DreINT0046722 @ danRer10
Intron Retention
Gene
ENSDARG00000087071 | chrna4a
Description
cholinergic receptor, nicotinic, alpha 4a [Source:ZFIN;Acc:ZDB-GENE-130530-903]
Coordinates
chr6:58519278-58523393:+
Coord C1 exon
chr6:58519278-58519344
Coord A exon
chr6:58519345-58522210
Coord C2 exon
chr6:58522211-58523393
Length
2866 bp
Sequences
Splice sites
5' ss Seq
GCTGTACAA
5' ss Score
-8.82
3' ss Seq
GCAACACTGTGTTTCTGCAGTGC
3' ss Score
6.33
Exon sequences
Seq C1 exon
AGGATAATGGGAATGTTTCGTCAATGAGGATCCCAGCGCAGTTTATCTGGAAGCCTGATATCGTGCT
Seq A exon
GTACAACAAGTATGTAAAAATGTGACATTACAAGAATGTGAACGCACACACACATACACACACACACACACACACTCACACACACACACACACTCACACACACACAGGAGTAGATTTAACCAATAAACGAGGTAAGCGCCCACTTAGAACCTCAAAATACTGAATCCACAACTTCTGGTTACAGCTGTGCAGAGACACAGACTCCGCCAGGGGGCGCCACAGCTGCTTTTTCTTATTATGTATCCATACAGTATGATGTCTTTAAACATAAATCCTGTGGGTTGAAGATTTGACAGAAATTGCATATTAAATGAGATTCTTGTTTTGAAATATTGTATTTATGCATCATAAATCACATTCTTGTATATTATGTTCAACTGTGCTTTAGTCTTGTGAGCGGGGTTAATTTGAAAGCAGACTGCGTTTATGATTCTACAATGATTAAATAAACATTTATATTAAATCAGTGGTTCTCAAACTGTGGGACGTGTATCACTGGTGGTACGCGGGCTTACTTCTAGTGGTACGTGGAGGAATCACTGAGTAATGAAGGAAAAAATGAATACAACTTTGATCAGTTGATGTGTACGATAACACCAATGTAGTGATCAACATTGGCTGTTCTGTAAAGCCTACGGTTAAAGCAATGTGTTTAAAATGTTTACTTTAGTGCATCGCGTCATCAGCTGCATAAAATCAATAGAACTAGAGAAAGAGGTGCGTGGTGCTTCCAGTGGAGATCCGTGCTAGACCAGAAGTCCCCTATACCCTCGGGCCACAGACCAGCACCAGTCTATGGATCAATTGGTACCGGCCCGCACAAAAAATCATTAATTCCGTTTTATTTATAATCTGAATAATTTAACCATTTATTTTGAAAAGTGACCTTATTCTATTGTTACATCTTGGTCACTTGAGTGCCAAAATTTAACCCACAGGCTAGCAAAATGAGTACTGCAGCATGACACGCTTGTGTATTCCAGCTGTCCCCAGCTGAAAACATCTTAACATTTCAGAATGCCGCACCGCGAGTCACATGACAAGAACCGACTGCTTCATATTTTGTATGGAAAATAATTTTGATGAATGACAATTATTCTGCCTCTTTTTCGAACGACGCTACTTTATTTCAATGCTGGTTATTATGGTGGTACTTGAAGAGACAATGTTTTTCTGAGGTGGTACTTGGTGAAAACAGTTTGAGAACCACTGTGTTAGATTACTCTATTGGAAAATAGCCAAATAGAACAGCTAACAGCTATCATAAACCTGGCGCAATGTGGCGCAAGGCGCGACGCAATTGTTGTTTGCTAGTTTCAGCTTGGCGCAGGAGTCAATTTGACGTTTTGCGCCACGCTGTTTAAATAGCAAATGCATTTGCACTCATATGTGCGCTCACAGGCGTTCTGGCCTAAAAAGGAAGGCGTTCTGAGGTGCATTATATAAACTATAATAGAGTTTTCAACAGACCAGAACAAAGCCGGTCTATTGTCCATCACAGAGCGCGTTAGTTTTGGCCTCACTTACACATTACTTAATACACACAAGATGTAGAGCAATACGCAAATATCTTTACATATGAAAAAGAATTAAAATATTAAGGATATATATAGGATATAATAAGAATAGATATAGAATATAAATATAAAGGATTAAAATATTACAAAACATATTATTTTCTAGCCTACATAAATATAAACACCACTGCCTTCATGCCTTCTTCATCTCGGGAGGCTTTTTCAGTTCATTCATAACAATTTGCTTTTGTATAATGTTATCATTATTAGCAGTATTATTTATTTTATATATATATATATATATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAGCAAGCTTAGATTTGCCCACCTGTCAGGTTTTAGACCATATGGGGCACAGCATGTGTATTTGGATATAACTCAGGTTTTTGAGCACACTTTGTTATTATTGTTCATTTATTCGTTTGCTGGAAATTAGAACTGAATTTAGAAATAGTTTTGAAACGAATCTTTGCGCTTAACAAACAAAATTGATTAATTATAGGCTAATTGATGTCTGTGGATACAAGGTTTCCCTATCCACGAGAGCGAAAGTGAAAAAGGATAATGAGAAGACTTATCTCTCATTCTCGCCTGCAGATGCTCTGTTTAACTGTGTTCTTGCTAGTGAAGTGTTCAGTTTTTCCACTTACAAAGTCCACCATGTAAATAGCTAATGCGCTTATGGCGCGACGCAGCTGGGTCTTAAAGGGAATGGGAGATGAGACTCTGATTGTTTTATTCTCAAAACACACCTATAACTCATTAAGAAAATAAGCTCAACCCTTTTAGACCATGCACCACAGCTCAAAGCGGATTTTTCCATATTTATATTAGCAAAAGTGGAATCTGACACACCCTGAATGCGTTTGCGCCCTGCGCTCTGCACTCTGCGCATGGTTTTCAAAATAGAGCCCATACAATATATCTGATCTAAATTTTTTGTAAAACAATAGCTTTGTGTTGAGGCAATCGTGTGAGAAGCATCTTTCTCCACTGATTCAGGGTGCTGCAAATCATTAAAAATACTTTAATGTTTTCAAGGTTTTGAAAGTGCTTAGATTTTGAATAAAGGGCTATACTGTAGAATATATCAAATAGCATCTGACATAATGTGAAGTTATGTAAGTGTGTAACTTGCCACACTTGTAAAGTGCTAGAAAGTTTTGAAGATGAATCTGAAAAGTGCTTGAAATGTACTTAAATTTGATTATGTAAGAACCTTTTAAGAAGCTCTGTACACTTATAAAACAATTTATTTGCCTCAAAATGTTATTTCACACAATCAGAAGTAAGACTAAAGAGCAACACTGTGTTTCTGCAG
Seq C2 exon
TGCAGATGGTGATTTCACAGTGACGCACCTGACTAAAGCTCACCTTTTACATGACGGAAGAGTAACCTGGATCCCTCCGGCCATCTATAAAAGCTCCTGCAGCATCGATGTCACCTTCCTCCCCTTCGACCAGCAGAACTGCACCATAAAGTTCGGCTCCTGGACGTACGACCGCAGCAAAATCGATCTGATCCGCATTGCAGACAGTGTAGACCAGCTGGACTACTGGGAGAGCGGAGAATGGCTCATAACCAGCGCTGTCGCCACATATAATGTGAAGAAATACGAATGCTGCTCTGAGGAATATGCAGACATCACTTATTCCTTCATTATCAGACGACTGCCGCTCTTCTACACCATCAATCTCATCATCCCATGTCTACTTATTTTATGTCTAACTGTATTGGTTTTCTACCTCCCGTCTGATTGCGGAGAAGAAGTCACCATGTGCATATCTGTGCTGCTTTCACTCACAGTCTTCCTCTTGCTGATCACAGAAATCATCCCGCCGACCTCATTGGTGATTCCTCTGATTGCAGAATACCTGCTTTTCATCATGATTTTCATCATACTTTTCATAATAATCACTGTTTTTGTGCTGAATGTCCATCATAGGTCTCCAGACACTCACTCAATGCCCCAATGGGTCCGTAGGTTCTTCCTGGACGTAATGCCGAGGTTTATTTTCATCCAAAGACCTCAAATTTGGCAGAAAGATGCTAAAGGGGTGTGTGATGATGCTCAGAAGAGCAATAAGAGATGCGTTGATTCTAATTGGAAAAACAGAGAAATAAAGGAAGAGTCCATTCGCATGAAGGTCTATTCCTCATGCTTAAATGCAGACATGCATTCAATTAAATCACCATCTCAAGCGTACAATAACTCTACATGTCCAAAAATGAAGCTTCATAAGGGTCGATCACAGAGTGTTCAGGTAAATTGTGGGGAGCGAGATGTAAATCTGTGTAACAGCAGCACACGTTTTCGCTCTCGCAGCATGCAGTACTGTAGTCTGCATGAACATGAGCAGCAGACATCTGCTGTGTTTAATGCTGATAAGTTCTCAAACATCTGTAAAGTAATGACCAGCACTGGGGAAAACCCTTCTCACGCTACGCGTCTGGCTATTGAGGGAGTGCAGTACATCGCTGAATATCTGCGTGCTCAACATGCTGATTTATCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000087071:ENSDART00000153740:5
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=0.015
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(10.7=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=29.1),PF0293211=Neur_chan_memb=PU(89.2=68.9)
Main Inclusion Isoform:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]