DreINT0103788 @ danRer10
Intron Retention
Gene
ENSDARG00000035505 | nelfb
Description
negative elongation factor complex member B [Source:ZFIN;Acc:ZDB-GENE-040426-765]
Coordinates
chr5:28951174-28952809:-
Coord C1 exon
chr5:28952667-28952809
Coord A exon
chr5:28951263-28952666
Coord C2 exon
chr5:28951174-28951262
Length
1404 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTCT
5' ss Score
2.68
3' ss Seq
AGGTATATACTGGATAACAGGGT
3' ss Score
0.5
Exon sequences
Seq C1 exon
GATCTGGAGGTGGTGACACGCTTTCTGCCTGCCATGATGTCGATAGTGGTGGACGACTACACGTTTACTGTAGAGCAGAAACTGCCGAGCGAAGAGAAGACTTCTCTCGCATACCCCAGCACCCTGCCTGAAACCTTCTCCAG
Seq A exon
GTGTCTGTTTTATCCCATGTTGCAACCAATAATAATTAAAAAACTATTATAAGAACTAAAACCACACACAGACTCCAGAATGTGTGACACTTATTGTGTTTTTAATGTTCATGAGGACAGAAAAATCTGAACTTTGTTTCATCATTTTATTTGAGAAAACTAGCATCATAAACACTGAAAGCAACGATCTTTTCAATATTTCATCTAAATAAAAGTGTGATTTAACTTGAAGTGTTTAAACAGTTTATTTAAGCAACTTATATGTGTAAAACTATGAAATGGTAATTAATAATCATATATTATACAGAAATTATTAAAAAACTTAATATTGATACAATTACAGTGCATAAATATAGTGCAAGTCAATATTCTAGTCAGGATTTTCCCATATGCACTTTTCAACAATTCCTAATCGCATCAGTTTGAATCACAACTGCTTAAGATAATTGCTGTAAAAAGTATATAATAAGACGTTTTTCACTTTCAGTCCTAATGAACAATTATGCGTAATTTATAAATGGAGCTAACGAGTGCTGAAAGTGATAACATCTTAACTTTAATTTAATTTACCATTGCAAGCTTCTTATGAAAATTGAATACTTTTAAGTATAATAAATAAGTCTTAAATTGAAATATTGTCTTGTAGGTCTTAAATTTCCTTTCCTTTGTTTATGTAAAGCTACCCAATTGATCCAACATATATCCTATCACCAACAAATACATCTCAATAAATCTTTTAGAACAGTCTTTTGTGCATACATTTAGTTTTTAAAGAGTTTTTAATGTTGTTAATTAAAAATATATGTATATAACTAGGGTTTGCTCATTCTTCATGGTCTTAATAAGTCTTAAATTTGAATTAATGAAACCCTGTTTAAGACTTCACTTAAAATGATTATATATATTTATATGTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGTATATATATATATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGTAATGTGTTACCAAAAATTCAATGTAAGCGGAAGCTTTACTACTTCCAGTAACCAGAATTTTTAGTTTTGGTCCAGAATTGTAATTTAATTGGATCATTATTATTTCTTTCTATCATCTTAGGTATATACTGGATAACAG
Seq C2 exon
GGTGGCGTGTGAGATTGGCCTTTACTATGCTCTGCATATTGCCAAGCTGAGGAATAAAAATGCTTTACAGCGGCTTCTGCCTGCATTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035505:ENSDART00000133949:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF062098=COBRA1=FE(10.0=100)
A:
NA
C2:
PF062098=COBRA1=FE(7.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGACACGCTTTCTGCCTG
R:
GCAGAAGCCGCTGTAAAGCAT
Band lengths:
212-1616
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]