DreINT0103786 @ danRer10
Intron Retention
Gene
ENSDARG00000035505 | nelfb
Description
negative elongation factor complex member B [Source:ZFIN;Acc:ZDB-GENE-040426-765]
Coordinates
chr5:28952888-28953639:-
Coord C1 exon
chr5:28953537-28953639
Coord A exon
chr5:28952984-28953536
Coord C2 exon
chr5:28952888-28952983
Length
553 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGA
5' ss Score
5.73
3' ss Seq
TGCTTTGTGTGGATTTGCAGGAC
3' ss Score
8.5
Exon sequences
Seq C1 exon
TGACCTTTCTATGATCCTCTGTGACCCCTTTGCCTGTAACACACTGGTGTTGAGCACTGTTAGGAACCTTCAGGAGTTGTTGAGTCAGGACGCCCTGCCCAGA
Seq A exon
GTAAGACCTCCAGCTTCATCTCTGCACTACACTACACATATTTCTTATTTCCATTGATTTTAGTGCTCTACAGTGTTGTTAATGTTAACTAAAATGTTGTACTGCACAATTTATTAACATGAACTAGTATCTTAATGATTTTTATTGTTAATATATAATATATTAATTAAATGTTAGATTAAATGAAAAGATTTGCTATTTCATTTACATAAACAAAAGTTATTAAATTTTATCATTTATATATGTATTATATGATTAATATAAATATAATGTATTGTGTTTGTTAATGGATTAGATAGTGTTGACAAATCACTGCTAATTTTAACACTAGAAAGACATAAGTATAAACATCCGGAAAAAAAAGAAATGTCTCATTAGTGGAAGTACTAACATTTCTAAAGCTGAATTAAAATAAAACTAATTATAAAACACAACAAAATTATTTAAAGTAAGTTAAAAACTGATAAAAACATCAAAGTATAAGCGATATGAACGCATACGGCAATAGTATATGTGTAATGCTGAAATATCTGTGCTTTGTGTGGATTTGCAG
Seq C2 exon
GACAGTCCTGACCTTCTCCTCCTGCTGCGGATGCTCTCTCTGGGGCAGGGCGCCTGGGACATGATCGACAGTCAGGTTTTCAAAGAGCCTCGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035505:ENSDART00000133949:7
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=0.000
Domain overlap (PFAM):
C1:
PF062098=COBRA1=FE(7.2=100)
A:
NA
C2:
PF062098=COBRA1=FE(6.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCTTTCTATGATCCTCTGTGACC
R:
CATTCGAGGCTCTTTGAAAACCTG
Band lengths:
198-751
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]