BtaINT0038396 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003132 | CHRNB4
Description
Bos taurus cholinergic receptor, nicotinic, beta 4 (CHRNB4), mRNA. [Source:RefSeq mRNA;Acc:NM_174517]
Coordinates
chr21:31523793-31525380:-
Coord C1 exon
chr21:31525271-31525380
Coord A exon
chr21:31524484-31525270
Coord C2 exon
chr21:31523793-31524483
Length
787 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TGCCTTGCCCCTGACCCCAGTGC
3' ss Score
6.97
Exon sequences
Seq C1 exon
GAATGGACAGACTACCGCCTGGCCTGGAACAGCTCTCGCTATGAGGGTGTGAACATCCTGAGGATCCCCGCAAATCGCGTCTGGCTGCCTGACATCGTGCTTTACAACAA
Seq A exon
GTAAGTGAAAGGTTTGGCCACGGTGGTGAGGGCCAAGCCTGGGGGTCCTCCAGTCCTGGGCTTCACCCAGACCTCCCAGCTGTCATGCTACAAGAGGAATTAGAGAAGCACAGAGCCAGCACCCTCAGTTACAGAGAGGAATTGGAGACCAAGAGATGGGAAGGATCTTAGGACTCAGGCACTGCTGGCACCAGGGCCAGCCTTCTGACCCCGAGTCTGGGGCTCTTTCTGTCCTCCATACCATCTTTTTGACTGTCAGTTGCACTGACTTGATATGCATATATATTTCTTTGTCTGTGTAGCACTGACTTGATATGCATACATATTTCAGGTAGGTGGAGGGGGCTAACAGACTTCCCAGGTCATAATTGTACTAGCAAAAGCATGAAATGATTATGAGTAGGTGGTGTAAAAACAGAAAGACCAGACTTCAAATCTTAGAGGTACTGCTTACTAGTTTTCTGAACTTGAAGACAGCTGACTTCTCTGAACCTTGGTTTTCCCGTCTGTAAAATGGGGACAATAATATTAATAATACCTACTTCATTGGACCGTTGTGAGCCTTAAATGAGCTCATCTACATAAAGCCTTTAAGCTGTTCATGGAAGGGTCTCTCTCTGCTGTGCAATTGCCAATTAAAGCAGGCCTTTCCACTGAGAGCATGGGGGGTTGGAAGAGTGACTAGTGAGAAATAATCCCACAGGGCTCTTTGGCCAGTTCTAAGAACAGCCGGACGTCATCTATGGGTTTCATGATGTTCTCCTCCGTGCCTTGCCCCTGACCCCAG
Seq C2 exon
TGCCGACGGGACCTACGAGGTGTCTCTCTATACCAACGTGGTGGTCCGCTCCAATGGCAGTGTCATGTGGCTGCCCCCTGCCATCTGCAAGAGCGCCTGCAAGATCGAGGTGAAGCACTTCCCCTTCGACCAGCAGAACTGCTCCCTCAAGTTCCGCTCCTGGACATACGACCACACGGAGATTGACATGGTCCTCAAGATGCCCTCGGCCAGCATGGATGACTTCACCCCCAGTGGCGAATGGGACATTGTCGCCCTCCCTGGGCGAAGGACAGTGAACCCACAGGACCCCAGTTATGTGGACGTGACTTATGACTTCATCATCAAGCGCAAGCCACTCTTCTATACCATCAACCTCATCATCCCCTGCGTGCTTATCACCTCCCTGGCCATCCTCGTCTTCTACCTGCCGTCCGACTGTGGCGAGAAGATGACGCTGTGCATCTCCGTGCTGCTGGCGCTCACCGTCTTCCTGCTGCTCATCTCCAAGATTGTGCCGCCCACCTCCCTCAACGTGCCGCTCATCGGCAAGTACCTCATGTTCACCATGGTGCTGGTCACCTTCTCCATCGTCACCAGCGTCTGCGTGCTCAACGTGCACCACCGCTCACCTAGCACGCACACCATGGCACCCTGGGTCAAGCGCTGCTTCCTACACAAGCTCCCCACCTTCCTCTTCATGAAGCGTCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003132:ENSBTAT00000052576:4
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(17.5=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(54.4=48.5),PF103294=DUF2417=PU(83.1=55.4),PF0293211=Neur_chan_memb=PU(45.7=48.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAACATCCTGAGGATCCCCG
R:
TCCTGTGGGTTCACTGTCCTT
Band lengths:
349-1136
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]