RnoINT0036298 @ rn6
Intron Retention
Gene
ENSRNOG00000013610 | Chrna5
Description
cholinergic receptor nicotinic alpha 5 subunit [Source:RGD Symbol;Acc:2347]
Coordinates
chr8:59586227-59590017:+
Coord C1 exon
chr8:59586227-59587055
Coord A exon
chr8:59587056-59588464
Coord C2 exon
chr8:59588465-59590017
Length
1409 bp
Sequences
Splice sites
5' ss Seq
GAGGTCTGT
5' ss Score
5.39
3' ss Seq
ATGTATTTGTTTTTTAACAGGTT
3' ss Score
10.42
Exon sequences
Seq C1 exon
TGCAGATGGACGTTTTGAAGGGGCCAGCACGAAAACAGTTGTCAGGTACAACGGCACTGTCACGTGGACGCAACCAGCAAACTACAAAAGTTCTTGCACCATCGACGTTACCTTTTTCCCGTTTGATCTCCAAAATTGTTCCATGAAATTCGGCTCGTGGACATACGATGGATCCCAGGTTGATATAATCCTAGAGGACCAAGATGTCGACAGAACAGACTTTTTCGACAATGGAGAGTGGGAAATCATGAGCGCGATGGGGAGCAAGGGGAACCGGACGGACAGCTGCTGCTGGTACCCCTACATCACGTACTCCTTTGTGATTAAGCGGCTGCCTCTCTTCTATACCTTGTTTCTTATTATCCCCTGCATTGGGCTCTCATTTCTGACTGTGGTTGTCTTCTATCTCCCTTCAAACGAGGGTGAAAAGATTAGCCTCTGCACCTCAGTGCTCGTCTCTCTGACTGTCTTCCTTTTGGTAATCGAAGAGATCATACCGTCATCTTCCAAAGTCATACCCCTGATTGGGGAGTACTTGGTGTTCACCATGATTTTCGTGACCCTATCCATTATGGTGACTGTCTTTGCCATCAACATCCACCACCGCTCTTCCTCCACACACAACGCTATGGCGCCCTGGGTTCGTAAGATATTTCTCCACAAGCTTCCCAAGCTGCTCTGCATGAGAAGTCATGCGGATAGGTACTTCACTCAGAGAGAAGAAGCCGAGAGTGGGGCTGGACCTAAATCTCGGAACACTTTGGAAGCCGCACTCGATTGCATTCGCTACATCACGAGGCACGTCGTGAAAGAGAACGACGTCCGCGAG
Seq A exon
GTCTGTGGCGAGTATAAACGCCCCCGCAAAGTGGGGCGTCTACACAAACCTTACCCTCCATTTCCCCAGAGCGCCTTGAATGATCCTGAAGAAAGTTTAGCAGTATGCACTTGAAGGGATAGTAATATTGCCATAGTTCTTTGGTTTTGGAATAATGTGCTGACTTAGATTTATCTTCCATAATGTTTCTGAATTTTTACCTTATAGTTTATCAAAAATTACTCTTTTTGAAGAATGAGTCTAATATGGACCTTAAAAGTGCAACCAAGATACTTTCCATAAAGACATCTTTTTGTAGCTTTTCCACAAAAGAATATTAGTAAAATTGAAAACAGCAAGGTGTATGGCTACAATCTTGCCCTTCAGGGGCTGAGGCAGGAGAATTGAAGGAGTCTGCCTTGGTGTACTTTAGCAGGTTCAAGGTTAGCGTGGGCTAAATAGGGAGAATATGTCTCATAAAAGCAAAGTGAAATAAATAGCATAAAAGTAAAGGAGCAAGGTGTTCTTATGTGTCATTTTATACTTCAAAGTTTTCTTGTAAAGCAGAAATAGTACCTAATTTGCCTAAGACAAAATTTGTTTAACATAAAAATAAGTTTGATTAGTTTGTTAAGGATAATTGGTAGTCAAAATGCAAAAATTGGACATGTTTTTACTAATGTTTTTTAATACAAGCTTTCAATTGTTAGTATTTTTATTTCTATTATATAATCTCTAACTACTAATATTTTCATATCTGAATTTATATTGAATGGTCCCATAAAGATATATAAATTCTAATTTTTTATTAATATTTGACATCCTTCCTTCCCTCCCTTTCTGCTTCCTCCCTCTCTTCCCCCCTCCTCCTTCCCTTCCCTTCCCTTCTCCTTCCCTTCCCTTCCCTTCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTATGATGGGACAGTCACCTTATAGTCCTTGCTAGCCTGGAACTTGATTTGTAGACCAGAATGGCTTCAGCCTATCAGAAATTCACCTTTTGAGGTTAAAGGCCTGTACCACAATGCCAAAGCCCCCATCTTCCACTTTTCTAAAGACAGTTTCACTATGTAGCTCAGGCTAGCCTCAAACTGTCCATTATTTTATTTAGGCCTCCTGAATGCTGGGATTTCAGCAAGTTATGACTTTAAATGAACTCTTCATTGTTATTCCAAGGTGCTGGCCTCAAACTTCCAATCCTCCTGCCTCAGTCTCCCAGGTAGCTGGTACTGCACACACCGCTATGGCTGGTTTACTTCTAACAAACTAATTCTTGCTGATTGTAGTATTCTGTGGCAGTATAATTATTATATATTACATATTATCATGAGATAATATATCTTAAAATATGGCTTTATGTATGTATTTGTTTTTTAACAG
