BtaINT0125058 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021020 | RIF1
Description
replication timing regulatory factor 1 [Source:HGNC Symbol;Acc:HGNC:23207]
Coordinates
chr2:44808895-44810921:-
Coord C1 exon
chr2:44810732-44810921
Coord A exon
chr2:44808988-44810731
Coord C2 exon
chr2:44808895-44808987
Length
1744 bp
Sequences
Splice sites
5' ss Seq
ACCGTAAGT
5' ss Score
10.43
3' ss Seq
ACTCTTGCTTTTGTTTTCAGAAA
3' ss Score
9.74
Exon sequences
Seq C1 exon
ACTAATTGAACAAGCCCCAGTTCAAATGGGAGAAGAGTCAATTAGGTGGGCAAAATTGGTCATACCTTTACTGGTTCATTCAGCCCAAAAAGTACATTTGCGGGGAGCCACTGCTCTAGAGATGGGAATGCCTTTGTTGCTTCAGAAACAGCAAGAAATAGCATCTATCACAGAGCAGCTTATGACTACC
Seq A exon
GTAAGTAATACTTTTTTGGATATTGCACTGTGAGGTTTTGCACCAAGCATAGGACTCATATTGGTGTAATTGCACTATGATCTAGGAAGTTCCTCTTTGAATTAAATTTAAGAATTGCTTGAATTAATATCACCCACTTCTAATTACGGTAAGGAAAGGAGCTGTCTATTCAGTGTTAACTGCAATCCTGGCATTTTATTTCATCCATAAAGAATGAAGAAATTGCATTTTTGGAAAAGGGAGAGTGTTATCTGATTCATCGCTATCTGGATTGTTACAGCATAATCCCAGGAGCTACAGATTTAAGGCATAAAAGTGCATGTAGTGTGTACAATTTCCCATTATTATTTGCCCAAAGTTTTAGGTTTTTCAGTCTTTCTTGTAACATTTATTGAGTACCTGTTATGTACTGGACATTGGTTTAGGTACTGTGTATATAGCAGTGAACAAAAGCAATTTGTTTTGGAGCTTATTTTCTAGTGGGAGCAATAAAAAAGTATGTAGTACATTTAGGAAAGAGATTATGGGAAACAGTGGGGACTGGATGAAAGTGCTTTCCAAGAGAAAGGGTGATGTGGTCAGAGAAGGAAAAAGAATAGGTGATTTGAAGGGGTAATAGGAGTTAGCTAATTGAATGATGAAGAGTAAACTTATTCAAGTTAGGAACCGTGGAAGCAAAGGCCTTGTTCTGATGTGCTAGGTTGTGTTCATCAAACACTGGGCAGTGTGATAGAGTGAATGAGGATGAGAGGGTAGAAGATGATGTCAGAAACAGGGCCAAGCCACATAGGACCTTGTAGACCATTGTAAGCACTTGGCTTTTATTGCTTTATTGCTTGGTTTTAAAGCATCTGGATTATATTGAAAACCATATTTGAAGGTTTTGAGTCTATGAGTGATATACGTACAGACTTGGCTTTTAAGGGGATCCCTCTGCCTATGTTAAATAAATTCTAGGCAGGGGTTGCATAGGAGCAGGGAACCCAGTTGGGAGATAGTACAGTAATCCAGGCAGAGGGGGAGACGTCCACATTCTAAAACCTGGGGATTTGTTTTTTTAGTTTTTTAAAATTCAGGATTCCTCATGGTAATGCCTGAGCTAAAAGTAACTCCAATGTTTTTGTGAGATTTTTAACTGATAAATATTTATTAATTTTTTAAGAGCTTATATAGGCAGTCCTTGAACAGCTCAAGTTTAACCCATGTATAATTTATAATTGACCCTCTGTATTCGTGGTTCCTCTGTGCCTTTGGATTCAGCCAACCACGGACTGTAGTACTGTGGTATTTACTGCTGAAAGATACCCAAGTGTAAGTGAACCACACAGTAACACACTTTATTCAAGCGTCCACTGTATAAGATTCTTAATGATAAATTTGAACTCAAATTTTCTCAGATGTATTACCCATGAAGCTATTAATGTATTTTTTAAGTTAATAGAAGTTAAAACATTATCATTTGAACTCTGATGATATGCATGCTGAAGTGTTTTAGGGGAAAGTGTATTGGTAGGGGAAAAGAAAGCTATATTGATGGATGGAAGAATGGCCTGATAAGTGATAAGACAAGCATAGTAAAAATGTCCAAGCATATACTTGGACATTTACTATAAACTGTCAGCTTTGCTATATGTGTGAAACTTCCTGATAAAATATTGGGAAAAATTACTTGGCTGAGACAATCAATGTAATATTGCATTCTTTTCAGGAGTCTTTTGGTAAATACTCTTGCTTTTGTTTTCAG
Seq C2 exon
AAATTACTTTCAGAACTCCAGAAACTGTTTATGAGTAAAAATGAGACTTATGTGTTAAAATTGTGGCCTTTATTTGTCAAACTTCTTGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021020:ENSBTAT00000027997:6
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(17.6=100)
A:
NA
C2:
PF122313=Rif1_N=FE(8.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATTGAACAAGCCCCAGTTCA
R:
TCCCAAGAAGTTTGACAAATAAAGGC
Band lengths:
278-2022
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]