HsaINT0066534 @ hg19
Intron Retention
Gene
ENSG00000162613 | FUBP1
Description
far upstream element (FUSE) binding protein 1 [Source:HGNC Symbol;Acc:4004]
Coordinates
chr1:78428455-78429400:-
Coord C1 exon
chr1:78429259-78429400
Coord A exon
chr1:78428616-78429258
Coord C2 exon
chr1:78428455-78428615
Length
643 bp
Sequences
Splice sites
5' ss Seq
AAGGCAATG
5' ss Score
1.24
3' ss Seq
TTACTGTCTTTTGATTTTAGGAG
3' ss Score
9.85
Exon sequences
Seq C1 exon
GCTGGTAATCCTGGTGGACCTGGACCTGGTGGTCGAGGAAGAGGTAGAGGTCAAGGCAACTGGAACATGGGACCACCTGGTGGACTACAGGAATTTAATTTTATTGTGCCAACTGGGAAAACTGGATTAATAATAGGAAAAG
Seq A exon
GCAATGTATTTTAAACTCTTAATGTTTTAACACATTATTCATTTTTCTGGACACTTTCTGTTGCTGTCGTAAACAAGTGGCAATGCTTTTTCTCTGACCGTATTTTAGTAGAAAAGAATTCTTATGTTAATATGTAACAAGTAAAACATAAATGAGGGATCTCATGTATATTTAGAGAAAGAGCAGGATTTTAATCTTACTAGCTTCTAGAGAAAGCGAACTAAGAGATAATTATTAGCATAAGAAATGTCTTTTGACCCAAAAAGTGGTTTGAGTGTTTTTGTTTGTGCATTTTGGTTTTTCCCGACTCATATTTTAAAAATTTGAATGTTTATAAGTGTATTAGTTTATATTTACACTGCTTTTAAAAGCAGTTAATTCAAATATTTTATTATAATCACATTAAGTTTATGTTTAAACATACTAAGTAAATGTAAATGTATTTTAAGAGAAGCATGAAATGCTTCCTAAAATTTGATTTTCAGTGTAGAATATTAAATGAAAAATCTTAATACAATATTGTCAATTAGGATACTGACCAAACCATATTTTTAATGGCCCATTTAATTGTGACCATTTTCTTCTAAATAGCTCCTAGTACACCCTTGAAACCTTTAGAGAAATTACTGTCTTTTGATTTTAG
Seq C2 exon
GAGGTGAAACCATAAAAAGCATAAGCCAGCAGTCTGGTGCAAGAATAGAACTTCAGAGAAATCCTCCACCAAATGCAGATCCTAATATGAAGTTATTTACAATTCGTGGCACTCCACAACAGATAGACTATGCTCGGCAACTCATAGAAGAAAAGATTGGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162613-FUBP1:NM_003902:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.875 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0001324=KH_1=PU(25.8=35.4),PF0395812=Secretin_N=FE(40.9=100)
A:
NA
C2:
PF0001324=KH_1=PD(72.7=88.9),PF0395812=Secretin_N=PD(43.5=92.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGGTAATCCTGGTGGACCT
R:
CCAATCTTTTCTTCTATGAGTTGCCG
Band lengths:
302-945
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)