DreINT0046803 @ danRer10
Intron Retention
Gene
ENSDARG00000034307 | chrne
Description
cholinergic receptor, nicotinic, epsilon [Source:ZFIN;Acc:ZDB-GENE-040808-32]
Coordinates
chr5:37841136-37842564:-
Coord C1 exon
chr5:37842360-37842564
Coord A exon
chr5:37841270-37842359
Coord C2 exon
chr5:37841136-37841269
Length
1090 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
3' ss Seq
TTGCATATGTCTCCCTCTAGTGG
3' ss Score
8.15
Exon sequences
Seq C1 exon
ATTTTCCTAGAAGTGGTCCCTCGTTATCTTGGCATGGCCCCCTTTGTGGATGAGGGGGACCAGGGTGGGGTGTATGAAATGAGGGAGAGGCGACGGAGTTCATTTGGGCTCATGCAGAGGGCTGAGGAATATGTTCTGAAACAGCCACGCAGTGAGATGATGTTTGATAAACAAAGAGAGAGACATGGACTCATGCGCACAATTG
Seq A exon
GTGAGAAATTCAGCCTTAACTTGTGTGTTCAAATATTGTTGCGTAGAAGTACGGCCTACTGAGAACAAAATTTGCGTGCATTAGGTCAGTTTTTGGAATAACTGTATAGAATTTGAGAGGGGAAGCATTTTCAGTGTAGTTTTGTCCAGTACAAACACCACAAACATTCTAAAATAAAAGCTTAAAGACTTAGAGGCATAATTTAGCCTAAAACTAAAATTGTCAACATTTACTAATCTTTTATTTGTTCCGAACTAGTTTGAGTTTTTTTGTTTTGTTTTTTTGAACATGAAAAAAGACATTTTGAAGAATGTTGAAACTGGTAACTGTTGAACACAGAGTAAGGAGAACAAAATACTAAGTTAATGGCTGCAGGTTTTCAACATTCTTCAAAATATCTTGCGTTCAACAAACAAACAAAAAAAAAACTTAAATTGGTGCATACATGATGACAGAAGTTACATTTTTGGGTGCAGTATCCCTTTTAAAACATGTTTCTGAAATAATTCAATGAAAGTTACAGCTTTATGCTTAAAAAGAAAAATATTGTCAAATATATAAGTTAATATAAATTTTTATTCAAAACTTAATTAAAAAGGTAAACATTTTATTGGACCCATATGTTTTTTTTTTTCTTTTGTGTAGTAAGAAGACATGCACTTTAATAAAACACATCCAGGTATCCAGAACTTTAAAGATAAGCTCATAAAGGGATTATAAAACAAATTCACATGAGTGGTTACATTTTTCACTATGACTTTGTGTTGTTCTCTACAGTATATATCAATAGTATCTGGATGCAGCCTTTATGATGCAAGCTGAGATTGCATCACTCAGTGAAGCAGTGTCAGACACAATGCACTCAAATGGAGCGAGTGATGTCAGTGTGATGGGTACGGTTAGGGGTGGGGTTAGGTGAGCCCATTAAAAAGCATTGGATACAGCCCAGATTGCACTGCACCAGGTCTGCATCCAGACCCCTCTCGTATAAATGTGTGTTGACATGTAAACATCAATCTTTTCTCGCCTGTCCCTTTAAAAGCACCCTTTCGATACAGATTGTAATGTGTTTGCATATGTCTCCCTCTAG
Seq C2 exon
TGGATGAAATTGATGTGAGCAGTACCGCAAACCTCTACAAGAGTCTGGCAAAGACGGCCCCAGAAATAAAAGAGTGTGTGGATGCCTGTAACTTCATTGCTGAATCCACCAAGCAGCAGAATGACACTGGATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034307:ENSDART00000136428:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(28.0=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(18.1=100)
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:
TTCCTAGAAGTGGTCCCTCGT
R:
ATCCAGTGTCATTCTGCTGCT
Band lengths:
334-1424
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]