HsaINT0140713 @ hg19
Intron Retention
Gene
ENSG00000080345 | RIF1
Description
RAP1 interacting factor homolog (yeast) [Source:HGNC Symbol;Acc:23207]
Coordinates
chr2:152324514-152325065:+
Coord C1 exon
chr2:152324514-152324660
Coord A exon
chr2:152324661-152324987
Coord C2 exon
chr2:152324988-152325065
Length
327 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CTCTCCTTTCTTCTATCTAGCAT
3' ss Score
8.94
Exon sequences
Seq C1 exon
GTTCGCCGTGTCTCCTTTGCAGATCCAATATACCAAGCAGGATTGGCAGATGACATTGATAGACGGTGCTCTATTGTTAGGTCCCATTCTTCCAATAGTTCTCCCATAGGAAAAAGTGTTAAAACTTCTCCTACTACACAATCTAAG
Seq A exon
GTAAGCTATAGGCTTTAAAATATACATATATGTATACCGACACAGAATTACATGTACATGATGTGTCATAAAATGAACTATATATGTGAAAAACTTCTTCCTTGGTTTAAAATATATTCTTTTGTCTGGTACACGGTAAGCAGAAAGGAAGAGAAGCAGAAAGGTAAGAGGCAGTAATGATCCAGCAAGTAATTGATTAGGTAGTAGATTACTCTTTTTATGTTTTTTGAACTTTTAAAGAAATGATTGCAGTCTAAGTTGTAAAAATTGTGAAATTATAGTCATCTAGGGTTCTGAGTGTTTTTTTCTCTCCTTTCTTCTATCTAG
Seq C2 exon
CATAATACCACTTCAGCCAAAGGATTTCTGTCCCCAGGATCACGTAGCCCTAAATTTAAGAGCTCAAAGAAGTGTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080345-RIF1:NM_018151:31
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.360 A=NA C2=0.503
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGTGTCTCCTTTGCAGATCC
R:
CTTCTTTGAGCTCTTAAATTTAGGGC
Band lengths:
214-541
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)