RnoINT0036353 @ rn6
Intron Retention
Gene
ENSRNOG00000019527 | Chrnd
Description
cholinergic receptor nicotinic delta subunit [Source:RGD Symbol;Acc:2352]
Coordinates
chr9:94291871-94293607:+
Coord C1 exon
chr9:94291871-94291985
Coord A exon
chr9:94291986-94293402
Coord C2 exon
chr9:94293403-94293607
Length
1417 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TGTCCCCTTGACTGCTAAAGTTC
3' ss Score
2.51
Exon sequences
Seq C1 exon
GTTCCTGCTTTTTGGCATGGTGCTGGTCACCATGGTTGTGGTGATCTGCGTCATCGTGCTCAACATCCACTTCCGAACACCCAGCACGCATGTTCTGTCTGAGGGAGTCAAGAAG
Seq A exon
GTGAGATTTTGATAAAAGATGGGACCCAAGTCCTGGCCAGGGGGATCTGTGAGGGTGATGGGTGTGATCAGAAGCACCAGGCTCAGAATCTCCAGACTTGTTGCCTAGATTGAGGACCTGGGTCAGCTCCTCAGCTCTGCTAAACTTAGATAGATAGATAGATGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGACAGACAGATAAGGGGACAGTTAGATAGCTCCGTGAGTTGGAGCACTTGCCACCAAGCTTGACCACCTGAGTTTGATCCCCACAACCCATGTGGTGTAAGGGGAGGACCAACTCCTACAGGATGCTCCTCCCTACCTCCTCCACGAGAGCACCGTGGCATGTGTACCCCTGCACACATATGTGCCCACATACATGTGTACATGGATAAATATAACTTTAAAATTAAAACAAAAGGTAAAAGTAAGCAGGTGAGGACACAGGGGACAGGGTGTTTGGGACAAGACTATCTGTGCTCTAAGCCACTGTGGGCCAACGGGTTCTTCTGGAACAAGTCATCTTCCAGATGATGATTCTGCAGCCCTTTAATGGGTTTTGTCTCTAATTGACTGAAGGAAGAGCTCAACATTTCGGCTTTTATTTGTTTGAGACAGGGTCTTACTGTATAACTCATAAACAGGAGAGGGGCACAGGTACACAGCTCAGTTGGCACAGTGCTTGCCTAGGGTGCACAAGGCCCAATACTGAGTGTGAACCCCCCTTAGCCTAGTGGGAGGATCAGAAGTTCAAAGTCATCCTCAGCTACACAGTGATATCTGTTTATCCTAGTATACATGAGACGCTAACTTAGAGGGGGGAGGGGGAGAGGGAGAGAGACAGAGAGAGAGACACACAGAGAGAGACAGAGGGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAGGAGGAGGAAGAGGAGGAAGAGGAGGAAGAGGAGGATCAGTGATAAAACGTATGTTCAAACTTTTAATTCTCCTGCCTCAACTTTCTGAATGCTAGGATTAAAGGCATGTAATCCCCACTCTCAGTTTCCTTTTGTTCTTAAGATTTATTTTCAGGGGGTTGGGGATTTGGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAACAAAAAACAAAAGAAAAAAAAGATTTATTTTCAGTGACTGAGTTCCGCTGTTGCTATGAGTAATGAAGGACAGTTGAAAGCATCCTACATCAGTCAGTGGGGAATCTGGGAGACAGACGATGGGGTCAGCCTGGGAGCTCTGCTTAGCAACCGGGTTCATCAGAGTGTATAAAGATGACTCCACATTTGTGAAATGGTCTGTCTTGTGTCCCCTTGACTGCTAAAG
Seq C2 exon
TTCTTCCTGGAGACTCTGCCCAAGCTCCTGCACATGTCCCGCCCAGAAGAAGAAGACCCGGGCCCCAGGGCTCTTATCCGGAGGACCAGCTCTCTGGGATACATCTCCAAGGCAGAGGAGTACTTCTCACTTAAGTCCCGCAGTGACCTCATGTTTGAGAAGCAATCAGAGCGGCATGGGCTGGCCCGGCGCCTCACCACAGCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019527:ENSRNOT00000026504:9
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=0.246
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(16.0=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(28.7=100)
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:
GTTCCTGCTTTTTGGCATGGT
R:
CCATGCCGCTCTGATTGCTTC
Band lengths:
294-1711
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]