RnoINT0036297 @ rn6
Intron Retention
Gene
ENSRNOG00000013610 | Chrna5
Description
cholinergic receptor nicotinic alpha 5 subunit [Source:RGD Symbol;Acc:2347]
Coordinates
chr8:59584571-59587055:+
Coord C1 exon
chr8:59584571-59584680
Coord A exon
chr8:59584681-59586226
Coord C2 exon
chr8:59586227-59587055
Length
1546 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
TTGTCGTGTGCTTCTTTTAGTGC
3' ss Score
8.24
Exon sequences
Seq C1 exon
GAATGGATAGATGTGAAATTGAGATGGAATCCTGACGATTATGGTGGGATAAAGATTATACGTGTTCCTTCGGACTCCCTGTGGATCCCAGACATCGTTTTGTTCGATAA
Seq A exon
GTAAGTTACGTTCTAAATATTACTCCCAATTTCCGAAAGAACACTTGTATTGCTACTAAGCACTAGTGATTTTTTTCCCTCTCATCTGCAAATTGTTTAGGTATGGAGTCAAGTGATCTATTTGTTGCATGGCTGTTGTGGGTCCTTTGCCTTTTTTGGTGTATTGTTGTTGTTGTTGTTTTAATCATAAAAGCGTTATCTGATTTCTGAAATAAGAAAAAAGACAAACATAGGAAGGAATAAGGGGAAGTAGGGGGAGAGATAACGGCTGCAGCTAACTTAACACACAGTAAGCTTGTGTGCCTGGCAGTGTGCTCACAGCACGCTTACACCGGGAGTCACCCGTCTTACTTGGCCCTTGTCTATGATCACAGAGCTCTCAGACAGTACTGTAAGGTTTCACCTCCAGACACTGGAATACACGTTTATTCCCTTATTCAAGTCAGACTTCCAGGTTTGGGGTGGGGGCTTGTTTTTTAGTTGAGGTTATAGTTTGTGATCAACCCAGTTTTCTGATATTATGTGAAGACATTGTCACGGTGGCACCATCCATTTTCCTACGTGAGTTTGTGGTTAATTGTCAGTTAGCAGCTGTATTCCCTGTCCACCACCCCTCCCAGGGCCATCTCCGAGTGAATGTGAGTGTTTGCATGTGTCCTAAAGCACGCTGCCTTGTTTGCACAAAGGCTTTTAGGGCAAGCGCTATGCAAAAAATGATCTTTTGAAACCTTTTACTTCCGTGCTCCTTGATATGGAAGGATGAAGAAGGCTCGTAGGGTATAACAGGGGCGGCTTCTGGCACATTCTCTTTACCCTCAGTAACGGAAAGCACTTTGTCCTATTTGCACAAAGGCTTTGGCATGCGGGCAGAGCAAATGCTGTGCAGAAGCCGACCTTTGGGAACCTTTCACTTCCATGTTGGTATGGAAGGATGAACACGCCTGCACGGTAGCGTGGTGCAGCTCCCTGTGCACCAGCTGCTGTCCGTGTTGAAAACATTCGTGTGACTCAGCATAGATATATTGCACAGTGCTGTGCAAACGCCAGGACCTGAAGAAACAGCAAGACAGTGAAGGAATCGGGTGCTTCCCCTGCATCGGGGCCACTCCGGCCCAGGAGAGCACCGGTGCAACCTGCATGGTGCAGACACTCTTTCCTCCAAGGGTAGAAGTCATCTCTTACTTGGGTGGAGGAGGAAGTCTAGGGATGTGGATTCAGGCTCTGCCTTTCTGCATGCCCAGTGTATAAACAGCCCGACCATATTTGTATGTAAAGAGGCGTCTTTCCCATTACTAAATTCTCAATGTCTTGAGGAACATGCATTTGCCCATCTCACAGTACAAAGGGAAGACTAGGTTCAGTCCTAGCAGAATCACAGGCTGGAAAGATGTCCACGAAGCGTGACCATGGGTGGAGCAGGCATTTGGGCAGACGGAAATTTCAAACTCATTTCCCACTATGACCCACAGGTTCCCTCTGTATTAGGCTTACGAAATGTGACCGTGGCTTGTTTGATTCTGGCACTATTGTCGTGTGCTTCTTTTAG
Seq C2 exon
TGCAGATGGACGTTTTGAAGGGGCCAGCACGAAAACAGTTGTCAGGTACAACGGCACTGTCACGTGGACGCAACCAGCAAACTACAAAAGTTCTTGCACCATCGACGTTACCTTTTTCCCGTTTGATCTCCAAAATTGTTCCATGAAATTCGGCTCGTGGACATACGATGGATCCCAGGTTGATATAATCCTAGAGGACCAAGATGTCGACAGAACAGACTTTTTCGACAATGGAGAGTGGGAAATCATGAGCGCGATGGGGAGCAAGGGGAACCGGACGGACAGCTGCTGCTGGTACCCCTACATCACGTACTCCTTTGTGATTAAGCGGCTGCCTCTCTTCTATACCTTGTTTCTTATTATCCCCTGCATTGGGCTCTCATTTCTGACTGTGGTTGTCTTCTATCTCCCTTCAAACGAGGGTGAAAAGATTAGCCTCTGCACCTCAGTGCTCGTCTCTCTGACTGTCTTCCTTTTGGTAATCGAAGAGATCATACCGTCATCTTCCAAAGTCATACCCCTGATTGGGGAGTACTTGGTGTTCACCATGATTTTCGTGACCCTATCCATTATGGTGACTGTCTTTGCCATCAACATCCACCACCGCTCTTCCTCCACACACAACGCTATGGCGCCCTGGGTTCGTAAGATATTTCTCCACAAGCTTCCCAAGCTGCTCTGCATGAGAAGTCATGCGGATAGGTACTTCACTCAGAGAGAAGAAGCCGAGAGTGGGGCTGGACCTAAATCTCGGAACACTTTGGAAGCCGCACTCGATTGCATTCGCTACATCACGAGGCACGTCGTGAAAGAGAACGACGTCCGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013610:ENSRNOT00000065771:4
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=0.008
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.6=100)
A:
NA
C2:
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)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCCTGTGGATCCCAGACAT
R:
AGGAGTACGTGATGTAGGGGT
Band lengths:
353-1899
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]