HsaINT0140703 @ hg19
Intron Retention
Gene
ENSG00000080345 | RIF1
Description
RAP1 interacting factor homolog (yeast) [Source:HGNC Symbol;Acc:23207]
Coordinates
chr2:152324514-152325270:+
Coord C1 exon
chr2:152324514-152324660
Coord A exon
chr2:152324661-152325154
Coord C2 exon
chr2:152325155-152325270
Length
494 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CTTCTGAAATTTATTCTAAGATT
3' ss Score
4.47
Exon sequences
Seq C1 exon
GTTCGCCGTGTCTCCTTTGCAGATCCAATATACCAAGCAGGATTGGCAGATGACATTGATAGACGGTGCTCTATTGTTAGGTCCCATTCTTCCAATAGTTCTCCCATAGGAAAAAGTGTTAAAACTTCTCCTACTACACAATCTAAG
Seq A exon
GTAAGCTATAGGCTTTAAAATATACATATATGTATACCGACACAGAATTACATGTACATGATGTGTCATAAAATGAACTATATATGTGAAAAACTTCTTCCTTGGTTTAAAATATATTCTTTTGTCTGGTACACGGTAAGCAGAAAGGAAGAGAAGCAGAAAGGTAAGAGGCAGTAATGATCCAGCAAGTAATTGATTAGGTAGTAGATTACTCTTTTTATGTTTTTTGAACTTTTAAAGAAATGATTGCAGTCTAAGTTGTAAAAATTGTGAAATTATAGTCATCTAGGGTTCTGAGTGTTTTTTTCTCTCCTTTCTTCTATCTAGCATAATACCACTTCAGCCAAAGGATTTCTGTCCCCAGGATCACGTAGCCCTAAATTTAAGAGCTCAAAGAAGTGTTTAGTAAGAAGTGCTTTAGTTTTCATGTCACTTTATATTTTCATGTTCAGTCAGTTGACCTCTGTGTAACAGCTTCTGAAATTTATTCTAAG
Seq C2 exon
ATTTCAGAAATGGCCAAAGAATCCATACCATGCCCAACAGAAAGTGTTTACCCACCATTGGTGAACTGTGTGGCACCAGTTGACATCATTTTACCTCAGATTACATCAAACATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080345-RIF1:NM_001177664:31
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.360 A=NA C2=0.058
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCGCCGTGTCTCCTTTGC
R:
CACATGTTTGATGTAATCTGAGGT
Band lengths:
262-756
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)