RnoINT0062939 @ rn6
Intron Retention
Gene
ENSRNOG00000043370 | Fubp1
Description
far upstream element binding protein 1 [Source:RGD Symbol;Acc:1591892]
Coordinates
chr2:257443255-257445094:+
Coord C1 exon
chr2:257443255-257443392
Coord A exon
chr2:257443393-257445019
Coord C2 exon
chr2:257445020-257445094
Length
1627 bp
Sequences
Splice sites
5' ss Seq
ACGGTAATA
5' ss Score
6.25
3' ss Seq
CTGTTTTGTTTTTTAAAAAGGAG
3' ss Score
6.74
Exon sequences
Seq C1 exon
CTAAGGCAGGAACGGATCCAAACTCGGCAGCTTGGGCTGCCTATTATGCCCACTATTACCAGCAGCAGGCACAGCCCCCGCCTGCAGCTCCTGCTGGAGCACCAACCACAACCCAGACTAATGGACAAGGTAACTACG
Seq A exon
GTAATAAAGATTTTATTTTCTATTTTAAAGCTAGAGCTTGCGTTTGGATTGATGGATGAAGTCATAATAAAACTTTCAGTCCCAGGAATTGTTGGGCCTTGTGCAGCACGGTATTAGATTGGATCCTCAGGCCTAAGGTTTTGAAGATTCATTTGTGACTTTGAGTAAGCAAACTGAGTCACTTTGAAATAGAGACAAACTTTAATAATAGTTGGAAGAATAATGCACTAAATAGTGAGACTGTTAACTGGTTTGTGCCCCATTTACTCCAGTACCCTGATATATGTCTGTTACAATTAGTTCTAAAAAGAACTACCAGAAAATGTACTTGGAGACATGAGGTCATACTACCCTTGTTATGTACCTGTATACTCATTCCAAAATAAATTACCATCGTGGACTTTAAAGTCACTGCTCAACATTGATATACCACTGTTACACACAGCCCGTGCTTAGATTCACCAACTGACCCAGTGGTTTCATTAGGTCTTTTAAGTCTCATCCAGCTAGAGCAGTTGGATCTTCTCTATGTCTCTAATAAGAGTGTAACTAAGTACCTTGGAATGACTAACAGCCTGGTATGTACTGTAAAGAATTACCTGGTGTTTTTTGGTACATCTTACTGGAATAATGTCACTGTCATATTCATTGAACTTTTGCCTCAGCCTTAGTATAATAAACCTTGCCTTAGTAAACTATTAAATAACTGTTAACTTTTAGCTATATTCGTTGTAGCTGTTAGCTGTTAGCTATATTCATTGTGTATTCATTGCTGTTGTAGCTGTTAGCTATATTCATTGTGTATTCGTTGCTGTTTTACTCCAAGGAATAGATTGCCCTTTTTTTTTAACTACTTTCATTATATTGTCCTAGATTTTGGGTGGTTGGGATTATCTTCAAGGTGGCTCTGGTGCCTTCTGACATTCTTCAGGTACTTCCTTAAGTACCTAACACAGTAAGATACTTTGTCTTCTGAGCTCCAATCAATAATTCATCCCTTTTCCCCCCCAGGATAGAATTTAGAAACCAGTCTAAACATACTCATTCCTCTTTAAAAGTCATGATTATAATCCTATCAGAATTAGACAGTATGTTTGGGGCTAGTAGTCATTTGTACTTTTTCATGCAGAAGACCCAGATTTGATTACTAGCACCCCAAGGTAGCTCAACACTGAAACTGATTCCAGGGGATCACCTTTGAAAGCACCAGTCACCTATGGTGCACAGATATACATATAGACAGAACGCTCATATGCAAAATTAAACAATCCGTATCTTTAACATGCAGGACCATACATGCCTATGAAAAATCACATGATTGCACACTGCTTTTTAATTAACATTTATTTCTGTTCTAGTGCTTCAAAGCTATTCATGATTTTTCTTAAAAAAAAAAACTTTCTTGTACTTAAAAATGGACAGAAACCTCATGTTCTGTATTTCTTTCATGTACATTTATTTACTGTCCCCAGTTTCTATGTCCACCTCTTCTGTACTCACTATTATGTATTCTCAGCACTTGCACAGCTCCGGGTAGATAGTGCTGATTACACTGGTGTAGAAGCAAAAGTGCAAAATAGCCTTCAGATACTTAAATCTTGTTTTGCCTGTTTTGTTTTTTAAAAAG
Seq C2 exon
GAGATCAGCAGAATCCAGCTCCAGCTGGACAAGTTGATTATACAAAGGCTTGGGAAGAGTACTACAAGAAAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000043370:ENSRNOT00000066199:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.745 A=NA C2=0.562
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF090055=DUF1897=PU(75.9=84.6)
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:
GAACGGATCCAAACTCGGCAG
R:
TCTTGTAGTACTCTTCCCAAGCCT
Band lengths:
198-1825
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]