BtaINT0038349 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017198 | CHRNA4
Description
cholinergic receptor, nicotinic, alpha 4 (neuronal) [Source:HGNC Symbol;Acc:HGNC:1958]
Coordinates
chr13:54716126-54719993:+
Coord C1 exon
chr13:54716126-54716277
Coord A exon
chr13:54716278-54719948
Coord C2 exon
chr13:54719949-54719993
Length
3671 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
3' ss Seq
TCTTCTCGTTCGTGCCCTAGGAT
3' ss Score
10.14
Exon sequences
Seq C1 exon
TGAGCAGCCATGCAGAGACCCGGGCTCATGCGGAGGAGCGGCTGCTGAAGAAGCTCTTCTCTGGCTATAATAAGTGGTCCCGGCCTGTGGCTAACATCTCGGATGCGGTTCTTGTCCACTTCGGCCTATCCATCGCGCAGCTCATTGATGTG
Seq A exon
GTAGGTTCTGGGGATGGGGTGGGGGTCAGCAACCCAGGGCCGACCTGTGTCAGGGAGGGATAGGCCTGGAGATGTCCCTGGGGCTGGGGGCAGCGGGCTGGATGAGCTGGGAGGGCTGCACTTGAGTCCCAGCTCTGCCTGAGTCCTGCACATACACCTAAGCAATGCAGGGGGCAAGGACTGTTCCATGCAGTGCCCTCCAAGGCCCTGCCCATTCCTCCCTCTCCATGTAGAAAAGCTTAAAGGCCCAGATTTGCAGCAGGGGATCAGGGCTGTGACTGTCAGAGACAGAGAGCAGGAGACTCATCTGTGGGGCTAGTGCAGGGTCTGGGGTAAGTCCTGGTACTGAGTTGGTCAGGGTGGGGCCGTGTGGTGCCCTGGCAGCCCCTCTTGACCTTCACCTTGCTCAGGAGGTTCCCCCAACCTGTCTGGAATGGGGCAACCTGGCGAGTCAGACAGGCTGTCAGGTGAGTTTACTTCCCTGGATGGGAACCAAGGAGGCTATTGGGAGGAGGTCAAGGTCCAGCCTCCGAGTGGCTGCAGCTCTGGAGGCGTGGGGGTGACCATTCAGGGTGGGGGCCTGTCCTATGGGTCTAACTGCGTGTTGGCTGCACATCCTGGGGCAGCAGCCAAGGGCCTTGGAGTGTGGGCTCCAGCCTGGCCTGGAGGAGTCCTCCAGGAGTTGGTTTGCTGGCTGCAAGAGGGTCTGAGGCTGGCTGGGTTTGGACTGGGGTTTCCAGTCAGCTCAGGTTCCAGGAGGAGCTGCCAGGGGCTGTAGATCTCTCCAAATATCCACCCCATGTCCCTGACAGGACCCCAACCCCAAGTGGGCTCTGTGAGGGGGGGGAGCCACCAGTTTCGGAGCCTGGAGATCCTGGTTTCCAGCTCGTGCCAGGTGTATTGAGTGGCCCCTTGGGGTCTTGGCCTTCTCACCTGTGGAATGGGATGAGTGAGCCAGCAACATCCGAGGGGCTTTGGGAGGTGAAGGGTGGGGGCTGTGGCCACGTTCACACTGACAGAAAGAGCCATGCTTGCGCCCCATTAGCAGAGAGACCCGGTCAGTCTCCCATCCTGGCCTGTGCTCTCAGGCCTCCTGGAACCAAGCCTCAAATGCTTCTTGTAAAGTACTCCTGGCTGGGGTGCAGCCAGAAGGCAGCTCAGGATGGCGAGGGTTCCGACCCACTGCGTTCGTAAACACTATTCCCAGTATGGCTGTGGCTTCATGTTCTGGGTCAGCTGCACTGTGGCCTGGCCTCCTGCCTGAGCTCCTGGGGTTTTCTCGTCCCCCGGCCACCATGTTGCAGCATCCCCCCCACTCCCACATCGCAGCATCCTCCTCCCCTCCATCTCCCTAGTTTGCCCAGGAGAGACAGCCGGAGCACACCAGTCCCGAAACCCCAGTGTGGGACCCACCAGTGGCCCCATGGCAGCACCGGGCTGGACAGGAGCTGCTCCAGCCCTACTGTCTGCAGCTGAGTTGGCCAAGGACACTCCTGCACACGTGTGCTGATGAGACGTCCTTGCCTGTCCTGGGTGCTGGCCTTTTGTGGAAGGGGCCGCCTCCCTGCCCACTCTTTGAAGGGCTGCAGTGTTTGCTGCAGGTTTGTGCCCTGGTGTGTGTGTGTTCGTGTGTGTTCACGCCTGCAGAGGAGGCTGGGAATCCCTGGGCACCTCTGGGCCCTGGACTAACATTTCAGGTGCCCGAATGTACGAAGGGCACTTCATACGGGTGGGGTGAACGGGTAGACAGCTGCAAGGGGGGTGTGTGAGGGGTGGGCACAAGGGGAAGGAGGCCAGGCCCGGCACCTGGAAGCTTGATCTGGGGGCAGGGAATGGGGCAGAGCCGGGCCAGCTTCCCCTGGGGGAATGGAAGGATGTGGTGGTGGGGGCGGCATCACTGCAGGACTGCATTGCCAAGGTCAAGGTCGTTGGAGTGGTGTCCGGGCCCTGCTCAGGTCATGCTTATCCTCAGTGTCCTCTGGCGGCATGTCCCAGGTGGCCCTGAGGGAGATCAGGACCAAGGCAGTGCCTGGGGTGGCAGGAGATGTGGTCCCTTCCCGTGACCCAGCCGACCCAGGGCTTGTCCCCTGGACAGGAGGGGAGACTCCCCGGCCTTGCCTTTGAATAACCATCTGCCCCCAGCCCTGGTCTGGGCACTGGGTGCTTCACTTCTTGACCATCCTCGCGTTTCTTTGGGCTGAGCAGTCATCCTGATGACCTGTGTGTCCCTGGTCTAGAGCCGACAAGGGAAAAAGTTGGGCCATCATAAAGTGGGGAGAGGCTGGTTCAAGCACCGCCCCCCAGAGCCTGTGTCCAGTCCCTCTACTCTCCCCAGGGGAACAGTCCCTGTCCCTCAGGCCCTGCGGGCACCCTGCTGTCTGAGAAGTACCCTCCATCAGCAGCAAGTGTCCCACCCCAAACCTTTTGCAAGGAGCCAGCCCCCTCCAGCCCCAACCCAGCTGCCCTCTGCCTGGGCTGGGTGCTGCATGGTCCCTGCAGGTTCAGGGTGGGGTAAGAGGACCCCTACATCCATGCACAGAGGCTGGCGTTCTTCTCCAGCCTGTGCTGGTGTCTGACTGCCTGTGTCCAGTGAACAGGAGGGCTGGGAAGAGGGGAGGAGGGCTGGGAAGAGGGGAGGAGGGAGCAGGGAGTGTGTGTGTGTATGTGAGTATGTGTGAGTGTGTGTGTATGAGTGTGTGTGTATTGTGTGTGTGAGTATGTGTGTGTGGGTGTGTCAGTGTGTGTCAGTGTGTACGCATGCATGTGAGTGTTGTATATGAGTGTGTGAGCGTGTGTGTATTGTGTGAGTGTGTGTGTCAGTGTGTATGTGTGTGTCAGTGTGTATGCGTGCATGTGAGTGTTGTATATGAGTGTATGAGTGTGTGTGTGCTGTGTGTGTGTGTGTTGTGTGTATGTGTGAGTGTGTGTGTATTGTGTGTGTTTATGCGTGCATGTGAGTGTTGTATGTGAGAGTGTGTGTGTTGTGTGTGTGAGTGTGTGTGTATTGTGTGAGTGTGTGTGTATGCGTGCATGTGAGTGTTGTATGTGAGTGTCAGTGTGTGTGTGTAGTGTGTGTGAGTGGTGTGTGTGTTCCAGCCCTTCTCGCCTGGCAGGGGGCTTCTCAGTGACCTGTAGAGGAGCCTGCCGGGTCTCCTGCTCCCGCCTCACCTGTTCTTGACCCTCACCTGTCTACCTCCAGGTCCTGAGGCTCTGGGCCTGGAGAGGCAGTTTGGCCAGTGAGTGGGTGGCTCAGGGGTAGTGGAGGGGGCAGGCTGGCCAGCTGGGAGGGAGTGATGCAGGTGGGCAGGACCAGCATGGGCTGCTGGGAAGAGGGCAGCTCCTCCAGCAGCTAGGAGCCCTGGGTGCTGCATACACCCTTACTTACGTAGCTGGAGAGGGCCAGGCCCAGCCACCTGTAAAGTCAGCTGGACACTGTCCACACTTTCCTTCTTAGAAGGGTCAAGGGGACTTACCCTGTGGCCCTCAGTCCCCTCTGGGCCTGCCATCCTGGGCTTGGTTGCCTCCAGGGGCGAGACACTCCCTCCCTCCTGAGGTCACCCAGTCCCCATGTTCGGCCCTGGCCCGTCCTTGTGGGTAAGGAAGCTTGGCCAGAGAGATGTGTCCTGAACCAAAGGGGATCACAACCTGCCTTCTTCTCGTTCGTGCCCTAG
Seq C2 exon
GATGAGAAGAACCAGATGATGACGACGAATGTGTGGGTGAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017198:ENSBTAT00000022855:2
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=PU(18.8=76.5)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.8=100)
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]
SPECIAL DATASETS
- Pre-implantation embryo development