DreINT0046789 @ danRer10
Intron Retention
Gene
ENSDARG00000038508 | chrnb3b
Description
cholinergic receptor, nicotinic, beta 3b (neuronal) [Source:ZFIN;Acc:ZDB-GENE-030102-4]
Coordinates
chr14:41158120-41160568:+
Coord C1 exon
chr14:41158120-41158229
Coord A exon
chr14:41158230-41159691
Coord C2 exon
chr14:41159692-41160568
Length
1462 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TATCACTTGCCTGCTTGTAGCGC
3' ss Score
7.31
Exon sequences
Seq C1 exon
GAATGGCTGGATTATAAACTGCGCTGGAACCCTGAGAATTATGGTGGGATCACATTTATCAGAGTCCCGTCAGAGAGCATCTGGCTCCCAGACATCGTTTTATATGAAAA
Seq A exon
GTAAGTTTGTCTGTCAATCATATACAACAGCAGTTTATTATGAAAAACATTCAAGGGTCATGAAATCACAAGGCTGTTTCTTACCACAGTTCTGAAAAATGCTAAAAAACAACAAAAAAAAGTGGAATTTATCATGACTCTCATTGAGTTTAAAAATACTTTTCACAAATGCTTGCTGCAATTCACTTTACAGTAACAAAATAAACATATATAATTACATTTAATATAAATGATAAAAAATAACATACATGATATAAAAAGGGGAAGCACAGTGGCTTAGTGGTTAGCACTGTCGCCTCACAGCAAGAAGGTCGATGGTTTAAGTTCTGCCTGGGTCAGTTAGCATTTGTGTGGAGTTTGCATGTTCTCCCTGTGTTCATGTGCGTTTGCTCCGGGTGCTGTGGTTTCCACCACAGTCCAAAGACATGCACTATATAGGTGAATTAAATAAACTAAATTGTCCCTTGTGTTTGAGTGTGTGAATGAGTGTGTATGGGTTTTTCCCAGTACTGGGTTGCTGCTGAAAGGGTATTCGCTGTGTAAAACATATGCTGGAATAGTTGCCGGTTCATTCCACTGTGGCGACCTCTGAAATAGAGACTAAGCAGAAGGAAAATGAATGAATGAATGAATTGTAGTGTTCCATTTAGTTGTGTTAATATCCATTTAATGTTTTTGCGACTATTTAAAATGTTATTTAAACTGTCCATTTAAGCTTGTTTTTTTTTTGTTTTTTTTTACGTTTATGTTCCATAATGGCAAAACATTCTGCTAACATTTTTGGATGAATGTTTACTGTTAGCTAGACCATTTAAAGCACATACAAAAAACATATACGGACAGTTCAACCAGAACAAGAAAATTCTGTGTAATTTTTTTTTTGTGAAAACTGATGCATTTTTTCAGGACTCTAGTGAAATATTACATTACAAATGTTTTACTTTTGAACAGTTTACTGCACAGTTAAATGTAAAATTATTAGCCCTGATGTGAAATTGTTATTCTTATAAAAATATTTCCCAGGTGATGTAAAATATGTCCCAAGTGACATTATGAAAGTGAAGTATATTGGTAAGCAGCAGCCACAGACATCTAAAATATATATTTTTCTACTATGAATGTCAACGGCTGCTGGTTTCAAACACTCATGGGAATATTCGTATTTGTGTTTAACAGAAGAAAGAAATTCCTAAAACCACTTGAGTGTGAGTAAATGTTCATTTTTGGGTGAACGACCCCTTTTAATTTGAAGTAATGCAAACTATTTAAAACAGGGGTGTCCAATCAGACACACCTGGGTTAGCTAATCAAGCTTACTAGGCTTTCTAGAAGCATCCTTGCAAGTTGGAGCCAAAATTGGCAGGACACTGGCCGTCCAGACCTGGTTAAAATAGATAATGGAGTTTATATAACATGTGAAGTCCTTCATGACTCTTTAACAGTATCACTTGCCTGCTTGTAG
Seq C2 exon
CGCAGACGGACGTTTTGAAGGCTCGATCATGACCAAAGCCATCGTGAGATACAATGGCCTGATCACCTGGACTCCTCCCGCCAGCTACAAATCTGCCTGCACCATGGACGTGACCTTCTTCCCGTTCGATCGGCAGAACTGCTCCATGAAGTTCGGCTCCTGGACCTACGATGGAAACATGGTGGAGCTAGTCCTTGTTAACCATCAGGTGGACCGAAGCGACTTCTTTGACAATGGCGAATGGGAGATTCTCAGCGCGACAGGGCACAAAGGCAGCCGACGGGACGGTCATTACTCCTACCCCTACATCACATACTCATTCATCCTAAAGCGCCTTCCTCTTTTCTACACGCTCTTTCTTATCATCCCGTGTCTGGGTTTGTCTTTCCTGACCGTTCTGGTTTTCTACCTTCCCTCGGACGAAGGAGAAAAAGTCTCTCTATCCACCTCCGTCCTGGTGTCGCTCACCGTCTTCCTTCTCGTCATCGAAGAAATCATTCCGTCTTCCTCTAAAGTGATCCCTCTGATCGGAGAGTATCTGCTTTTCATCATGATCTTCGTGACACTCTCCATCATCGTGACGGTGTTTGTTATTAACGTTCACCATCGCTCTTCAGCCACGTATCATCCCATGTCTCCGTGGGTTCGTACTCTGTTCCTCCAGCGGCTGCCGGATTTGCTGTGTATGAGGGGAAACACCGACCGCTACCATTACCCGCAGATGGAGCCCCAGAGCCCTGATCTGAAGCCCAGGAGCAAGAAAGGGCCACCTGGGCCTGAAGGAGACGGTCAGGCGCTGATCAACATGCTGGAGCAGGCCACTAACTCTGTGCGCTACATCTCACGGCATATCAAGAAGGAGCATTTTATTAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000038508:ENSDART00000050037:4
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=0.096
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.1=38.6),PF0293211=Neur_chan_memb=WD(100=49.5),PF0293211=Neur_chan_memb=PU(61.2=17.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATAAACTGCGCTGGAACCCTG
R:
GCTGAGAATCTCCCATTCGCC
Band lengths:
353-1815
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]