HsaINT0140707 @ hg19
Intron Retention
Gene
ENSG00000080345 | RIF1
Description
RAP1 interacting factor homolog (yeast) [Source:HGNC Symbol;Acc:23207]
Coordinates
chr2:152271337-152273202:+
Coord C1 exon
chr2:152271337-152271433
Coord A exon
chr2:152271434-152273074
Coord C2 exon
chr2:152273075-152273202
Length
1641 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAT
5' ss Score
7.25
3' ss Seq
TAAAACTGCTTGTTTTTCAGAGG
3' ss Score
7.94
Exon sequences
Seq C1 exon
ACTCACATTTCCAGTCAAAACTCGGAGCTGAGTAGTGCTGCTCTACAAGCCCTGGGGTTTTGCTTATATAATCCCAAAATTACCTCAGAATTATCAG
Seq A exon
GTAGATAAATTTCTTATGACTTAATATTTTTAGAGTATAAAGTATAAGTTTTAAGTATAAGTAGTTTGATGCTGTTAAAAGTACTGTTATGTCTGGATTAGTTTCAGAACCTGTAGTTTAAGGTTTGCTTTTAAGAAAGAAAGAATGGCTGGGTGTGGTGGCTCACGCCTGTAATCCTAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACATGGTGAAACCCCGTCTGTACTAAAAATACAAAAAATTAGCCGGGCACCGTGGCGGGCGCCTGTAGTTCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGACGTGAACCCGGGAGGCGGAGTTTGCAGTGAGTCGAGATCGTGCCATTGTACTCTAACCTGGGTGATAAGTGAGACCCCATCTCAAAAAAAAAAAAGAATGTTTAGATTATCATTACCTACACATAGCTCTAACTTCGATACTACAAAATTTGCTCTTAAAAATAATGGTATTTGACAAAAGATTAGCCGGGCGTGGTGGCAGGTGCCTGTAGTCCCATCTGCTGGGGAGGCTGAGGCAGGAGAATGGCGTGAACCTGGCAGGCAGAGCTTGCCACTGCACTCCAGACTGGGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAAGGATATTGCTGGGTGCAGTGTCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTAAGGTCGGGAGTTCGAGACCAGCCTGGCCAACCTGGAGAAACCCCGTCTCTACTAAAAATACAAAAAAAATTAGCTGGGTGTGGTGGCGCATTCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGATGGAGGTTGCAGTGAGCCAAGGTGTTGCCATTGCACTCCAGCCTGGGCAAGAGTGAAACTCCGTCTCAAAAAAAATCAAATGAAAAGGGTATTTAAACATGATTGCTGTAAAAAGGGAAACTTTTATTCAGGCATATGCACTAAGGAATATGCTGAATTGAAAAGTTCTTTGACATGATAAATGTGGGATAATTTGGAACTAAAAGTGGTAATGAAAGCACAGAACCTAATGCTTTCCAAGTTTTCAAGTAGTCTGCACTGTTGCTCCATAGTTAGATGATTTCCATTGTAAAGGAAACCCTTATCTTTAGAGAAGGGAAGTTAGGAATAAAGATGTCAAAGTTGTTACCATCTGTTTTTGAGGGAAAAGCTGCTGCCTGCTCTTTTTTATACATGGAAGTGTTAGCAACCTAAAGCAGGAGTTGTTCATTTTGGAGCAGAGATGCAGGATTGAAAACATCTTACCAAAAATTGTCTTGTATGTTCAAACCTACAGTGATATCTAGTTATTTCAGTTGCACAAGATATCTGATTTGGTGTCTGTTGTTTTATTTTCTCTCAGTATATCCTCCCCTCTAATCTGAATTTTGTGTTTTTGGGAGAAGTTTGGTATCAGCATTGGTTCTCTGATCTGTTCTCTGGATATACATTTAATTTTATGATTGATGAGTATATTGTTTTCTCTAGTTTTATATTTGAGACTTTAAAGAGTATCACCTATTCTATACAAAATTAAAACTGCTTGTTTTTCAG
Seq C2 exon
AGGCAAATGCTCTAGAATTGCTTTCAAAATTGAATGATACCATTAAGAATTCAGACAAAAATGTACGTACTAGAGCACTTTGGGTGATATCTAAGCAGACATTTCCCTCTGAAGTGGTTGGCAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080345-RIF1:NM_001177664:4
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=PD(29.1=92.6),PF122313=Rif1_N=PD(35.2=92.6),PF053776=FlaC_arch=PD(45.5=55.6)
A:
NA
C2:
PF032249=V-ATPase_H_N=FE(29.4=100),PF122313=Rif1_N=FE(19.1=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:
ACTCACATTTCCAGTCAAAACTCG
R:
TTTGCCAACCACTTCAGAGGG
Band lengths:
222-1863
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)