RnoINT0062959 @ rn6
Intron Retention
Gene
ENSRNOG00000009139 | Fubp3
Description
far upstream element binding protein 3 [Source:RGD Symbol;Acc:1307004]
Coordinates
chr3:10221395-10223434:-
Coord C1 exon
chr3:10223307-10223434
Coord A exon
chr3:10222754-10223306
Coord C2 exon
chr3:10221395-10222753
Length
553 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGT
5' ss Score
6.84
3' ss Seq
CCTCTCCCTCCCCCCCACAGGAG
3' ss Score
12.64
Exon sequences
Seq C1 exon
GTCACACCACCAGTGCTGCCCCACAGGCCAGCTCCCCCCCAGACTACACGATGGCCTGGGCCGAGTACTACAGGCAGCAGGCCGCCTTCTATGGGCAGACTTTAGGGCAGGCTCAGGCCCACAGCCAG
Seq A exon
GTCTGTAGCCAGTCCCCAGCACCGTGATGCCACCCAGCCTTGTGCTTTCCTAGTCCCAGGGTGAGCACGGTGGCCTATAGGGTCTCCTCTGTCCCTCCACCTTGTCCCAAACCTTGAGCTTGATCAGATGCTGCTCTCTTTCTAGCTCTAGGCCTGGCAACCCTAACTCTAATTGCCATGGGTCTGTGGTAAACAAGGACCACTCCAGTGGTAGTCCTTGCAGAGAGTGGCCAGGCTGGGGCCTTTACCTGCACAGCACCTTCGGGGCCGAGCAAGTGGAGGGCCAGCTTGGCCTCTCAGTGTGTAGAAACGTGGAGGGCTCTATGTAGTCCTCAGCCAGAAGGAGCTCTCCTTGGACCTTGGGGGCAGGGCTCCCATAGGTACCTTTTGCCTTGTAGGAAGCTGGTGGTAGGCCTGGTGACCCAGAAGAAGCCCTCCCCTTGCACCCCCCTTTGCCCCTACATCTTGCCCCTAGAACCTGAGGTGCTTAGAGTCCAGTATCTGGTGGTGTGAGGTGCTGGTCTTGGGCTGACCCTCTCCCTCCCCCCCACAG
Seq C2 exon
GAGCAGTAGATGGGCATCTGCCGCGGCTCTTCCCCGAAATCAGTGTGAGAGAAACCTGTTTGTTACAGAGATTTTTAGATTTGCAAACCTTTCGATGAAGACCTTTGTTTTGTTCTGTGAAACACTATATTTAGATTAACAGAAATTTTCTAAAAATTAGGAAAATTAGTTACTAAACATTGGTAATTTTTGTGTCATGATTTCTTTGTAAATGTGTAAGCTCTGGAGCTCTTTTGGAGCAAAACCTGCAAGCTCAGGTGCCGGAACTCTCCTCAGAGCCTGACATTTCATCAAATGATGGGTTTGTCTTGTGTCTTTTTATTTACAGTTTTGGGTGGTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTTGTTGGTTTTTTGTTGGGTTTGGGGGGGTTTGGTTTTTTGTTTTGTTTTGTTTTTTGTTTTTTTGTTTTTTTCTGTTACAACAGAAAAAATGGCTTGGAAGTCTTAGGTGGTAATGTAACAAATTCTTTAAAAATTTTTAAGCAGTATTTAAATATTCATAAATGTAAATTCATTAAGTGTTTCACCTCTAATTTCTTGTATCTTGGCTGTCTGGTTTTATTGCATTTTTTAAAAAACTGAACTATTATGTATTGTAATTAATGATGTGAATTTTGAACTGAGACGGGTCCTTGTGTTGTGGAGGGTCAGTCGTGGGCTGTATCATTTCTAGCGTTTGGATGGTGATACGGAGATGCTGTCCACCTTCCTGTAAGCTGCCCGTCTCCATTGCCCAGGGCGGTTGTGTGTCTAAGACCTCCAAGCTGGTTTTAAAAACAAAAAGCCTTTCTCTATTCTCAGAAATATAAATACTGTTATTTTTAATATTAAAAAGAAATTGAATATAACTTTAACACACACTGTGGACATTAAACCATATAAAAATGTAGTGACTATTTTTTAATTCCAGGTGTTTTTTGCTTTTTTCCTTAAATATTTTCTTAATATTTGTCAAATTAACTAGATAAATAAATAAATCTAGTATTAACCACAGTATGAGTTAAATAATTTTGATTTAATAAAAGGGATGATTTCCAATGTTTACTGTAGTGTAACTTGTACAGATAACATGTATTTTTAAAGAAAAGACGAAATTGACGCTATTTTCTCTTGCGTTTTGAATTGACCTGAGGAACGCTCGTTTGAAACGCGCTCGTCCCAGTTTGCGGTTCCTGTTCTCCTCGCAGTGCTTGCAATGTCTAACCATTAAACAGCATTGGACATGTTATGCATGTGGTTGTTTTTTAAAGGTGTTCTTTTTATTTGACTGACAATTCATTTTACACTCTATATAATAAAATTTCCACAAGACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009139:ENSRNOT00000021871:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.651 A=NA C2=0.289
Domain overlap (PFAM):
C1:
PF090055=DUF1897=PD(30.3=23.3),PF090055=DUF1897=WD(100=74.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGAGTACTACAGGCAGCAGG
R:
TCAGGCTCTGAGGAGAGTTCC
Band lengths:
351-904
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]