RnoINT0062932 @ rn6
Intron Retention
Gene
ENSRNOG00000043370 | Fubp1
Description
far upstream element binding protein 1 [Source:RGD Symbol;Acc:1591892]
Coordinates
chr2:257435347-257435774:+
Coord C1 exon
chr2:257435347-257435448
Coord A exon
chr2:257435449-257435671
Coord C2 exon
chr2:257435672-257435774
Length
223 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
ATATACTTTTACTTCCTAAGGTC
3' ss Score
7.18
Exon sequences
Seq C1 exon
CAAGCCAAGGAAATGGTATTAGAATTAATTCGCGATCAAGGTGGTTTCAGAGAAGTGCGGAATGAGTATGGCTCCAGAATAGGAGGAAATGAAGGGATAGAT
Seq A exon
GTAAGTAAGGAGTCTGGAGTGGGTGTGTCCTAATCCATGAGTGCAGTGGAGTTCTTCCTGTTTGAGTTAAATGGTCTTGTCTTAACATCATGTCCCTTTTCTTCATTTCTTCCTTGGAGTCTTCTTATCTTGTTTTTATGATCATTTAATATGTTTACTTTTATGACTATATGGAGATGATTTTTTGAGAAATGTCTTATAAAATATACTTTTACTTCCTAAG
Seq C2 exon
GTCCCAATTCCAAGATTTGCTGTTGGCATTGTAATAGGAAGAAATGGAGAAATGATTAAAAAAATACAAAATGATGCTGGTGTTCGAATTCAGTTTAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000043370:ENSRNOT00000066199:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.294 A=NA C2=0.343
Domain overlap (PFAM):
C1:
PF0001324=KH_1=PD(7.7=14.7),PF0001324=KH_1=PU(3.2=5.9)
A:
NA
C2:
PF0001324=KH_1=FE(54.0=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:
CAAGCCAAGGAAATGGTATTAGAA
R:
TGGCTTAAACTGAATTCGAACACC
Band lengths:
204-427
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]