BtaINT0038352 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017198 | CHRNA4
Description
cholinergic receptor, nicotinic, alpha 4 (neuronal) [Source:HGNC Symbol;Acc:HGNC:1958]
Coordinates
chr13:54723241-54727493:+
Coord C1 exon
chr13:54723241-54724576
Coord A exon
chr13:54724577-54727170
Coord C2 exon
chr13:54727171-54727493
Length
2594 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
CCGTGTGTGTCTGTCTGCAGGTG
3' ss Score
12.49
Exon sequences
Seq C1 exon
TGCGGACGGGGACTTTGCCGTCACCCACCTGACCAAGGCCCACCTCTTCCATGACGGCCGGGTGCAGTGGACGCCCCCAGCCATCTACAAGAGCTCCTGCAGCATCGACGTCACCTTCTTCCCCTTCGACCAGCAGAACTGCACCATGAAGTTCGGGTCCTGGACCTACGACAAGGCCAAGATTGACCTGGTGAGCATGCACAGCCGCGTGGACCAGCTGGACTTCTGGGACAGCGGTGAGTGGGTCATCGTGGACGCCGTGGGCACCTACAACACACGCAAGTACGAGTGCTGTGCGGAGGTCTACTCGGACATCACCTATGCCTTCATCATCCGGCGCCTGCCGCTCTTCTACACCATCAACCTTATCATCCCCTGCCTGCTCATCTCCTGCCTCACCGTGCTTGTCTTCTACCTGCCCTCCGAGTGCGGCGAGAAGATCACCCTCTGCATCTCCGTGTTGCTGTCGCTCACCGTCTTCCTGCTGCTCATCACCGAGATCATCCCATCCACCTCGCTGGTCATCCCGCTCATCGGCGAATACCTGCTCTTCACCATGATCTTCGTCACGCTCTCCATCATCATCACCGTCTTCGTGCTCAACGTGCACCACCGCTCCCCGCGCACACACACCATGCCCGCCTGGGTCCGCCGCGTCTTCCTGGACATCGTGCCGCGCCTGCTCTTCATGAAGCGGCCGTCTGTGGTCAAGGACCACTGCCGGCGGCTCATCGAGTCCATGCACAAGGCGGCCAGCACTCCGCACTTCTGGCCGGAGCCCCAGGGGGAGCCCGCCCGGTCTCCGTCCCTGACCTGTGGGGTGGACCAGCCCATCAAGCCCCAGCCAGCCCGTACAACACCCTCTGACCAGGTGCCGACTCTGCAGCCTTCAGAGACCGAGAAGGCCAGCCCCTGCCTATCTCCTGGGCCCTGCCGTCCACTCACTGGCACCCAGGCCCCAGGGCTCACCAAAAGCCGGTCCCTAAGTGTCCAGCACGTGTCCAGCCCCAGCAAAGCGGTGGAGGACGGTGTGCGGTGCCGGTCCCGGAGCATTCAGTACTGCGGGCCGCGAGAGGAGGCCGCCTCACCGGCCGCCCACCTGGCGGATAGCTCCCCCTCCTCTCCGACCAAGGCCCCCTCAGCCGAGCTCCCGCCCCCAGACCAGGCTGCCTCCTGCAAATGCCAGTGCAGGAAGGAGCCGGGGGCCCCAAATGCCACGCTCAAGACCTCCAGCACCAGAGCACCACCCCTGCCCCTGTCGCCAGCCCTGGCACGGGCGGTGGAGGGCGTCCAGTACATCGCAGACCACCTGAAGGCGGAAGACACAGACTTCTCG
Seq A exon
GTAAGTCTCCACCACAGCCACCTGGAGGAGGGGGACTCGCTGCCCTCTCCATGTCATGGGGCCCCACCACCCCATCCACTTTGAAGGAGGAGGTGACTGGTGAAAGACAGAGAAACCAGGACCCCAACCCGGCTGTTCCCTGTGCCCCAAGCCTCCATCAGCTTGGGGGCAGGAGGTACCCCCAGTTGTGGCCCTGTTGGAGCAGAGTGGACCTCTTGTGTCTCCTTTGGGCTTCAGGGCACAAGGAGCCTGCCTGCAGGTGGGGTGTTAGGCAGCCCCCAGCGCCATCTGCACCTGGTGAGCACCTCCCTCGACCTCAAGTGCCCCCCACCCTGCTGTGGGCCCCCCGGGGAGGGTCTGCGGTGAGAGGTGCTGAGAGGAGATGGGATGAGATTGAGTGGCCTCTGTGGCCTAGCACGGGGAGAGGAGAAATCAGGCCTGGCACACAGGACCCTCTGGCCAGCACCCTCATGCTTGGCCAGAGAGAGGGCGCCTGAGGTCTGGATGAGCAGGGCAGGTGCTCAGACACGGGTCATAATCAGGGCCCTGTGGAGTCAGGGACTGCAAGGGTGAGTCCAGGCTGAGGGCCAAGCCCCAGTTCAGATCCTGGGTGGGGTGGGGCAGGGGAGCACATAGGCGGGTGGGGGAGGGCACCGCTCAGTCTGCTTGGTCATTACTGGCCGCTCAACCTGGGCTGTGACCTTGCCCCACATCAGCTTCCTCCTGCAGGAACGAAGGCCTGTGGGCAGGCAAGACACTGCAGTTCCCTCCCCGACCTCTTCATCCCTCTGCCTCCTCGGGAACAGCCCGTGATCGTTTCCCAGACACACATGATCCCTGGGGACTGTCTGTCCTGTGGCTGGGCCACCCCACCTAAAAGCGAGTCAGTCTCCTAGCTGCCCTCTGAATCCCAAGGGGTTGTGAAGTCATCCGAGGGTTTCTGGAAGGTTCCACCGGGAGACGCTGGCTCTGGGCCCGTTGTGTTCCCCAGTTCTTGAGGAGCTCTGACGTGCGGGTCTGAGGGGCTGCTGAGAAGAGATCGATGCCTTTGAAGTGTCACCAGGATCTCGGAGGCGCCCAGTGGTTCTTAGTGCAGGGCCAGCCCCTTGTCCCCAGACCCCTCCATCCGCATCACAGGCCCAGCTGTCACAACCTGGTTCTGGTTCCGGCATTGTGCCCAGGTTCTGGGAAGCAAAGCAACTTCAGAGGAACCGACCTGGGATGGGGGCTGGGCGGCTTTGTGAGCAGCGTTTCAACCTCCGAGGGGGCGGCTGGAAAGACTGCTCCTGCTCGGATGCGGCAGCACCACTGGCTGCTTCATAGAACAGAGGGTCCTGTCGCTCCCTGGCTTACAAGTGACCCCATTTGCTCTGGTTACCCGAGAATAAACTCGGCCCTTTCAGCTTTGGCTTAAAACTGTCACGATGCAGCTGATTACTTTAAACATCAGAGCAGAAAACCACAGTGAAAAGTTCTCTTTCTCTCAAGGCCCCCAAAATGGGAGGCTGAGCCTGCCCTTGGCCAGGCCTGTGGGCCCTGCTAGGGTCCAGCGGGCCGGAGCCCAGGTGCCCCTCCTTTCTGGTCACTCAAGTGCTGACAACCACCCACCCAGGACCCGCCTGTGGCCTCCCTAAGGCTTTGTCTGGGGGCACCCCAGGTGGGGTTGGGACCCACTCCCCCAGCGTGGACATGTAACATGACCTGTCCTGCCTCTGGGCCTCTGTGTACCCCCCTGCAGCCCAGATGGTCAGCCACCTTCCTTGTCGGGTCCAGGGAGTGGCCGCAGGTGGTGGGCTCAGTACGTTCCTCACCTCGAGCCTGGGGTCCCCTCCCTTGTCCCCGGGGAGCCCTCCACCCAGCAACTGCACGCTCAGAGCCTGCTGGCAGCACAGGGCTGTGCCTGTATTCACGTCTGATCCTCACCCTCAGGGTCTTTGGGGACAGACCTGAGCGTCCCACTGACCATGAGGGGCTCAGGCCACCTGAGCAGCCAGCCGTGAGCCCTGCCCTGGGCAGAGGCAGGAGTGAAGGACAGCCAGCTGTGAGCACTGCCCTGGGTTTCTTGCTGGAGGTCAGCTCCCCCCGCCACTATCCAGGATGCTCTGGCCCTTGCCTTGCACTGTGAGGGGCTGTGGGTGCCTGCTGACTCCAGCCTCACTGGCTCCATCTGTAAATGCGGGGGCTGGGTGGTCCCCATGGTGCCACCAACTATCAAAAACCCAGAGCACACTTCACCGTGTCATAGCCTGGACCCTAGCCTTCCTTCAGAGGCGTCCCCACCACTACCTCCTGGGAGCTCAGGCACCTGCCCGGCTGGTGGAATTGGTAGGGCCACCATGCTGGACCCCATTTCCCTCAGTGGCTTTGCTGCCACCCCCATAGACAGTGTTGGCACCTACAGCCCAGAGTTTCTGAGCCCAGACTTCAGACAAAGCCCTTTCGCTGCATCCCCTCCACACCCCTTACCCAGCACAGCTATGCCTGCAACCTTGGTGACCCTGGTGGCAAGAATAGGAACAGAGGTTCTAGAAGTTTCTTGCTGTGGCGAGGCCTGAGGGAGGCAGCTGGGAGTGACCGTGTGTGTCTGTCTGCAG
Seq C2 exon
GTGAAAGAGGACTGGAAGTACGTGGCCATGGTCATTGACCGCATCTTTCTCTGGGTGTTCATCATCGTCTGCCTGCTGGGGACTGCTGGCCTCTTCCTGCCTCCCTGGCTGGCCGGCATGATCTAGGGGCCCGGACTCGGGACTTCCTGAACTCGATGGGGTCATGCCACTTACCAGATTGCCCCCCATCCTCTGTCTGCTATGAGACGGCCTTGGAAGGAGCCTCTGACCCCTGGGGACCCCTGGGGACCCCTGGGGGACTGGTGAATGCCCGTTTGTCTGCAGGGCGGTGTCACTGCCTGTCTTATTAAAGTTTAACCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017198:ENSBTAT00000022855:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.287 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=25.8),PF0293211=Neur_chan_memb=PU(90.7=72.4)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(8.7=73.8)
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