HsaINT0140708 @ hg19
Intron Retention
Gene
ENSG00000080345 | RIF1
Description
RAP1 interacting factor homolog (yeast) [Source:HGNC Symbol;Acc:23207]
Coordinates
chr2:152273075-152273415:+
Coord C1 exon
chr2:152273075-152273202
Coord A exon
chr2:152273203-152273320
Coord C2 exon
chr2:152273321-152273415
Length
118 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TTATTTGGTTCGTTTTTTAGGTA
3' ss Score
11.58
Exon sequences
Seq C1 exon
AGGCAAATGCTCTAGAATTGCTTTCAAAATTGAATGATACCATTAAGAATTCAGACAAAAATGTACGTACTAGAGCACTTTGGGTGATATCTAAGCAGACATTTCCCTCTGAAGTGGTTGGCAAAATG
Seq A exon
GTGAGTATAGTTTTTGGGTATGCCATCTTAACTATATGCCAATTAAAAGAAAAAACTATAATGCCAATAAAAACAGTTCAGGCTTATTTCATTTGTATTTATTTGGTTCGTTTTTTAG
Seq C2 exon
GTATCCAGTATAATTGATTCATTAGAAATACTGTTTAACAAAGGAGAGACGCATTCTGCTGTTGTTGATTTTGAAGCATTAAATGTTATCGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080345-RIF1:NM_001177664:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF032249=V-ATPase_H_N=FE(29.4=100),PF122313=Rif1_N=FE(19.1=100)
A:
NA
C2:
PF032249=V-ATPase_H_N=PD(4.9=21.9),PF122313=Rif1_N=FE(14.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCAAATGCTCTAGAATTGCT
R:
TTAATGCTTCAAAATCAACAACAGCA
Band lengths:
210-328
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)