DreINT0046740 @ danRer10
Intron Retention
Gene
ENSDARG00000055559 | chrna6
Description
cholinergic receptor, nicotinic, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-090312-91]
Coordinates
chr1:21799417-21800761:-
Coord C1 exon
chr1:21800652-21800761
Coord A exon
chr1:21800477-21800651
Coord C2 exon
chr1:21799417-21800476
Length
175 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
TACTTTTTTTTCTGACACAGTGC
3' ss Score
7
Exon sequences
Seq C1 exon
ATATGGAATGACTACAAGCTGAAGTGGTCACCAGCAGAGTTTGATGGAATTGAGTTCATCAGAGTCCCATCCAATAAAATCTGGAGGCCTGACATTGTACTTTACAACAA
Seq A exon
GTGAGTCTTTCAACCTAACACTAAAGCTGTATACATATGTATGAATTAATGTTTATTGTAAGTTTGGCAATATTCCTAGGTCCCTCATTTTGTTTTGAGTGACATGAACACAGAGTTAATAGTCCGATAAAATATTAATTGATTAATGCTTTTCATACTTTTTTTTCTGACACAG
Seq C2 exon
TGCTGTTGGGGACTTCCTGGTGGAGGACAAAACCAAAGCCCTTTTGAAATTTGATGGAACCATCACTTGGGTCCCACCTGCAATTTTCAAATCTTCCTGCCCTATGGACATCACTTACTTTCCTTTTGACTATCAGAACTGCTCTATGAAGTTTGGTTCCTGGACGTATGATAAGGCCAAAATTGACCTGGTTCTTATCGGCTCTAAGGTCAACCTTAAAGACTTCTGGGAAAGTGGAGAGTGGGAGATCATTGATGCACCGGGTTATAAGCATGACATCAAGTACAACTGCTGTGAAGAGATCTACCCAGATATAACCTACAGTTTTTATATACGCCGACTACCCCTCTTCTACACTATCAACCTTATAATCCCCTGCCTCCTCATCTCTTTTCTGACAGTACTGGTTTTCTACCTTCCGTCAGACTGTGGCGAGAAGGTGACCTTGTGCATCTCTGTACTTCTATCTCTCACTGTGTTCCTTCTTGTCATTACGGAAACCATCCCATCTACTTCACTTGTGATCCCTCTGATTGGCGAGTACCTTCTCTTCACCATGATCTTCGTAACCCTCTCTATTGTTATCACTGTCTTTGTACTGAATGTGCACTATCGCACCCCTATGACCCACACTATGCCCAGCTGGGTCCGCACTGTCTTTCTTCGAGCTTTACCCCGCATCATGCTCATGCGCAGGCCTCTTGATCTATCAGAGTCCTCTGGAAAAGGAGGACTAGAAACTGGGGGCTCGTCCGGGACAGGAGCAGGGCGCGGAGGAGAGGGGAAGAAGAGAAAGAATAGTGGATCCCAACAGGGTGCAATGAACTCTCTGGAATTTGGAGAGGGGAAAGCAGCATTGGAAGGAAAGAAAGGAGGATGCCCATGTCATCCACTGAAAGAAGCAACTGAGGGAGATTGTGGGAAAGTCAGCCGTCAATTAAGTCCACAGGCTATTAATACAGTTGTGGCTTTCTCTGTCGTGTCACCGGAGATCAAACAGGCTATTGAAAGTGTGAAGTACATTGCTGAGAACATGAGGAGCCGCAACAAAGCTAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000055559:ENSDART00000031546:4
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=0.110
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=32.5),PF0293211=Neur_chan_memb=PU(87.5=65.3)
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:
TGAAGTGGTCACCAGCAGAGT
R:
ACGTCCAGGAACCAAACTTCA
Band lengths:
258-433
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]