Seq C2 exon
GTTGTTGAAGATTGGAAATTCATAGCCCAAGTCCTTGATCGGATGTTTTTGTGGACGTTTCTTCTGGTGTCAATCATTGGGACTTTAGGGCTTTTTGTTCCTGTTATTTATAAATGGGCCAATATAATAGTCCCAGTTCACATTGGAAACACAATTAAGTGAAACCAAGAAATTACCCTGTGGATTTAGTGAGCAGTCATGCAGCTCTTAGGACATGTATGCTGTTATGGAAATGTGAAGGTAGTTACAATTTGACATAGGCTATAACAGATTAGCAATTTCTAACATTGGCTTAATGTTGTCCATTAGAACTGCAGTAATAACCTCAAATAGCAACAACACATTGTCTGCCTGCACTAGTGAAGGCCTAGCATCTGCATCCTGGCAAACCCTACCAATTTGCAACCAATGATGAAGGCCATCCTTGGAGTGCTGGAAAACTCAACTGTATTTGAAGACTATTTAAAACTCCCCCCAAATTTAGTAGGAACATATATATGTGTGGTTTTGAATTTTCAGAATGGGTCTTTGGGTCTTGTTAAATTGTCTGGGCTAGCACAAAACCTCCTGAGTAGCTGGGACCATGGGTGTGCTCCACTTTGCCCTGTTCTGTATTCACAGATATAAAATACATCATTATTTTATAGGAGGTAGACCCATTACTTGGTTTAATAATAACTTAATGTCAGTTAGGTTTAATTATAACCTTATGTCAGCTAATGTTCTATTGCTGTGAAGAGACATCATGACCATCAACTCTTATAAAGGAAAACATTTCATCAGTGCTGGCTTACAGTTTTTGAGGTTTAGCCAATTATCACAGTGAAAGCATGATAGCATCCAGGTAGACATAATGCTGGATCCAGGAGTTCTCTACATCTGGATCAGCAGGCAGCAGGAAGAGAGAGAGAGCCACTGGACCTGGCTTGAGCATCTGAAACCTCAAAGCCCACCTCCAGTGACACACTTCCCCCAACAAGGCCCCACCTCCTAATAGTGCCACTTGCTGGTGATCAAGCATTCAGTCTATGGGTCTACGAGAGCCATTCCTATTCAAACCACACTTAATAGGATGCTATTCTTTACTGACATTTTTAATAAGCGACAAATGGTAACTAGAAACATCGTAGGCCCACTTTACTCTTTATATGGTAATATGGATTGGCTTTTGTATTAACTAGTTTTACAGCCTATCTGAAAACATGTAACAGGCAACTCCTGCAGACACATTCTTTGTAATGACTTTATAATCCTGCAGTGGCATGTTCCGGTAATGACTTCAGTCTCCTCGTCCACACTCTCCGGTTAGTAGAGCCATTTATGTACATCGCATATCCCTGATTTCAGAGCAACGGTGCAGTTGCACAGGTTCCCACCTCAAAATGGGATGCCATGACTCTGTCTGGATAATTCTGTGGAAAAACCATTCTGAGCTGGATACGGTGCCTCATACCTGTCATGTCTACTTTCAGGAGGCAGAGGCAGGGGAATTGCTGTGAGTTGTTGGTCAGCCTGGGTTACAGTATGAGACCCTGTCTCAGAAAACCAAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013610:ENSRNOT00000065771:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.008 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(54.9=40.4),PF0293211=Neur_chan_memb=WD(100=48.0),PF0293211=Neur_chan_memb=PU(54.8=14.4)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(42.5=57.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGAGTACTTGGTGTTCACC
R:
CATCCGATCAAGGACTTGGGC
Band lengths:
348-1757
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]