HsaINT0140707 @ hg38
Intron Retention
Gene
ENSG00000080345 | RIF1
Description
replication timing regulatory factor 1 [Source:HGNC Symbol;Acc:HGNC:23207]
Coordinates
chr2:151414823-151416688:+
Coord C1 exon
chr2:151414823-151414919
Coord A exon
chr2:151414920-151416560
Coord C2 exon
chr2:151416561-151416688
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:ENST00000243326:3
Average complexity
IR
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:
PF122313=Rif1_N=FE(8.9=100)
A:
NA
C2:
PF122313=Rif1_N=FE(11.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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