTCCTGACATCAGGGTCTTTTCCAATGAGTCAGCTCTTCGCATCAGGTGGCCAAAGTATTAGAGTTTCAGCTTCAGTGTCAGTCCTTCCAATGAACACCCAGGATTGATCTCCTTTGGGATGGACTGGTTGGACCTCCTTGCAGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCAAAAGCATCAATTCTTCGGCGCTCAGCTTTCTTTATAGTCCAACTCTCACATCCATATATAACCACTAGAAAAACCATAGCCTTGACTAGATGGACCTTTGTTGGCAAAGTAATGTCTCTGCCTTTTAACATGCTGTCTAGGTTGGTCATAGCTTTTCTTCCAAGGTGTAAGCGTCTTTTAATTTCATGGCTGTAATCACCATCTTGCAGTGATTTTGGAGCCCTAAAAAATAAAGTCAGCCACTGTTTCCACTGTTTCCCCATCTATTTGCCGTGAAGTGATGGGACCAGATGCCATGATCTTCGTTTTCTGAATGTTGAGCTTTAAGCCAAGTTTTTCACTCTTCTCTTTCACTTTCATCAAGAGGCTCTTTAGTTCTTCTTCACTTTCTGCCATAAGGGTGGTGTCATCTACATACGTGAGGTTATTGATATTTCTCCTGGCAATCTTGATTCCAGCTTGTGCTTCATCCAGCCCAGCGTTTCTCATGATGTATTCTGCATATAAGTTAAATAAGCAGGGTGACAATATACAGCCTTGACGTACTCCTTTTCCTATTTGGAACCAGTCTGTTGTTCCATATCCAGTTCTAACTGTTGCTTTCTGACCCGCATACAGGTTTCTGAAGAGGCAGGTCAGGTGGTCTGTTATTCCCATCTCTTTCAGAATTTTCCACAGTTTATTGTAATCCACACAGTCAAAGGCTTTGGCATAGTCAATAAAGCAGAAATAGATGTTTTTCTGGAACTCTCTTGCTTTTTCCATGATCCAGCAGATGTTGGCAATTTGATCTCTGGTTCCTCTGCCTTCTCTAAATCCAGTTTGAATATGTGGAAGTTCACGGTTCATGTATTGTTGAAGCCTGGCTTAGAGAATTTTGAGCATTACTTTGCTAGCGTGTGAGATGAGTGCAATTATATGGTAGTTTGAGCAGTCTTTGGCATTGCCTTTCTTTGGGATCAGAATGAAAACTGACCTTTTCCAGTCCTGTGGCCACTGCTGAGTTTTCCAAATTTGCTGGCATATTGAGTGTAGCACTTTCACAGCATCATCTTTTAGGATTTGAAATAGCTCCACTGGAATTCCATCACCTCCACTAGCTTTGTTCGTAGTGATTCTTCCTAAGGCCCACTGGACTTCACATTCCAGGATGTCTGGCTCTAGGTGAGTGATCACACCATTGTGATTATCTGGGTCATGAAGATCTTTTTTGTACAGTTCTTCTGTGTATTCTTGCCACCTCTTCTTAATATCTTCTGCTTCTGTTAGGTCCATACCATTTCTGTCCTTTATCGAGCCCATCTTTGCATGAAATGTTCCCTTGGTATCTCTAATTTTCTTGAAGAGACCTCTAGTCTTTCCCATTCTGTTGTTTTCCTCTATTTCTTTGCACTGATCACTGAGGAAGGCTTTCTTATCTCTCCTTGCTAGTCTTAAAGCTCCCAGGAAACTTGAAAGTATAGTCAACATGGAAAAAATCCCAATAGTCCCAACCTACTTATTTTTTATTTTTTTAAAGATTTTTTTTTTGGATATGGACCATTTTCAAAGTCCTTCCTGAATTGTTACAACATCACCTCTGTACTGCTTTGGTCCCCTGGCAGAGCAGCATGTGGGACTCCAGCTCCCCAACCAGGAATCAACCCCACACCCCCTGCATTGGAAGGTGAAGTCCCATCTGCTGAACTACCAGGAAAGTCCCCAAGCCCCTTCCTTTATGGGGGGGGGATAGGATACACAAGATCCCCTCCTAGGTATGTGACAGCACTGGAATCTGTTGCTTTGTCACAGCTGACTAGGAAACCCTGCGGCTCCTCATGGTGACAAGGCTGGACATGTCAAAGTTTCACTCTGTCTTCTCAG
Seq C2 exon
GAGAGCGACCAGCCAGACCTGAGCAACTTCATGGAGAGCGGAGAATGGGTGATCAAGGAGTCGCGGGGCTGGAAGCACTGGGTGTTCTATGCGTGCTGCCCCTCCACCCCCTACCTGGACATCACCTACCACTTCGTCATGCAGCGCCTGCCCCTCTACTTCATCGTCAACGTCATCATCCCCTGCCTGCTCTTCTCCTTCTTGACCGGCCTAGTGTTCTACCTGCCCACAGACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018253:ENSBTAT00000024298:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(31.2=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(24.0=62.5),PF0293211=Neur_chan_memb=PU(15.3=27.5)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]