DreINT0046785 @ danRer10
Intron Retention
Gene
ENSDARG00000052764 | chrnb3a
Description
cholinergic receptor, nicotinic, beta polypeptide 3a [Source:ZFIN;Acc:ZDB-GENE-040108-1]
Coordinates
chr1:21698060-21701283:-
Coord C1 exon
chr1:21700380-21701283
Coord A exon
chr1:21698674-21700379
Coord C2 exon
chr1:21698060-21698673
Length
1706 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCTT
5' ss Score
3.62
3' ss Seq
GGTCTGTGTTTCTCTTTCAGGTT
3' ss Score
12.63
Exon sequences
Seq C1 exon
TGCTGATGGCCGATTTGAGGGATCTCTAATGACTAAAGCCATTGTAAGGTTTAACGGTACCATCATGTGGACTCCTCCTGCCAGCTATAAATCCGCCTGCACCATGGACGTCACCTTTTTCCCCTTTGACAGACAGAACTGCTCAATGAAGTTTGGATCATGGACATACGATGGCACTATGGTGGATCTGACCCTTGTTGACGCTTACGTGGACCGTAAAGACTTCTTTGACAACGGCGAATGGGAAATACTCAATGCCACTGGCCAAAGAGGCAGTCGACGTGACGGCATTTACTCTTATCCTTACCTCACATATTCATTCATCCTTAAGCGTCTCCCTCTGTTTTACACACTCTTTCTCATCATCCCGTGTCTCGGTTTGTCGTTTCTCACTGTGCTGGTCTTCTACCTTCCATCAGACGAAGGGGAAAAGCTTTCCCTCTCCACTTCCGTCCTTGTGTCTCTCACTGTGTTTCTTCTCGTCATTGAAGAGATCATTCCGTCTTCCTCTAAAGTCATTCCTCTGATTGGAGAGTATCTACTTTTTATCATGATCTTTGTCACTTTCTCGATCATCGTAACTGTCTTTGTCATCAACGTTCATCACCGTTCCTCTGCCACTTACCATCCCATGGCACCTTGGGTGAAGAGTCTTTTCCTCCAGAGATTACCCAGACTGCTGTGCATGAGAGGACACACTGACCGATATCAGTACCCGGACATCGAGCTGCGGAGCCCAGAGCTCAAACGAGGGATGAAGAAAGGGCAACAGAAGAGTGCTGGAGGAGGACGAGCTGGAGTTAAGGAGGATGAAAACCAGGCCTGGATTGCCCTGTTGGAGAAAGCCACCCACTCAGTGCACTACATTTCCAGACACATCCGGAAGGAACACTTCATCAGAGAG
Seq A exon
GTGCTTTATGGATTTTTTTCAGCATTAGCATTTAGGTTAATGATTTGTTCACATATGCTGTGCTGTTCACATGGGTTTTTCTCCGGGTGCTCCGGTTTCCCCCACAAGTCCAAAGACATGCAGTACAGGTGAATTAGGTAGGCTAAATTGTCTGTAGTGTTTGTGTGTGAATAAGTAGGTATGGACGTTTCCCAGTGATGGGTTGTAGCTGGAAGGGCATCCCCTGCGTAAAACATGTGCTGGATAAGTTGGTGGCTCATTCCGCTGTGCCGACCACAGATTAATATAGGGACTAAGCTGAAAAGAAAATGAATGTATGAATGATGCTGTGCTGTGCTGTAAACCAAACATTCATTCATTCATTTTCTTTTCAGCTTAGTCCCTTTATTAATCCGGGAGTGCCAACTTATCAAGCACATTTTTTGGATGCCCTTCCAGCTGCAACCCATCTCTGGGAAACATCCACACACACAATCACACACACACTACGGACAATTTAGCCTACCCAATTTACCTGTCCCACATGTCTTTGGACTGTGGGGAAACCGGAGCATCCGGAGGAAACCCATGTGAACGCAGGGAGAACATGCAAACTCCACACAGAAACACCAACTGAGTCGAGGATCAAACCAGCGACCTTCTTGGCGTGAGGCGACAGCACTACCTACTGCGCCACTGCGTCGCCCTTGTAAACCAAACAGTAAAATTAAATTACAATTAAATTAAACAAGTTCATTTCACTCCAATAATTAAAAAAATAATTACTTAATAGAAATAATTACATCAACTCAAAAGTTCTGTGTATTAAGGTGAACTTAAACTCATTGAGTAGAAGCAGATTGCTATTTCTCAGCATATGTTGCATCAGACTGTTTAAGGAAAATCTGTACTGAAATTAGGTGTTAAGCTGCAGTCACACTAGAGTAACAAGTTTCCCTATACTGGGTTGTGGCTGGAAGTACATTCGCTGCGTAAAACGTATGCTGGAAAGTTGGTGGTTCATTCTGCTGTGGCTACCCGTGGTTAAAAAGAGACTAAGCCGAAGGAAAATGACAAAATGTTTTATAAATGTATTATTTTAAACTTTAATGTAATTTAATAGTTTTAAATAAGTGTTTATGTGTCAATTTAAGAAAAAAACTTATAAACAATAACAGAAATTAAGGCAAGAATGCTTCCTGCATGAAAGTCCCCATGCTAATTTTCTGCAGCAAAATTTACACAATTTACTGTGTTAGCTCACAGATGAACAGTTAATCTATGCGAGTTCATCCACTGAGAAAGATGTTTGTCTTCGTTATCCTTAATCAAAATCTGTAAAAATATTTCCACCCTGGAATGCATCCATTATCTGATGATGTCAGTTTGACAGCTTGGGTAGAATATTCTTAATCACTCTGACTATCCCTCCTCTATGAAGATAGTGAGGAGTGCAAAATAAATGCAAATTAGCTATCTAGCTAATTATCTATCTAGCTAATTCTGACACAATATTTGTGTTGTGCATAATAAACTAATCCAATGAAAACTACTACATTTTCCCTTTCAGTAAGAAATACATCACAATACCGAAGTAATGTTGAGCTTTCAAATCACACATTCAGTTTGTTACTGATATAAATTCTATGAAACATGCTTTGTTATTAAGATGAAAAACATTTTAATGATGTAATGTATTTACCGTTTGGTCTGTGTTTCTCTTTCAG
Seq C2 exon
GTTGTTCAGGATTGGAAATTTGTGGCTCAGGTGTTGGACCGGATTTTCCTGTGGGCCTTTCTCACAGTTTCTGTGCTTGGGACCATCCTCATCTTCACCCCAGCTTTGCAGATGTTTTTTAGCACATCTTAAAACCCTTTTAAAAATCACCTTTACCCCCAGTAACGTTCTTATGACCCTAAGAAATAAATGTAGTTCCCACAAGATTACGGTAATCCCTCTGTAAGTCTTTTTTTGACCTAGCCACATCTATAATCCCTCAAAATTCTGGGAGGAAGCAAAACTCAGCAGAAATGAAGTGCAGGAGTTTTATTTTTATTTATTTTTGCCAAGTTGACACATTATTAAATAAAGTTTGAATATCTCTATAAGGCATCTTGGTTTAGAAACCCTCAAAAATGTGACTTTACACTTTGTATGTCACTGTTTAACTATGTCTCTTAGGCCTGTCATTTTTGCTTTCGGGTTTTATTGATATTTTATTTTTAAAACTAGAACTGTGCTCACTATCCATGTAATACTGTGCTGTGTAATTATGTTACTCAATAGATAGCAAACTATTATGGTTTTTAATTTATCTCTCTTTTTGAAATAAAAATGCTGTCTGTGGGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052764:ENSDART00000074678:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.036 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.1=37.4),PF0293211=Neur_chan_memb=PU(84.6=59.9)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(14.5=70.5)
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:
GACTGCTGTGCATGAGAGGAC
R:
ATCTGCAAAGCTGGGGTGAAG
Band lengths:
343-2049
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]