HsaINT0140685 @ hg19
Intron Retention
Gene
ENSG00000080345 | RIF1
Description
RAP1 interacting factor homolog (yeast) [Source:HGNC Symbol;Acc:23207]
Coordinates
chr2:152296541-152298505:+
Coord C1 exon
chr2:152296541-152296641
Coord A exon
chr2:152296642-152298418
Coord C2 exon
chr2:152298419-152298505
Length
1777 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
AAACCTTTTATCTCTCATAGGTC
3' ss Score
9.41
Exon sequences
Seq C1 exon
GTAACAAAAAAGAGAAACCAGGTTCTGAAGTTTTGACTCTCTTATTAAAGTCTTTGGAAAGCATAGTAAAGTCTGAAGTATTTCCTGTATCAAAAACGCTG
Seq A exon
GTAAGTATAATACCCGTATGTTGGACTTTAAAAACCATTTTCTGAAGTTAAATTTTATATAGAAGATATTTGCACAAATCTAGTTTGGGAAGACTTTTTTATATCAAGCATTCATCAGCAGTTTAGTCCTATTGCAATAAGTGCCATTCTATTAACTGTAGAGTCATTTGAAACCTTTTTAATAGTGACTATAACAACAGCCACAAAAGTCTTCAACGTGGTAAGAAAAAAGTATCCGCCATACAGAGAAAAACTAGGGTAAAGGACATGAAACTTGAACTGAAGAAACTCAGATGTCCTTTAATTTTATGACAAGATTGCTGAAAACTACTAATAGTTGGTACTTTGTTTTCAATTAACTGTTTTTAACCAAGATAATGACTTTGGTATTAAAACCCCTTTTTTTTTTAAACCCGTGTAGTACAGGAAGAAAAGTGAATTGGATATGATTTTGAGGATATGGGCATCTCAAAATAAGCTCCAGTGGAACAAACAATACCCTTAAATTCTGATTTTGTTTCCTTTATGTATTTTGATAGTTACTTGTTCTGTAGCAGTATAGCATAGTGGTTAATAGCAAGGGCTCTGGAGCATACTAGGTTGAATACCAGCCTAACTATTCATTAGCTGAGTAAATTTGTGCAGTTTATCTATTCCCTTGGCTTTGCCTAACCCCATATGTAAAGAGGGAATGTAGCAGTAGTTAAAGACTAAGTGAATTGATACATGGAAAGTACTATGGGCCAGGAACAAACTAATACTGTCTATTATTATTACTAATCTGTTTCAGGTGACAGTGTGTGAAAATGTATTTTCACTGACATAACTCTTCTATGACATTTAAGTTATGTAGTGCATGTTCATACCAGTATATTACCACTGGGCATGGTGGCTCACATCTGTAATCCCAGCACTTTGGGAGGGCAAGGTGGGCAAATTGCAAAAATTAGCCAGGCATGCTGACATGCCTCTAGTCCCAGCTTTTATGGAAGCAGAGGTGGGAGAATCACTTGAGCCCATGAGGTTGAGGCTGCAGTGAGCCAAGATCGTGCCACTGCAATCCAGCCTGGACAACAATGAGACCCTGTCTCAAAAAAGAAAAAAAAGACAGTATGGTAGTATTTTTGGAGAGCAATTTGGTAGGCTCAGTCAGTTTGATTTAGCAATCTTAGACCCAACTATTAGCAGTCCTTTGAATATTTGCTTTGGGTACCAGTATAATTAATTGCAGAATTTCTATTAGTAGTATAAAAAAACATAGAAATAGCCCCAAGGTCTCTTAATAGAAAAATGGTTGAATAAATAATGGACATTCATATAGCAGTATTTTTATATATTGATGCAAAAATTCCGTAACAAGGTAAAATGAAGGTTAGTTGCAGAGTTTAATATCATTAGTGATTTACAGTGTAATGGCTTTAATGGTTTAAAGGAATGTGTGTATAACTGGCTGCCCAAGAAGTTGTGTGTTTTTCTGTGTACTTACATATACAGAAATTTAGAAGGTCTAGGAAAATAGACTCTGAACTGAAAATATTATCGTTGGAGATTAAAGACTTTACCTGCTTTTTATATTTCTGTGTTTGAACTTCTAAAACGGATGCAGATATATTCATGTTAGTGAATGAATGTATTTGATCTTTTTTAACTAATGAGATTATATTTACGTTAATGAATGAACATTACTTGTAATTGTTAGAGATATAGTTAACACTCAGATTTTTATTAGATAATATTTTTACGGCTAATTTACTGTAAAACCTTTTATCTCTCATAG
Seq C2 exon
GTCCTCATGGAAATTACAATTAAAGGACTTCCTCAGAAAGTATTAGGTTCACCAGCATATCAGGTTGCTAATATGGATATTCTTAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080345-RIF1:NM_001177664:15
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:
NO
A:
NA
C2:
NO
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)