RnoINT0100354 @ rn6
Intron Retention
Gene
ENSRNOG00000009377 | Nelfb
Description
negative elongation factor complex member B [Source:RGD Symbol;Acc:1307832]
Coordinates
chr3:2423385-2424030:-
Coord C1 exon
chr3:2423935-2424030
Coord A exon
chr3:2423528-2423934
Coord C2 exon
chr3:2423385-2423527
Length
407 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGA
5' ss Score
6.56
3' ss Seq
TCAGACATTCCTTCTGCCAGGAG
3' ss Score
5.18
Exon sequences
Seq C1 exon
GACAGTCCCGACCTCCTCCTCCTCCTTAGGCTGCTGGCACTGGGCCAAGGTGCATGGGACTTAATAGACAGCCAGGTCTTCAAGGAGCCCAAGATG
Seq A exon
GTATGAGGCCCGGGTCCTCCTTTCTGCTAAATTATGGGAGTGCAAGGGTGGGGGCCTTCTGGTAGCACAACTCTACTCCTAGAGTCATTTTTAGGGGAGCTCCCATCAAGGGTGTTTGGGTGTCTTGGTGGACTAGCTGCAGGGTAGAAGCTATTCTAGGGGCTGGGATCCAGATGGGGCTTTGCAGGTGCAGCCATGATGGGGGCATTCAAGAATATAGCAGTAGACATGAATCTCAGGAAACAGGAAGGAGGGATTTGGGGGCCCAATGTCCAAGAAATGTGAGTTTGAGGCAAGTGTATTGGGTGGATAAGGGCTAGATGTACATGGCTGAGTGGGTTAGGGTGTCTGCTGAGAGCAGCCAGGCGCACTGGGACCTTAATGGACTCAGACATTCCTTCTGCCAG
Seq C2 exon
GAGGCAGAGCTCATCACCAAGTTCCTGCCGATGCTCATGTCCTTCGTGGTGGATGACTACACTTTCAACGTAGATCAGAAGCTTCCAGCTGAGGAGAAAGCCCCAGTCACATATCCCAACACGCTTCCTGAAAGCTTCACCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009377:ENSRNOT00000012978:8
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=0.021
Domain overlap (PFAM):
C1:
PF062098=COBRA1=FE(6.5=100)
A:
NA
C2:
PF062098=COBRA1=FE(9.9=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:
GACAGTCCCGACCTCCTCC
R:
CTTTCAGGAAGCGTGTTGGGA
Band lengths:
230-637
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]