DreINT0046784 @ danRer10
Intron Retention
Gene
ENSDARG00000052764 | chrnb3a
Description
cholinergic receptor, nicotinic, beta polypeptide 3a [Source:ZFIN;Acc:ZDB-GENE-040108-1]
Coordinates
chr1:21700380-21702765:-
Coord C1 exon
chr1:21702656-21702765
Coord A exon
chr1:21701284-21702655
Coord C2 exon
chr1:21700380-21701283
Length
1372 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
GCTGTATGTTTCTCTCTTAGTGC
3' ss Score
8.22
Exon sequences
Seq C1 exon
GAGTGGACAGACTACAAACTGCGCTGGAATCCAGAAGACTATGGGGGAATCACATCTATCAGAGTACCCTCAGAAACGATTTGGCTGCCAGATATTGTCCTTTATGAAAA
Seq A exon
GTAAGCCTATTATGACCATATAAAATGTCATACAGGTGCACATATTTCATACTGCAGTTGCTGATCTTGGTTTTGGTGCATTTGTTCGGATCTTTTAAAAAATGTGTTTAATCTCTTGAAATATTCAAATCTGCATTATGTCATGGAAAGACAGATTAAATAACTGCTTGATTGTAACTGATGGGGCTGGCCGATTAATCGAAAAGTAATTGAAATTTTGAAAAGTTGTGTAGCGCCATCTAACGCCAAGGAGTGATTTTGCATAATCTTCTGCTTGACGGCAGTGAAAATCGATTGGTTTTTGAATCCGGAAAAACATCTTGTAAAACGCTGACGATAAACGCAAACGAAAAGCAACCCGGTGTGTACGAGCCTTTAGCCTTACTCCTCGTTTTGCACGTTCAAATGAAGGTGTAGGGATGTCCAAACTCTCTTTATCTTAAAGGTGTAGGCCTAAGTGGAAGGGCTACATAGCCCTTGAAAGAGAGATTTCCCTGAATACACCAGCCACAACGGCTGCATAGCACTAAAATAAAAATTGCCAAATTTTGCTATCTGTAATAATAACTCCTGTATAGTAGTTCTACAACATTCTGACACTTGATGACACTCGAATACCCTGTCAGAAAAGTTTATTGGCTGAGAATGAGCTTTTTACAGTGTCTACTATAATGTTAATGTTGTTTCCTTGTGTTTACAATGATGAATATGGCCAGGGTGTAAATGCACAGTACAGTTATGATCTTATTGCCACATTAGATTGTTATGATAACATGATATTATCCTGAATATATTATCCAGGGTAATAGATATTATCCTATTATCCTGATTTTTTAGCATTTACTACAGCAGTCTCGATTGTCTGATCTCATATGAAGCAAGAGACTGTGATGAAGTGTGCAGGTGCTGTAGTGGTGTCCCATTTCAGAGGGGTAAAATTTAAAGCCCTTTCCCTTCACACTCTGTTTGAATGGGGAAGGGGTAGGGTACAAAAACAGAATTGGGATTAGGCCTATATACTGTATTTGCATATTTTTTAATAAAAAAGCTGAACCTAGTGGCATTGACATTTCGTCACCTTATAATTACAAGGTTCTATCTGACATTTTTGTCAAAGTTGAGTTATTGACATAATCTTAATCAATGACAACATATTTACATTATGGGATGTTTTTTTATAAGTTTTTCACATTTTAAGACTTTTTATTTCAAAAAACAAATGTTAAACGCATACTGTTTGCTATGGAATGCAAAAACTTTGAAGCTCAAAATCATTAAGAACGCAGATAGAACCTTATAATTCTAAGGTGACGATTTGTAGTCACATTGTCTTCAAAATAATTGCTAATATCGCTGTATGTTTCTCTCTTAG
Seq C2 exon
TGCTGATGGCCGATTTGAGGGATCTCTAATGACTAAAGCCATTGTAAGGTTTAACGGTACCATCATGTGGACTCCTCCTGCCAGCTATAAATCCGCCTGCACCATGGACGTCACCTTTTTCCCCTTTGACAGACAGAACTGCTCAATGAAGTTTGGATCATGGACATACGATGGCACTATGGTGGATCTGACCCTTGTTGACGCTTACGTGGACCGTAAAGACTTCTTTGACAACGGCGAATGGGAAATACTCAATGCCACTGGCCAAAGAGGCAGTCGACGTGACGGCATTTACTCTTATCCTTACCTCACATATTCATTCATCCTTAAGCGTCTCCCTCTGTTTTACACACTCTTTCTCATCATCCCGTGTCTCGGTTTGTCGTTTCTCACTGTGCTGGTCTTCTACCTTCCATCAGACGAAGGGGAAAAGCTTTCCCTCTCCACTTCCGTCCTTGTGTCTCTCACTGTGTTTCTTCTCGTCATTGAAGAGATCATTCCGTCTTCCTCTAAAGTCATTCCTCTGATTGGAGAGTATCTACTTTTTATCATGATCTTTGTCACTTTCTCGATCATCGTAACTGTCTTTGTCATCAACGTTCATCACCGTTCCTCTGCCACTTACCATCCCATGGCACCTTGGGTGAAGAGTCTTTTCCTCCAGAGATTACCCAGACTGCTGTGCATGAGAGGACACACTGACCGATATCAGTACCCGGACATCGAGCTGCGGAGCCCAGAGCTCAAACGAGGGATGAAGAAAGGGCAACAGAAGAGTGCTGGAGGAGGACGAGCTGGAGTTAAGGAGGATGAAAACCAGGCCTGGATTGCCCTGTTGGAGAAAGCCACCCACTCAGTGCACTACATTTCCAGACACATCCGGAAGGAACACTTCATCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052764:ENSDART00000074678:4
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=0.036
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.1=37.4),PF0293211=Neur_chan_memb=PU(84.6=59.9)
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:
ACAGACTACAAACTGCGCTGG
R:
TTCCCATTCGCCGTTGTCAAA
Band lengths:
351-1723
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]