HsaINT0066540 @ hg19
Intron Retention
Gene
ENSG00000162613 | FUBP1
Description
far upstream element (FUSE) binding protein 1 [Source:HGNC Symbol;Acc:4004]
Coordinates
chr1:78413591-78414985:-
Coord C1 exon
chr1:78414840-78414985
Coord A exon
chr1:78414460-78414839
Coord C2 exon
chr1:78413591-78414459
Length
380 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAA
5' ss Score
7.46
3' ss Seq
TATGTATCTCTTCTGCACAGGGC
3' ss Score
8.31
Exon sequences
Seq C1 exon
GTCAGGCAGTTCCTGCTCCGACTGGGGCTCCTCCAGGTGGTCAGCCAGATTATAGTGCAGCCTGGGCTGAGTATTATAGACAACAAGCAGCCTATTATGCCCAGACAAGTCCCCAGGGAATGCCACAGCATCCTCCAGCACCTCAG
Seq A exon
GTATAATGTAATTGCTAATTTGTTGATTTCTACTCCAGTCTGTTTTCTGCATGTTTACTGTTTGTCTGTTTGGGAGTGTTTGCCTTTTAAATTTTTATCTGGCAAAGTATAATAACTATTTAAATGAAGTACTACGGTGTATTGTTTGGGTTTTTTTGTTTTTTATAATGCTTTCCAGCATCTGAGTGGTGAATATTTCTGCAATGCCTTTGATTTTAAAAATAAATTTTCTTCCCCCAGGGATTTGCAAATCATGCAAGAAGCCACCACCATTTATATTAACCACTTTTTCTTTCTTAAAGGATTCACTCCTGAATTAGCTCCATTTCAAGGATTTTCTTTAACTTTTTGTGTATTTCTTATGTATCTCTTCTGCACAG
Seq C2 exon
GGCCAATAATAAGAAGTGGACAATACAGTATTTGCTTCATTGTGTGGGGGAAAAAAACCTTTGTTAAATATATGGATGCAGACGACTTGATGAAGATCTTAATTTTGTTTTTGGTTTAAAATAGTGTTTCCTTTTTTTTTTTTTTTTTTGAAAATGTACAAAATATCTATCACTACTGATAGGAGGTTAATATTTCTGTGTAGAAATGAAAATTGGTTTGTTTTTAGTATTTAGTGTAGATGTACACATTCCAGCAAATGTATTTGCAATTATGTGGTTGATGCTTTGTGATATAAATGTACTTTTTCAATGTATACTTTCACTTTTAAAATGCCTGTTTTGTGCTTTACAATAAATGATATGAAACCTCCTGTGTCGGTAAGTTGGATATGTGGGTATTTAAAGGATTCATAATTTCTTAGCAATGATAAATTAAGATACATATACACAAATATATAAGCTTTCCCCATGAAATATTGAGTTTTTAAACACTGGCATGTTTTTCCCCCCTTGCAGTATAGTGGTAGATTGGAGGATCTTTTCCATTTATTGTATTGGCTCTTTCAGCACAAGTAATCCTGATATCTTCATTTTTTTTCCTTCTGTTTGATTAAAAACTGCATGTGTGTACAATGATCTTTTGGCATACTTCCATTGCATTAACAGTGAAATTTCCTTTTATACATGACCACTGTTTCAGACCTGTACTGCTGCTATAACAGTTAACCTTTCTGTTCTTAATTTGATAATACTTGATTTCCAAGACTGTTTCGGCATAACTAATTTTAAACAGTTTTCAGATAGTGAATATGAGTAGTCTAATAAGAACAGTTTTTTTCCATGTGAAGCAACTCTTTCAATGTATATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162613-FUBP1:NM_003902:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.788 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF090055=DUF1897=PD(17.9=10.2),PF090055=DUF1897=WD(100=67.3)
A:
NA
C2:
NO
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:
TTATGCCCAGACAAGTCCCCA
R:
CACAAAGCATCAACCACATAATTGC
Band lengths:
342-722
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)