RnoINT0036303 @ rn6
Intron Retention
Gene
ENSRNOG00000012283 | Chrna6
Description
cholinergic receptor nicotinic alpha 6 subunit [Source:RGD Symbol;Acc:69281]
Coordinates
chr16:68864394-68866718:+
Coord C1 exon
chr16:68864394-68865369
Coord A exon
chr16:68865370-68866491
Coord C2 exon
chr16:68866492-68866718
Length
1122 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
ATCCTTTGTTTGCTTTGCAGGTA
3' ss Score
10.79
Exon sequences
Seq C1 exon
TGCCGTCGGCGACTTCCAGGTCGAAGGCAAGACCAAAGCTCTTCTTAAGTACGATGGGGTGATAACCTGGACCCCGCCAGCCATCTTTAAGAGTTCCTGTCCAATGGACATCACCTTCTTCCCATTTGATCATCAAAACTGCTCCCTGAAATTTGGGTCCTGGACTTACGACAAGGCTGAAATCGACCTTCTCATCATTGGCTCTAAAGTGGACATGAACGACTTTTGGGAAAACAGTGAGTGGGAAATTGTCGATGCCTCTGGCTACAAGCATGACATCAAGTACAACTGCTGTGAAGAGATTTACACAGATATCACCTACTCGTTCTACATCAGGAGACTGCCCATGTTTTATACCATCAATCTCATCATCCCCTGCCTCTTCATTTCCTTTCTCACCGTGCTGGTCTTTTACCTTCCTTCCGACTGTGGCGAGAAAGTGACTCTTTGCATCTCGGTTCTGCTTTCTCTAACTGTCTTTTTGCTGGTGATTACAGAGACCATCCCATCCACGTCTCTCGTGATCCCACTAGTGGGTGAGTATCTACTGTTCACCATGATCTTTGTCACGCTGTCCATTGTGGTGACCGTGTTTGTGTTGAACATACACTACAGGACCCCAGCAACGCATACCATGCCCAAGTGGGTGAAGACCATGTTCCTTCAGGTCTTCCCCTCGATTCTGATGATGAGGAGACCTCTGGACAAGACAAAGGAAGCAGATGGTGTTAAGGACCCCAAAACCCACACCAAGAGGCCGGCCAAGGTCAAGTTTACTCATCGAAAAGAACCCAAGCTTCTAAAGGAATGCCGCCACTGCCATAAGTCAAGTGAGATAGCGCCTGGCAAGAGGTTAAGCCAGCAGCCTGCACAGTGGGTGGCAGAGAATTCAGAGCACCCACCTGATGTTGAAGACGTGATCGATAGTGTTCAATTCATAACAGAAAACATGAAAAGCCACAATGAAACAAAGGAG
Seq A exon
GTAAAAGTGGACCCCTTTTCTCCAGCCAGCTGCACCCCTACTAGGCCTCAAGGCTCTTAGAGCGTCAGTGGGAGTTACATCTGTGGTACAGTCAGGCAACATCACCTAAGGCCAGCTCTATTACCATGCAGCCTTTCAGGACCTGGGTGTTAGTTTAGGGAGCTATGGTGAGATGGTCTATGTCGCCCTACAACAAATCTTCAGCCTGCATTTACTTACGGTGAGATCTAGCTACAGTACAAATGCAGGACAAGCTTGCCTCATGGAACAAGCCTCCAACAAAATGAACAGTGACAGAGTGAGGATGGGAAGAGAGACTGTAGAAATCGTTATTAATAAAAATCCCTGTGGCAGGTTTGTTACCGGCCCCAATGGTTTATGTTCCCGAATGAAACACACACACACACACACACACACACACACACACACACACACACTGAGAATGCCTGTCATAACACAGGTCACAGGACAGCAATGGCCAGTGAGCCTGCCTCCTGGTTGGCATCTTTTAAAACATTGAAATACATTTACTGTTGACTTACCGGGCCAGGCAGGTCCCCTAATACACAACCCACAGAGACCATAGCAGAAGGTTAGAAGTTTGGAACTGGAAAGATTCCAGATGTGCAATAAGCTCTCCCTGTTAGCATCCCTCGGAGGCCTAGAGGCTACTTATTCCTGTACAGGGGATCCTGGCTGTATCCTACACCCTCTGGCCTGTCCTCTCACTGCTTCACTCAGATTCCCCAAAGAGCCAGGCTCTCCTGGTGCACTCGCGACAAGAGCTTGACTCTCAAGCAGATACTGTGTGGGAAGTGTCCCTGGAGCCAGGAAAGGACCTTTATCACAGGAAAGGGGTCACAAAAGTCTTTGGCACAGTTCATAGCCATCTCTGTGAGGCACCAATGGTGTATATGACTGCCATGGTGTATATGACTATTTACCCTCCTTAGGCCATAGACCCCACATAGGATACACAGGCAAACATACTAGCAATTACTGATTTTTTTTAAAAGGATTAGAGAAAATCACTTTGAAAAAAGGACGTATTCATAAAACATAGCCTGTTTTCCTATGGTCTTGACTTTTAATGCTAGCCTTGATCCTTTGTTTGCTTTGCAG
Seq C2 exon
GTAGAAGATGACTGGAAATACATGGCCATGGTGGTGGACAGAGTCTTCCTCTGGGTGTTTATAATCGTCTGTGTGTTTGGAACTGTGGGGCTCTTTCTACAGCCACTGCTTGGGAACACAGGAGCGTCTTAATCGGGATTTTCCTTTTGCCTTCTAAATCTTTTAAATGTTTTTTCCTCCACTACTTACCACAAGAAAAAGTCAAGTTTGCAGTCTCCTAAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012283:ENSRNOT00000016452:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.104 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=35.3),PF103294=DUF2417=WD(100=51.5),PF0293211=Neur_chan_memb=PU(86.0=62.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.1=70.5)
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:
CCTTCAGGTCTTCCCCTCGAT
R:
CCACCACCATGGCCATGTATT
Band lengths:
353-1475
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]