RnoINT0036272 @ rn6
Intron Retention
Gene
ENSRNOG00000018286 | Chrna1
Description
cholinergic receptor nicotinic alpha 1 subunit [Source:RGD Symbol;Acc:69277]
Coordinates
chr3:60445666-60447045:-
Coord C1 exon
chr3:60446806-60447045
Coord A exon
chr3:60446204-60446805
Coord C2 exon
chr3:60445666-60446203
Length
602 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGC
5' ss Score
6.12
3' ss Seq
AATGCCTCTGTTTTCCCCAGGCG
3' ss Score
10.64
Exon sequences
Seq C1 exon
GTTTTTATCGACACTATCCCAAACATCATGTTTTTCTCCACAATGAAAAGACCATCCAGAGATAAACAAGAAAAAAGGATTTTCACAGAAGACATAGATATCTCTGACATCTCTGGGAAGCCGGGGCCTCCACCTATGGGCTTTCATTCTCCACTGATCAAGCACCCTGAGGTGAAAAGCGCCATTGAGGGTGTGAAGTACATTGCAGAGACCATGAAGTCAGACCAGGAGTCTAACAAT
Seq A exon
GTAAGCTGTATGGCTCCCAGGCCACGCCTCTGGGTCTGTCTGTCCGTCTGTCCATCTGTCTGTCCGTCCATCCGTCCATCCGTCCATCCATCCATCCATCCATCCATCCATCCACCTATCTATTCATGACAGGGTTTCTCTGTGTAGTCAAGGGTGTCCTGGAATTCGCTCTGTAGACCAAATTGATCTCCAACTCAGATGTGTTCCTTCCTCTGCTTTCTGAGCGCTAGAATCAAAGGCGTGTGCCACCACCTCCAGGCTAACACACCTCGGGGTCTAAATGATCAAATGCATAAGTGCAACAAGGAGGTTGATCTGACCTTGACCAATGAGTTGGCTTTAAGCTCCAGTTACTGACTTGAGATGTGCCGTGTTGACTACCCCCGGCAACTATAGTAAGTCATTTTTGGCTTAAATTAGCTATGCAAAACCCAAAGAGTATAATATCGGCCTCAGGGGTTGATTTACATATTGAAGATATGTAGTACAAGATGAGAACTACATATTGGAGATTTACATATTGAAGGCCAGGCCTGTGGGGGATGCTATGAGCCTGTGTCCCATCTTAGTGGACTCCCGTCCAATGCCTCTGTTTTCCCCAG
Seq C2 exon
GCGTCTGAGGAGTGGAAGTATGTCGCCATGGTGATGGACCACATCCTCCTCGGAGTCTTTATGCTGGTGTGTCTCATCGGGACGCTGGCTGTGTTTGCAGGTCGGCTCATTGAGCTACATCAACAAGGATGAGCAGAAGCTGAACTAAGCCTCCCTCTGCCCCAGCTGCAGCCACCACCAGGAAAGATAGAAGAGAGGAAGGCCTGTCTACTTGAATCCTTTCGCGCTTACCAAGCACACAGTGTGCTACATGTCCTGTTAATGATAGTGGTCTCTGCTCACACTGCTATGTCCTTAAAGTATCTCCCCTTTGCTTCTGCTTTTAACACCATGGGTCTCCTTAAAGAGGGAACCCTTTGTAGTAAATAAAAGTGAGTCCTCGGGCTGGAGAGATGGCTCAGCGGTTAAGAGCACCCGACTGCTCTTCCAGAGGTCATGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTATAAAGAGATCTGATGCCCTCTTCTGGTGTATCTGAAGACAGCTACAGTGTACTTATAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018286:ENSRNOT00000024706:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(31.9=57.5),PF0293211=Neur_chan_memb=PU(52.2=45.0)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(44.9=70.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCCATTGAGGGTGTGAAGTA
R:
TAGCAGTGTGAGCAGAGACCA
Band lengths:
350-952
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]