HsaINT0140702 @ hg19
Intron Retention
Gene
ENSG00000080345 | RIF1
Description
RAP1 interacting factor homolog (yeast) [Source:HGNC Symbol;Acc:23207]
Coordinates
chr2:152319398-152324660:+
Coord C1 exon
chr2:152319398-152322634
Coord A exon
chr2:152322635-152324513
Coord C2 exon
chr2:152324514-152324660
Length
1879 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
ATCCTGACCTGTGTTTTCAGGTT
3' ss Score
9.6
Exon sequences
Seq C1 exon
GAGGAGCAAATGGACAGTGACATTGTCATTCCTCAAGATGTCACGGAAGACTGTGGTATGGCTGAACATCTTGAAAAGTCCTCCCTTTCGAATAATGAGTGTGGTTCTCTTGACAAAACCAGTCCAGAAATGTCAAACAGTAATAATGATGAAAGAAAAAAAGCTTTAATTTCATCAAGGAAAACATCAACTGAATGTGCATCTAGTACAGAAAATTCTTTCGTTGTCAGCAGTAGTTCAGTTTCTAATACCACTGTTGCTGGAACTCCCCCATACCCTACAAGTCGGAGGCAAACCTTTATTACTTTGGAGAAGTTTGATGGTTCAGAAAATAGACCTTTTAGTCCATCCCCCTTGAATAATATTTCATCAACTGTTACAGTGAAAAATAACCAGGAAACCATGATTAAAACAGATTTTCTACCAAAAGCAAAGCAAAGAGAAGGGACTTTTTCAAAATCTGATTCTGAAAAAATAGTGAATGGAACTAAGAGATCAAGCCGGAGAGCTGGTAAAGCTGAACAAACAGGGAATAAAAGGTCTAAGCCCTTAATGAGATCTGAGCCGGAGAAAAATACTGAGGAATCTGTTGAAGGCATTGTAGTCTTAGAAAATAACCCACCTGGTTTGCTTAATCAAACAGAATGTGTGTCAGATAATCAGGTTCATCTTTCTGAATCTACAATGGAGCATGACAATACAAAGCTTAAAGCAGCAACAGTGGAAAATGCTGTATTATTGGAAACTAATACTGTAGAGGAGAAAAATGTAGAAATTAATTTGGAATCCAAAGAGAATACACCCCCAGTAGTAATATCAGCAGATCAAATGGTAAATGAGGATAGTCAGGTTCAGATAACTCCAAATCAGAAAACCCTTAGACGGTCTTCAAGGCGACGTTCAGAAGTAGTAGAGTCTACCACTGAAAGCCAAGATAAGGAAAATAGTCATCAAAAAAAGGAACGACGTAAGGAAGAAGAAAAACCTCTTCAGAAGAGTCCATTGCATATAAAAGATGATGTGTTACCTAAACAAAAACTGATTGCTGAACAAACTCTACAGGAGAATTTAATTGAGAAAGGAAGTAATTTACATGAGAAGACTCTTGGGGAAACTAGTGCTAATGCAGAAACTGAACAAAATAAAAAAAAGGCAGACCCTGAGAACATTAAGTCTGAGGGGGATGGTACCCAGGACATTGTAGATAAGTCCTCTGAGAAACTAGTCAGAGGCCGAACACGGTATCAAACTAGAAGAGCATCTCAGGGTTTGCTTTCCAGCATTGAAAACTCAGAATCTGATAGTTCGGAGGCAAAAGAAGAAGGTTCTAGGAAGAAGAGATCTGGAAAATGGAAAAACAAAAGCAATGAAAGTGTTGACATTCAAGATCAAGAAGAGAAAGTGGTGAAACAGGAATGTATAAAAGCTGAAAATCAGTCACATGATTATAAAGCAACTTCTGAAGAAGATGTAAGCATAAAATCTCCGATTTGCGAAAAACAAGATGAAAGTAATACTGTAATATGTCAGGATTCTACAGTAACTTCAGATTTGTTGCAAGTTCCTGATGATTTACCAAATGTGTGTGAGGAAAAAAATGAAACTAGCAAATATGCAGAATATTCCTTTACAAGTCTACCTGTGCCAGAATCAAATCTAAGGACTAGAAATGCCATTAAGAGATTACATAAGCGAGACTCTTTTGATAATTGTAGTTTGGGAGAATCCTCAAAAATAGGGATATCAGATATTTCTTCGCTTTCAGAAAAAACTTTTCAAACACTTGAATGCCAACACAAGAGAAGTAGGAGGGTGAGGAGATCTAAAGGTTGTGATTGCTGTGGGGAAAAATCACAACCTCAGGAAAAGTCACTCATTGGGTTAAAGAATACAGAAAATAATGACGTAGAGATTAGTGAAACAAAAAAGGCAGATGTGCAAGCACCTGTAAGCCCATCAGAAACTTCTCAAGCTAATCCATATTCTGAAGGACAATTTTTAGATGAACATCATAGTGTGAATTTTCATTTGGGTCTCAAAGAGGATAATGATACTATTAATGATTCATTAATTGTTTCTGAAACCAAATCAAAAGAAAACACTATGCAAGAATCTCTTCCTTCTGGAATAGTAAACTTTAGAGAGGAAATTTGTGATATGGATTCTAGTGAAGCAATGTCTCTTGAAAGCCAGGAGTCACCTAATGAAAATTTTAAAACTGTTGGCCCGTGTTTAGGAGACTCGAAAAATGTTTCACAGGAATCTTTGGAGACAAAAGAAGAAAAACCAGAAGAAACCCCAAAAATGGAACTGAGTCTAGAGAATGTTACTGTTGAAGGAAATGCATGTAAAGTAACAGAATCCAATCTAGAGAAAGCAAAAACTATGGAATTGAATGTAGGAAATGAAGCTAGCTTTCATGGACAAGAGAGAACCAAAACTGGTATTTCTGAAGAAGCAGCAATAGAAGAAAATAAAAGAAATGATGACTCTGAAGCAGACACAGCTAAACTGAATGCCAAAGAAGTAGCAACTGAGGAATTTAATTCAGATATTAGTCTTTCTGATAATACTACACCTGTAAAATTGAATGCTCAAACTGAGATTTCTGAACAAACAGCAGCTGGGGAACTAGATGGAGGAAATGATGTATCTGATCTACACTCATCTGAAGAAACGAATACCAAAATGAAAAATAATGAAGAAATGATGATCGGCGAGGCAATGGCTGAAACTGGCCATGATGGTGAAACAGAGAATGAGGGCATAACTACCAAAACCTCAAAGCCTGATGAAGCTGAAACAAACATGTTGACTGCAGAAATGGACAACTTTGTTTGTGACACAGTTGAAATGAGCACTGAAGAAGGAATCATTGACGCTAATAAAACTGAAACAAATACTGAGTATAGTAAATCTGAAGAAAAATTAGATAACAATCAAATGGTAATGGAAAGTGATATTTTACAGGAAGATCACCATACTTCACAGAAAGTGGAGGAACCATCACAGTGTCTGGCATCTGGAACAGCTATCTCTGAGCTAATAATAGAAGACAATAATGCATCTCCTCAAAAACTAAGGGAACTTGATCCTTCACTTGTGTCAGCAAATGACAGTCCTAGTGGCATGCAGACACGCTGTGTCTGGTCTCCTTTGGCTTCTCCGTCTACGAGCATTTTAAAGAGAGGACTAAAAAGATCCCAAGAAGATGAAATCTCATCACCTGTTAATAAG
Seq A exon
GTAAGGGGAATGAGGCTAAATATTAAGGAACCCAGTATTTGGTTGGGATATTTTGGCCATACAGTGACCTCTGGTGAATGACAAAATATTACAATTATATGGCCACTCATTTGATTATTTACCATAATGGTTGCTAGGGAAAAGGTAGGTAGAAGAAAAGGTTTCGAAAAAAGGAGACTGAAGCCTTTTAGATAAGTCTTTCATTTTACAACACTAAAGATCTTTATGCAGCTGTGCACATTGTTCACCTTTGGCAAAATTGATAAGGCTCCTAGCATCTTTTCTGCTCCCCATACCATAATATCATATGAGGAAACAGATTTAGGAATGCAGGCAACACTGCCATTGATAAAGCAGATTTAGTAGTTGTGTGTTGGAACATTATGCTGTTTTACGTTTTACATACATGTTCCAGACCATATCTAATTAAAAAAAAAAACTCATGTGCCTTCATCAACTTGTAGATGTGATCTTATTTAGTTATTTATATCCCCATTTCCTCAGCTAAATTATAGATCTTTTACTTTAGAAAAGATGGATTATCTATATATCTGCTTTAGCTTCAGGCCTTGTGCCTTGCACATAGTTTGTTGAATGAATGAATAAAAAAATAGGAAAAGTTAAATGTATTTACGTAACTCAACTTGTCTTATACTTAACAAAATAGATATCCTGAAAAGGTATGATGTTGGCATTCCTTAATTTTGAACTTGAACCTGCTATTCATTGTAGAATACATTTTATATATACAAGCATGAATATATAGACATGACACCTTGTTTTTTGCCTTCAACAAACAACACTTTGAAAGTATTCCTTTGGCCAGGCTCGGTAGCTCACACCTGTAATCCCAGGCATGGGATTTGGGAGGCCAAGGCAGGTGGATCACCTGAGGGTCGGGAGTTCAAGACCAGCCTGACCAACATGGAGAAACCCCATCTCTATTAAAAATACAAAAATTAGCTGGGCCTGGTGGCGCACACCTGTAGTTACAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGATGCAGAGGTCGCAGTGAGCTGAGATTGTGCCACTGCACTCCAGCCTGGCGACAGAGCGAGACTCTCAAAAAAAGAAAAAAAAATGTTCTTTCAAAATCCCTGTTACTCTTATTCATGTGTCTGAACTTTGCAAGATACACTGAAAATTCTTCTGCTGAGAATCTAGAGATTAAGTTGTTTTTTGTTTTGTTTGTTTGTTTTTTGAGATGGAGTCTTACTCTGTCTGTAAGACAGAGTAGTGCAGTGGCACGATCTTGGCTCACTGCATGCTCTGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCTTGAGTAGCTGGCATTACAGGCATGTGCCACTAAGCCCAGCTAATTTTTGTACTTTTAGTAGAGATAAGGTTTCACCATGTTGGTCAGGCTGGTCTTGAACTCCTGACCTCGAGATCCACCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGCGAGCCACTGCGCCTGGCACATTTCTGTTTTTACATCAGTCTTCTTTCTAGTCTGGTAATCCCATAAAGTTCCTAGAATCAGATCGTACACTTTTAACTGCCACATCTGGCTTCGTTAAGTTTTTGTTACTGTGCCTTTTTCACAATCTTTGGTATTATGCAGAGACAGTTTAAAATATAGAAAATTAGAGTGAATTGTGGTATTGAGTTAATGTGATCTGTGAAGGCAGTCGCTAGGAACTGTGCAGCTGACTTCTGGTGAAATAAATTTTCTAAACCCACATTCTATTTTTGGGTAACCTCATAATGAAAATTTATGGTGTAATTTTTTAAAAACTTTAATTTTGTTAAGTAAAATCCTGACCTGTGTTTTCAG
Seq C2 exon
GTTCGCCGTGTCTCCTTTGCAGATCCAATATACCAAGCAGGATTGGCAGATGACATTGATAGACGGTGCTCTATTGTTAGGTCCCATTCTTCCAATAGTTCTCCCATAGGAAAAAGTGTTAAAACTTCTCCTACTACACAATCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000080345-RIF1:NM_001177664:30
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.876 A=NA C2=0.360
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:
GGAACCATCACAGTGTCTGGC
R:
TGGGAGAACTATTGGAAGAATGGG
Band lengths:
344-2223
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)