RnoINT0036291 @ rn6
Intron Retention
Gene
ENSRNOG00000011202 | Chrna4
Description
cholinergic receptor nicotinic alpha 4 subunit [Source:RGD Symbol;Acc:2346]
Coordinates
chr3:176536863-176542820:-
Coord C1 exon
chr3:176542711-176542820
Coord A exon
chr3:176538241-176542710
Coord C2 exon
chr3:176536863-176538240
Length
4470 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
TTTCTCTTGTTTCCTGCCAGTGC
3' ss Score
10.39
Exon sequences
Seq C1 exon
GAGTGGCACGACTACAAGCTGCGCTGGGACCCTGGTGACTACGAGAATGTCACCTCCATCCGCATCCCCTCTGAACTCATCTGGAGGCCTGACATCGTCCTCTACAACAA
Seq A exon
GTAAGCCATGTGGGCCCGGGGTGGGGGGGTGAGCTCAGGACCCACACATCGAGGAAGCTGCTAGGGTCAAAGAAGACCAAATGGAGAGGAAGCCCAATGGCCACCAGCACCTGGGAATACCTGCTCTGGGTTCTGGAGAACTTCTAGTTCTGCTGGTCTCCTAAGAGCAGAGAATGGATTCGACATCCTCTTCTGGCAGCGACTACCAGTATCCCATCTCAAGCCGGTGTCCTTAACCCCCACCATGCACAAGTCACAGTTTGGTTGACTAATGACGCAGGGGACTTTGGGAGTAGGTAAAGAGCAAGAGACGAGGCTGCTCTATAGAGCCTCGCCTCCGCTCTTCTTCGTCCTGCCTTCGTGCTGTGTATCCAACACTGGGCATTGAGCCAGTGGGCAAACCTGGTTCTCAAGATCAGCTCACACCCTGTCTCAGCTCCTGGAAGCTAAAGTCCACATGGAGACAAATCCAGTTAGTGGTGACAAGACAGGGGGCGAGCATCTTCACACTTCTCTCCCGGGGAACCTCACAAGAAGACCAGGACTGGGAGCAGCTGGCTTCCTGAGCTGAGTCTCCCCGAGGTGATGCTCTATTCCCTCAGGGTCTGGGTGGGCAGCAGCTTCTGCAGTGCTTACAGACAAAGCAAACAGAAGCTCTTCTACCCCCTAGTCCCAGCCATCTGCCAGCAGCCCCCTCCAGCCCCTGGGGTGCCCGTCTGACCTACAAATGCTCCTATTTGATTAAGAATGACTGGGATTCTCTTCCTCTTTAATTGAGCGGAGTACTAGCCACATCCGCGGCTTGTAGAAGGCACTGAAGGTGGTTTTCCAGAGTGTGTTATGGGTGGGCTTAAGGAGGAGCATATGTGTCAGAGAATGGCAAGGTCTACAATTCCTGCTCTTCCTTCAGAATGGCTCTCTGTCTTCTGCAGCAATCCAGCTGAACCTTGAACCCTGGAAGGCTTCTAGCTACTGGGTCTTTCTGGGGTCCACACTCTGCTTGATCCTCCCTCAAACCCTGGGATCAAGTACTGAATCTACTCTGGGCAGCCTGTTGGACCCATGACAAGGAAGGACATGCATTTCCTGGGTGGTATTTGTTAAGCAGAGGACTAGGTGGAGATAGCCCAGTACTCAAGCTCCTACAGACAGGCACCCAGTAGTTTCCACCCCTCTAAGGTCACCTTTTTATCTCTTCTACCTGCTAGGATACTGTGAAAGGGGCAACCCCCCCCACACACAGAGACCCTTTTATGGGGCTGGGATGAGCACTTGAGGTCTATCTGAACAGGACTTGGAGCTGGCGAGGGTTGATAGGACTCTGGTACTAACAGGGAGGAAGGCCATTTCCAGCAGCTGCTTGCCAGATGGCTGGTCCCAGTGCTGGATACGGGAGTCCCCACTCTTTTGTTGATGTGGGGCTCCCTCTCCTGGAAGCCCAGAAGCTCTCCACCTGGTACAGGGCAAACAGTTGCCTCTGGAATGCCTCCTCATGGGATGGGGCCTCTTAGGGGTAGGCAGGATCTGGGACCCATTCTCTCTCAGCTACTGGCTAGCTCATTGAATCCACTAACACACACTGGATGGCTCTAGGACCCAAATACTTGTGCTTCCTCTTATTTCCTGGGGACTCTAAGGTGCGGAAACTGAGGATCCATCATCCTCACCCTGCATCAGCAGCTTCGGCCATGAAATGTTGACAGCCTACTTGAGGAAACCTGCTGTCCTAGTTCATGGCTGGGCTGCCAGTGGTCCCTGAGACAGCAATATCCTTTGGGCATTCTGAGAACCTTACCCTTGGCCGCACGAGAAGAAGGAGCAGCCAGAAGTAGGACACAGAGTGCTGAGCCCTGTGGACTTTACTGTCACCTTCTCCACAACTGGGGTTTCGTGGCAGTGCCATATGGAAGCAGGGCCAGAATTTGAAGGAGCTGGGCTGCACTGCAACCCTCAGAGAACTCCAGTGCACTTGGGACCTGTCTGCAAACACAAGCCCAACAGCAACTCCAGAGGGAACAGAGGGAGCCGTACACTCAGGTTTAGATGCTCTGGAAAACTCACAAGGGGAACCCAGACAGGCTAGGCAGGGCGGGGAGAACAGAGAATGGCGAATAGTACTGGTGAAGGCAGATGGAACCACGGTAACCTGAGCTCTGACTGCTGAACCCCATTGTGTCTCCAGGGTAGGAAACCTAGACCCAGCCACCCAGACTGCAGATGGGAGCCACCGATTCAAGTGAGCCCCGAGGGCCTCCTGTCTGCCAACTGGTTGCAGCCTCCCCTGCCTGCCCTCCAGAATGTTTACAAGGCGGAGGATCCACTCTCTGGCTGTGGGAGAATTTAAATTTGTGCCTGGAGTGTTTAGGCTTTGATTTTTTGGAGAGATGGGACCGAGAGAGGGAAACAAAACCAAGCCTGAATCTGCACGGCCCGAAATGCGCCACAAGATCCACCCCCATGTACCCGGAGGGAACCTCGGCTTCTGTAGAAGCCAGGCTGAGCTCTGTGCACTGTGCAGCCAGGAACCTTATCAGGGTGCATGTAGAGAGCGGCGTTTCCAGTCCCTTCCACATGCAGCATGACTACCGGTGACACTGGCCCAGGGTGGGTTAACATGCTGGAGGGTCCAGGGTTGACACCCAATGAGATCATGAGAAGCTCAAGTCTTCTGGACTTGGGCATGGTACTTCAGGATTTTGGCTAGCAAAGGAAGAGCCACTAAAATTCCCAGGAGGCCACCATGGGCCCTGGTCTAGACCTGATAAAGCTCATCAGGATAGCAGGGCCAGTTGGCTGATGAAATTCACGGATCCTTCTGCCTTAGAACCTTGAAGGATACTAGCCAATGACCCGGACCGGTGAATGGAGGTGGGAGAAGTAATGGACAGAAGGGGTCTGGACTGCTGGGTGAACAGAAGGTTCTGGAGTCTGTGTCTCTGAGCTACACTGTCTTATGAGTGTTGAGACCAAAGGGATGTGTGCGGGTGCCATTACTGAGGGATTTAATTAGGCTTCAGAGAGCTCGGTAGCTATAAATTGAGGTTTCCCGTCAGTGTTTCTGAGCTGAAGCTGGCAGGGTTTGCCCAAGCGCGTTAGCGCATTGCACTCTCACGGTCTGTGAATGCTAATCTAGGGCCCGGCCTGTGAAGAAGCCAAGGCCTAAAGAGTGGCATCGCAGCCCAGGTTCCACAGGGCAAATAGAATTGAGGCTGGGCTCTGAAAGACCAGTTCTGGGGAGGGCTGTGGAGGTGAGCAGGGTGAGGAAGGCTTCTTGAGAGCAGCTTCCCGGTGTCAAGTTCCGATAATGGGTAAACTGAGGCACAGCATCACTGCTCGTGAAGCTCAGAGGCCAAGGCTGGAACTCTGCTCGAGAGGAGGGGCCTGAAGGACAGCAGCCCCGGGTTCCACTGCTTAACCTGACAAACATCCCCCAAGGCAGAGAGAGGCAAGAAGCCAATAATCAGACACTGGAGGCTGAATTAGACAGCTGGAGTCCACATCCAGACTCTGCCATGACCTGTAGTGAGGTGGCCTCCAGTACTTGGAGCCAGTGGAGAGGAAGATACCTTAGTCTCCAGTGGCAGGAGGTCAGGGTTGATCCACCCTGAGTTTGCGCTTGGTCCACGGTGTTTGTCCTGGGAGTGACCGTGGGCACGATGCATTGTTATGTGCATGCCTGGGTCTTCTGTATGGATAAGATGGGCAGAGAGGCCAACTGGCCTCCAGCAAGATGATCCATTAACCAGGACCCGATGAGCAGCTGTTTGATGTGAGGTCCTTTTCATGGGTGATGGGGACGAAATGTTGCGTATCTCACCCCTCTGCTCCTGGGCCCAGCAGGTACCTATTCTCCTGGATCAGGCCTCTGGGTCCTCTTGTCCTGTCACTGTAGACACATACTCTCCATGCCCAGTGAGCTTGCTATGGTCCTGCAGGGACCTCCAGGATATCCATAGCACGCTCCAGGGTCTAGTTGTCAGCTCCTAAACTGAAAAGGACAGGCACCAGCCCCTCCCCTCGGTCCATGAGACACTCAGGTGGAAACCAGGGGAAGGCAAAGGGAAATTTCCACAGTGCCACAATAAGCAGAGGTGACTCAGGCCCCTTGGAATGGAGGTACAAATGCAAATTCATGGAGGCAATGGGTGCTCAGGAGAAGCCAGTGGTTTGGTCCCACCCTGCACCTTCGTAACAGCAAAGAACAAGGACTGTAACACTAACTCTGCTCACTGGGCATGCGCACCATTCATCCCTGCCTTCTCCAAACCACCTGCCACCTTGAATCAAGGGTGAGAAACTGAAGCACCCAGGTGAGTGACGGCCCAGACCACACGCACCACTACACACAGTCCTGCACCGTGTGGGTGGCTGTCAGAGCTGTCGGTACAGGCTGGGAGGTTTTCTCTGCAATGTTTATGGGTGTGGTCCATGGAGGGGCAGAACTCATTGCTTTCTCTTGTTTCCTGCCAG
Seq C2 exon
TGCGGATGGAGACTTTGCAGTCACCCACCTGACCAAGGCCCACCTGTTCTATGACGGAAGGGTGCAGTGGACACCCCCAGCCATCTATAAGAGCTCCTGCAGCATCGACGTCACCTTCTTCCCCTTTGACCAGCAGAACTGTACCATGAAGTTTGGATCCTGGACCTACGACAAGGCCAAGATTGACTTAGTGAGCATGCATAGCCGTGTGGACCAACTGGACTTCTGGGAAAGTGGGGAGTGGGTCATCGTGGATGCTGTGGGCACCTACAACACCAGGAAGTACGAGTGCTGTGCCGAGATCTATCCTGACATCACCTATGCCTTCATTATCCGACGGCTGCCGCTATTCTACACCATCAACCTCATCATCCCGTGCCTGCTCATCTCCTGTCTCACCGTGCTGGTCTTCTATCTGCCTTCAGAGTGTGGCGAGAAGGTCACACTGTGCATCTCGGTGCTGCTTTCTCTCACCGTCTTCCTGCTGCTCATCACCGAGATCATCCCGTCCACCTCGCTGGTCATCCCGCTCATCGGCGAGTACCTCCTCTTCACCATGATCTTCGTCACCCTCTCCATCGTCATCACGGTCTTCGTGCTCAATGTGCACCACCGCTCGCCACGCACACACACGATGCCCGCCTGGGTGCGTAGAGTCTTCCTGGACATCGTGCCTCGCCTCCTCTTCATGAAGCGCCCCTCTGTGGTCAAAGACAACTGCCGGAGACTTATTGAGTCCATGCACAAGATGGCCAACGCCCCCCGCTTCTGGCCAGAGCCTGTGGGCGAGCCCGGCATCTTGAGTGACATCTGCAACCAAGGTCTGTCACCTGCCCCAACTTTCTGCAACCCCACGGACACAGCAGTCGAGACCCAGCCTACGTGCAGGTCACCCCCCCTTGAGGTCCCTGACTTGAAGACATCAGAGGTTGAGAAGGCCAGTCCCTGTCCATCGCCTGGCTCCTGTCCTCCACCCAAGAGCAGCAGTGGGGCTCCAATGCTCATCAAAGCCAGGTCCCTGAGTGTCCAGCATGTGCCCAGCTCCCAAGAAGCAGCAGAAGATGGCATCCGCTGCCGGTCTCGGAGTATCCAGTACTGTGTTTCCCAAGATGGAGCTGCCTCCCTGGCTGACAGCAAGCCCACCAGCTCCCCGACCTCCCTGAAGGCCCGTCCATCCCAGCTTCCCGTGTCAGACCAGGCCTCTCCATGCAAATGCACATGCAAGGAACCATCTCCTGTGTCCCCAGTCACTGTGCTCAAGGCGGGAGGCACCAAAGCACCTCCCCAACACCTGCCCCTGTCACCAGCCCTGACACGGGCAGTAGAAGGCGTCCAGTACATTGCAGACCACCTCAAGGCAGAAGACACTGACTTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011202:ENSRNOT00000009041:4
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=0.217
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=25.0),PF0293211=Neur_chan_memb=PU(91.1=73.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]