DreINT0046770 @ danRer10
Intron Retention
Gene
ENSDARG00000022532 | chrnb1l
Description
cholinergic receptor, nicotinic, beta 1 (muscle) like [Source:ZFIN;Acc:ZDB-GENE-060811-1]
Coordinates
chr7:22321910-22323883:+
Coord C1 exon
chr7:22321910-22322057
Coord A exon
chr7:22322058-22323697
Coord C2 exon
chr7:22323698-22323883
Length
1640 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
AGTCCTCTCTCTTCCCTAAGAGA
3' ss Score
6.24
Exon sequences
Seq C1 exon
GTGGCGTACTTTCCATTTGACTGGCAGAATTGCTCAATGGTGTTTCGTTCCTACACATATGATTCCTCAGAAGTGGACCTACAGTATGGTCTAGATGAAGACGGAAATGAGCTCCATGAAATAGTGATTGATGAGAATGCTTTCACTG
Seq A exon
GTAAGTGTCCTTCTTCCTGAAATTTTCAACATATTTTCCAGCTCCAGTTACTAGTATGAAACAAGAAAGATGGTTCTTTTTATGTGTATCAAAGGCACAATTTGCAATTTTAGCCACTAGAGGGCACATTTACAACAAACAATGGTGTATTTTGGTGACACTGTGACTGTGCGTGGAATCATGGGAGTTGTGGTCTTTGATACATACTACAAGACATGGTTAAGCTAAAAATACTCATTATCATGGTAATATGAAGCAGAGTAAAGCTGAAAATGAAACAAAAGTGCTAAAGCAATTGTTTATGAGAGACAAGTGCAATCCGACATGAAAGAAACAAAACTTGTATTATGTCACAATCGCTTTTGGGGGATTTTCAGTCATGATCATGTAGGGAAAAACAGCACTGTTTTACTCTATTACAGTAAATACATTTTAGGTTTCTATTATAATGCTGATATGTGCACTCTAATAACAGTGTTTCCATGTTTTCTATAAAACCAAACTGGTGTTGCTAAGAGCAAAAGTTAATAATGTGGCAACCCTAGATGTTTGGCAGAAAGATCTGGGATGCTCAATCAGTGCAGACACTTGGACACACACGTGGCAATATGCTGGCAATATATCAATCTGTAATAGAACTAAAAGAACAACAGTTCAAACTTTTGCATCATCTCCGAATTACACCATCACATAGATATAAGCTTAATTCATATTATTCTCCATTCTGTTTAAAGTGCAAAGTTGAAGAAGGTGATTTTATGCATTTATTTATGTATATATGCATTTATGAATACTATTGGAATTATATATATGTTAAAGGCTTTTGGGTACAGATTTGTAGTAGACGTGTAGATGTGACTTCGACTCTCTTAACTTTTTGTCAGGTGTTGCTGATAATCATTTGAAGAGTACAACAAACAGGAAGTTGTTTAACTTTCTTACCTATTTTGCCCGTAAGAGTATATTTCTTAAATGTATATCGAATAAACCACCAACAGTATCAGAATGGCATAAAGTAATCAAATGTCATTGGAATATATTACCCACTGGTCAATGGGAAAAATTATAATTTTTATTATTACATTCTTTCCTTGAGTATGTGGGTGCCAGCATTTCAGGTACTTTTTTTGCAAATCTTTAGATCACCATAAACCTTGGTTAATGTATGTATTCTTTTATTATTGTTATTACTTTGTGTATTTTTATTTGTCTTCTTTTTGATCTTTATTAAGTGCTGTGATGTTGAGAAATTTGTTGGCTGTAATCTGTGGTTATTATTCTGTTGTTTTGTTCTAATAAAGACAAAATAGAGGCATTGAGGGTGTATGATATAATTAGTATGGCAATAGCATAGCAACTAGGTAAAATAGCTTATATCTCTTGATTTGAAAATTTTTCTAAACATTTAAGATAATGCAAGTAAATAAATCAGCAAAAAAAAACATTACATGAGATATCTTAATGAGATATCTTTGGATATCTTTATGAAGAAGTCTTACATATTGAAATTAAAATAATTCCTCAAGCAATCTTTTTGTAGCCTGTCTACTGTTGCCAAGTATTCTAGCAACTTGGCACATGGCACACCGTCTCTTTCCTTCTGTCTCTCTTTCTCTCATTAGTCCTCTCTCTTCCCTAAG
Seq C2 exon
AGAACGGCGAGTGGCAGATTTGTCACAAGCCCAGCAGAAAGAACGTCCAGGATGACTTGTATGAGGACATCACCTTCTACCTGATCATTGAGAGAAAGCCTCTCTTCTACGTCATCAACATCATCGTGCCCTGCATCCTTACCAGTGTGCTGGCCATTTTTGTCTTCTACCTGCCACCTGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000022532:ENSDART00000149144:6
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(23.2=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(15.6=52.4),PF0293211=Neur_chan_memb=PU(9.3=34.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGCGTACTTTCCATTTGACTG
R:
CTGCACCAGGTGGCAGGTAG
Band lengths:
334-1974
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]