DreINT0046790 @ danRer10
Intron Retention
Gene
ENSDARG00000038508 | chrnb3b
Description
cholinergic receptor, nicotinic, beta 3b (neuronal) [Source:ZFIN;Acc:ZDB-GENE-030102-4]
Coordinates
chr14:41159692-41162886:+
Coord C1 exon
chr14:41159692-41160568
Coord A exon
chr14:41160569-41161807
Coord C2 exon
chr14:41161808-41162886
Length
1239 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
CTGTGATTTGTCTTTCACAGGTT
3' ss Score
11.19
Exon sequences
Seq C1 exon
CGCAGACGGACGTTTTGAAGGCTCGATCATGACCAAAGCCATCGTGAGATACAATGGCCTGATCACCTGGACTCCTCCCGCCAGCTACAAATCTGCCTGCACCATGGACGTGACCTTCTTCCCGTTCGATCGGCAGAACTGCTCCATGAAGTTCGGCTCCTGGACCTACGATGGAAACATGGTGGAGCTAGTCCTTGTTAACCATCAGGTGGACCGAAGCGACTTCTTTGACAATGGCGAATGGGAGATTCTCAGCGCGACAGGGCACAAAGGCAGCCGACGGGACGGTCATTACTCCTACCCCTACATCACATACTCATTCATCCTAAAGCGCCTTCCTCTTTTCTACACGCTCTTTCTTATCATCCCGTGTCTGGGTTTGTCTTTCCTGACCGTTCTGGTTTTCTACCTTCCCTCGGACGAAGGAGAAAAAGTCTCTCTATCCACCTCCGTCCTGGTGTCGCTCACCGTCTTCCTTCTCGTCATCGAAGAAATCATTCCGTCTTCCTCTAAAGTGATCCCTCTGATCGGAGAGTATCTGCTTTTCATCATGATCTTCGTGACACTCTCCATCATCGTGACGGTGTTTGTTATTAACGTTCACCATCGCTCTTCAGCCACGTATCATCCCATGTCTCCGTGGGTTCGTACTCTGTTCCTCCAGCGGCTGCCGGATTTGCTGTGTATGAGGGGAAACACCGACCGCTACCATTACCCGCAGATGGAGCCCCAGAGCCCTGATCTGAAGCCCAGGAGCAAGAAAGGGCCACCTGGGCCTGAAGGAGACGGTCAGGCGCTGATCAACATGCTGGAGCAGGCCACTAACTCTGTGCGCTACATCTCACGGCATATCAAGAAGGAGCATTTTATTAGAGAG
Seq A exon
GTAAGAACTGGTTGAGACGTGCTAAGATGAAGGTAAAGGAAAGTGTTGAATGCATAATTTGAATGCATTTATCCATCCATGTCAATCTATCTGTCTACCTATGTTCATCCATCCATTCATCGATGTCAATCTATCTGTCTACCTATATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCTAATTTCTATCTATCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTATCTGTCTGTCTATCTATCTATCAATATCCCTAGCCGTCTATCTATCTATCCGTCCGTCTGTCCGTCCGTCTGTCCATCCATCCATCCATCCATCCATCCATCCAATCATGGATTTTATCCAGCAAATAAATTCTTCCATATCAGCTTAAAGGTATTCAGTAATTTTTGTTCAGTTTCAAAAAACAACAAAAAAAACAAAAAAAAAAAATGGAACAAAATATGAATCAATATTTTATGATTAATAAATGTTTTAAGCATCAGATCAGTAAAAAAATCAAAGTATCTAAAAGTTATTTCAAGGACATGAACATTAAATATTTTTTCATTGAACTTTTTTTTATAGTAGAATTTGTCATATATTTTGCCATTTTGAACTACTGGTCAAAAAATTGGGGTAAGTTTTATTTATAATAAATATTTATTATAAATAAAATGTTTTAATATATATTCTTATAATATATATATATATATATAATATATTCTATTCCTTTTCTTTTTCTTTTTTTTGATAAATACAACTTTGGTGAGCAGGATAAACTTATTTTAAAACGTTTAAAAATCCTACTGACCCCAAACTTTTGACTGGTAGTATATAGATACTCTAAATAAAATACCTAATAATTGTATTAATTAAAATACCCAAGAATATGCTGGATTTACTAAATATGGGTTAGAGTAAATGTAAATATTTTTTTATTCTAGAAAGGTTTGATAACATTTTTTTCCAGACAGATTTATTTATTTACTTTTTGGGACATTTGTTTATATTTTTGACAGTTGGTTGGAATAACACATAATGAATAATAAACACACAATAGTAAATTGTAAATCCAGAGAAGCTCTAGAATTTTCCATTATGTACTGTTCACTAATAATATATGTAGTTCAATGTAGTTTAGCTATAAAGACTGAAGATATTGCTGTGATTTGTCTTTCACAG
Seq C2 exon
GTTGTACAGGACTGGAAGTTTGTAGCTCAGGTTCTGGACAGGATTTTTTTGTGGGCTTTCCTCACCGTCTCTGTGCTCGGCACCATCCTGATCTTCACTCCTGCGGTGAAGATGTTTCTGAGCACTCCTCCACCTCCGTCTCCTTAACACTCATCCACCAAAATCAGCAATCAAGACCTGAATACTGTACTTACAGTAACATACACACAGCACTCAGTATTAGGTAGACCTTCTTTCACTACTTTGAGATATATATAAAATGTATTATTATTATTATTATTATTATTATTTGTTGATTGTTAGGTCTGTCTTTTTTACACATATTTCCTAAACAACTTTTAGCAATTACTTGCACATACAAAATGCAGTAAAAGTAACAGTGTACAAATCATTCCAGAATTGCGGGTACATTGAAAACATTTTGCATTTATTTTTCTTGACTGGAATGACATAAAGCATACAAATAATGAACAGTAAATGTAATACAATAGCTAATTGTTGTTTAACTTATAACAAGCTCATATTATATAATTGTTTTTAAATAAAAACAGAAGTGAATGAGAGATTCACTAAAATATCACAAAACAAAGTTCATGTAACTGAAGACAGAAAAGAAGATATAAAGAATTTAGTACACTGTTAACTGACATCCATGGTAGTAAAAACAGATACAACATTTTTCATAAAATCTTTTGTGCACACAGGAAAGAAAATGGTTTGGAACCAGTCAAGTATGTGTAAATAATAGCAAAATGTTAATTTTAGTGAACTATCCCTTTAAGGAGACAAGTGGATGCAGACAATAAGATGTGAATCATCAGCAGGAAGAATGAGTGAATTGTTGGATCCTGACACAGGTTCAGTTTATGCCAATGTGTGCAGAAACATTTCATCACTGCAAACTCAAATATCCAAACGTCAGGTTTAGATGTAAATGAGCTGTAACGTTTTGCCAATATGCAACTTCTCAATGTGCAGAAAGCTATGCAGTAACAATGTTTTGTTATGAATGCCGAGTCCCGTAACTATAGCTAACTTGTACCTCCATAGTTTATTAAAAACGTGCAAATGAAATCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000038508:ENSDART00000050037:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.096 A=NA C2=0.125
Domain overlap (PFAM):
C1:
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)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(36.5=63.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGTCTCCGTGGGTTCGTACT
R:
GTGAAGATCAGGATGGTGCCG
Band lengths:
344-1583
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]