DreINT0046815 @ danRer10
Intron Retention
Gene
ENSDARG00000086647 | chrng
Description
cholinergic receptor, nicotinic, gamma [Source:ZFIN;Acc:ZDB-GENE-030131-3805]
Coordinates
chr2:45243435-45244745:+
Coord C1 exon
chr2:45243435-45243568
Coord A exon
chr2:45243569-45243731
Coord C2 exon
chr2:45243732-45244745
Length
163 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
TTTCTTCTTCTTCTGTTTAGAAA
3' ss Score
8.91
Exon sequences
Seq C1 exon
AGAATGGTCTGGGGGGAAACACGGCACAGGATCTGGAGTGCAGTTTAGCAGCGGCCTCCCCTGAAGTGCAGCAGTGTGTGTCCTCCTGCAAACACATCGCAGAAAGCACCAAGCATCAAAATGACTTCCAAAGT
Seq A exon
GTGAGTTACTGCACCACAGTCTTCCAAACATGAGGTTAAAAAGAGTCTCTCATTATACAAGATAAACACTCTCAATGTTTGCGTTCGGGTTTAACTTCTCAATCCCAGACAAACTGCTGTTGACGTCTGAATTCCAGACATCCTTTCTTCTTCTTCTGTTTAG
Seq C2 exon
AAAAATGAGGAATGGTTTCTGGTCGCCAGGGTGATTGACAGGATGTGCTTCTTTGTCATGGCGCTGCTGTTTATCCTGGGCACCATCGGAATTTTCCTGACAGGACATTTTAACCAGGCGCCGTCCCAACCCTTCCCTGGAGATCCCAAAAAATATCTTCCTGAAATCTCAGCTGGAGACATCCCCGGCTGAACAAAGGTGTAAAACAACATGGCGGACACAGAGAAACTCCAGCAGAAGACTGGAGCACTTGCCTGAAGAGACTCTGGAGATAAAAATGTGGTGTTTTGCTGTAATTTAACTCTCAGCACTGCAATATGGCTGCACTGTAGCACTAATGAATGTGATCTTCAGAGAAGAACGCTGGTTGAATTTGGAGCCATCCAAGACTCGGAAAGGCTTTGTTGAGTTGCTTGTAATAAGGAAAGTCATGTTATTTGCTTGTCCATTTCTTTATCAACCCTACTGTTTGATATTGCTTCAACATTTGATTATTTTCCTGAGATAAATATGTAACATTTAAAAGCATGGTCTGCTACATTTCTAGCCTTAAGCCACTATGCTTTGTCTGTTATAGATCGTTTGATAGTACTCAGTGCGTTTTTCACCTACATCGCATCAGTGTTAAGTTACTTCAGTATTTATTTACTAAATACATGATTACAGTCGTATTTAAACAACCTTTCTAATTCAGTTGAGAAATTCATCTTGATTACTCAATAATTACTTAAATTACTTGACTAAATATTATTTATAAATCTCAGTACACAAAAAATAAAATTCTTATTTCCTTCAATTCAAACACTGCCTTTTGTTTGAAAAAATTAACATTCAAGAGTGTAAGTAATATTTTTACAAATGCACAAAACTTTTCAAAAAAGTAATAACACCATATTTCACATATAATAGCATAAATTTAACTTTTAATTAAAAACTTTTTTTGTTGTAGAGAAATTGAGTTGATATGCAAAATGTCTGAATAACACAAAATAAATATTTACAATGACTCAGCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000086647:ENSDART00000123966:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.079
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(17.1=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.1=48.4)
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:
ACACATCGCAGAAAGCACCAA
R:
TTACACCTTTGTTCAGCCGGG
Band lengths:
247-410
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]