RnoINT0036282 @ rn6
Intron Retention
Gene
ENSRNOG00000017424 | Chrna2
Description
cholinergic receptor nicotinic alpha 2 subunit [Source:RGD Symbol;Acc:621533]
Coordinates
chr15:42822788-42825179:+
Coord C1 exon
chr15:42822788-42823817
Coord A exon
chr15:42823818-42824962
Coord C2 exon
chr15:42824963-42825179
Length
1145 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TAGCTCATTTCTAACTTCAGGTG
3' ss Score
6.1
Exon sequences
Seq C1 exon
TGCAGATGGGGAGTTTGCGGTGACCCACATGACCAAGGCTCACCTCTTCTTCACGGGCACTGTGCACTGGGTGCCCCCAGCCATCTACAAGAGCTCCTGCAGCATCGATGTGACCTTCTTCCCCTTCGACCAGCAGAACTGCAAGATGAAGTTTGGCTCCTGGACATATGACAAGGCCAAGATCGATCTGGAGCAGATGGAGAGGACAGTGGACCTGAAGGACTACTGGGAGAGTGGCGAGTGGGCCATTATCAATGCCACCGGAACCTATAACAGTAAGAAGTACGACTGCTGCGCGGAGATCTACCCCGATGTCACCTACTACTTTGTGATCCGCCGGCTGCCGCTGTTCTATACCATCAACCTCATCATCCCATGCCTGCTCATCTCCTGCCTCACTGTGCTCGTGTTCTACCTGCCTTCCGAGTGTGGAGAGAAGATCACGCTGTGCATCTCGGTGCTGCTATCTCTCACTGTCTTCCTGCTGCTCATCACGGAGATCATCCCGTCCACCTCGCTGGTCATCCCACTCATCGGCGAGTACCTGCTCTTCACCATGATCTTTGTCACCCTCTCTATCGTTATCACAGTCTTCGTGCTCAATGTACACCACCGCTCCCCCAGCACCCACAACATGCCCAACTGGGTAAGGGTAGCCCTGCTAGGCCGGGTGCCCAGGTGGCTGATGATGAACCGGCCCCTGCCACCTATGGAGCTCCATGGCTCCCCGGATCTGAAGCTCAGCCCCTCATACCATTGGCTAGAGACTAACATGGATGCTGGAGAAAGGGAGGAGACAGAGGAAGAGGAGGAAGAAGAAGATGAAAACATATGTGTGTGTGCAGGCCTTCCAGACTCTTCGATGGGTGTCCTCTATGGCCATGGCGGCCTGCATCTGAGAGCCATGGAGCCTGAGACCAAGACTCCATCCCAGGCTAGCGAGATTCTGCTGTCACCTCAAATACAGAAAGCACTAGAAGGTGTACACTACATTGCTGACCGTCTGAGGTCTGAGGATGCTGACTCTTCG
Seq A exon
GTGAGTTGGGAAGGGCCCCTCCATGGGTGATCCTGCCAATTTATCAGGGAAAAATCCCAGCCCAGCCCAGAGTATCCCCTTGGGTAACTCCTTCTCTTCTTGTAAGGATCAGTTTCCCTCAGTCATGTCCAAGGAATCTGGACTCAATCATGAGAGAGAAACACTAGCTAGAAGTTCTTTGGTAACTTCCTGGCCGATGGCAGCATACCACAGGGTCTATCCCACTCTGTTCAACTTAAGTAGGAGAGGATGAGCAGAAATTGGGGAGCTCAGATACTATTCTCCATCTGCTTTGGCTTTTGCTGAGAAGCTTTTCTATGGGAAGGTGGGGGAAGGGGAGGTAGATAGAGAGACTGCTCTGCGCAAGGACAGAAATCCAGGTACAAATGTATCAACTTTGTGCATCGCTGGCCCTCTACATTACCCTGTGGTAGAGGGTCTCCTCCATCTGGGCTCTGGGCATTCTGTGACTTTCCCTATTCACTTGCAAGCCCTGCAGATTATCAACTGAATCAGGGTGGGCTCCCCTCCCCAGTGCACATAGCAAGTACTTAGTGTTCAGAACCTGATCGTCCCCTTACCAACCAAAGGAGTGAAAGGTCTGTGGTTATTGTGGGATGGTCTTACTGAGTAGATAAGAACATTGATCATTAATTTGGAAATGACTAAGAATTTAAATCTTCTGGGTTGGCCTATGAGCTGAAGAAATGCAAAGCCCAGCTCTTCCACATTGACTTGCCCTGGGCTACAACCTGCCTCTTTCTGCCCCCTTCAGGTGTGTGGGTAGGTAGCATGGGACAGCACATTATTGGGCAGCTATCTGACTGCTGTGAGCTACAGTTAGATTTTCCTGATTTTGAAGGCCCATGCCCTCTTGGTAGTCCTAGTGTCTCCTCATGTCCCTCTGGACTCCTGAACCTGGCAGTATGTGGAAATAGGGAAAGACACAATGGGATTCCCAGGGATGCATCAGTCCTGAGTTAAGCCTGTTTCTCACTCCATCCATCTCTATGTGTGGGATAACCTTGGCTTCACAAGCCTTCTGTAGTCTGGTGACTGCTGCCTTCAGTGGGGCTGGATGTGGAGGGATAGTTCCTCTTCCCAAAGCCTGGCTCTTATCACTGTTAGCTCATTTCTAACTTCAG
Seq C2 exon
GTGAAGGAAGACTGGAAGTATGTGGCCATGGTGGTAGACCGGATATTCCTCTGGCTGTTCATTATCGTCTGCTTCCTGGGGACCATCGGACTCTTCCTTCCTCCATTCCTGGCTGGAATGATCTAACTTCATGTCCTTCATGTTGGCTCCAAGGTGGCCTTCGTAACTATCTTCTAGTCTTCTGTGAATGGAGCCATCTCTAGAATACTCTTTTGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017424:ENSRNOT00000023475:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.084 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=33.4),PF103294=DUF2417=WD(100=50.0),PF0293211=Neur_chan_memb=PU(87.0=64.2)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.2=73.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATGTGTGTGTGCAGGCCTTC
R:
CCACCTTGGAGCCAACATGAA
Band lengths:
357-1502
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]