BtaINT0125049 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021020 | RIF1
Description
replication timing regulatory factor 1 [Source:HGNC Symbol;Acc:HGNC:23207]
Coordinates
chr2:44812125-44813819:-
Coord C1 exon
chr2:44813723-44813819
Coord A exon
chr2:44812253-44813722
Coord C2 exon
chr2:44812125-44812252
Length
1470 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TTTTTTTGCTTGTTTTTCAGAGA
3' ss Score
10.29
Exon sequences
Seq C1 exon
ACTCACATTGCCAGTCAAAACTCAGAGCTCAGTAGTGCTGCTCTACAGGCCTTGGGGTTTTGCTTATATAATCCCAAAATTGCCTCTGGATTATCAG
Seq A exon
GTAGGTTTGTTGTGATGGAATATTTTTAGAGTTTATAGTTTGATATTGTTAAATGTACTGTTATTTCTCAATTTCACAACCTGTAGTTTAGGGTTTGCTTTTGAGAATGAGTCTGTAGATTATATCATTAGATTATATCATTGTAGTAAAGTTTCTTAGACATAGCTCTAGCTTTGATAACTATAAAATTTGTTTTAAAAGAAAATACAGTAAGCCTATTTTAAAATGTTGAGAAACCATCTTGATAATAAACATACCTGTTTTTGAAGTTTATAATTAGATAGAATTAATTTTGGGAGGTGGATGGGTCATTTATTTTATACAAGCATGTGTTAAGGAATTTGCTATTAGAAAAGTTCTTTTACATAGTGGTAAATTAGATAATTTGGAGCTAAAAGTGGTAATGAAAGCACAGGATCTGATGCTCTTCTGAGTTTTATAGCATCCTTGACCCTCTGCATCCTCAGATGCAAAACTCATGGAGATCTCAGTACTACACCATTTCATGTAAGGGACTTGAGCATCTCCTGGTTTTTGATATTCCTGAGGGGAAGTCCTAGAACCAATCCCCCATGGATATCAGGGGAGGACTATAATCCTAATTGTTGCTCTATAAGTAGCTTCTCATAGTATAGGTATGGGGATGATCTTTAGAGATGGATAATTAGGAATAGGGAATAAAGATATCAGAAAGTTGTTACCATCTTTTTTTCCGAGGGAAAAGTTTCCACTTATTTAATATACAGAAATGTTAGCAATCTGAAGTAGGAGTTGTTCATTTTGTAGCAGAGATACAGGATTTATAACATCTTGCCAAAAATTGACTCGTACGTTCAAACCTAATCAATCAGTTCAGTTGTGTCCAACTCTTTGCCATCCCATGGACTGTAGCACGCCAGGCTTCCCTGTCTATCACCAACTCTCAGAGCTTGCTCAAACTCATGTCCATCAAGTTGGTGATGCCATCCAGCCATCTCATCCTCTGTCATCCCCTTCTCCTGCCTTTAGTCTTTCCCAGCATCAGGGTCTCTTCAAATGAGTCGGTTCTTCACATCAGGTGGCCAAAGGGTTGGAGTTTCAGCTTCAGCATCAGTCCTTCCAATGAATGTTCGGGACTGATTTCCTTTAGGATTGACTGGTTTGATCTCCTTGCAGACCAAGGGACTCTCAAGAGTCTTCCCCAACACCACAGTTCGAAAGCATCAAACCTAATAATAAGATCCTATAGAAATATTTTAGTTGAAAAATTATTGATTTCAAGTCTATTATCTGTTTTCACTGAGTATACATTCTCTCTGACCAGAATTTTGTGTTTTGGGGGAAAGTTTGATTATTAGCATAAGTTTTCTGGTCCTTTTCTCTGGATATGCATTTAATTTTAATGACAATGACAATTATTTTTATCTGTTACGGATTTTAAAGGATGTAAAAGATTCTGCATAATTAAATTTTTTTTTGCTTGTTTTTCAG
Seq C2 exon
AGATAAATATTCAAGAACTGCTTTCAAAACTGAATGATATTGTTAAAAGTTCAGATAAAAATGTACGTACTAGGGCACTTTGGGTGATATCCAAGCAGACGTTTCCCACTGAAGTCGTTGGCAAAGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021020:ENSBTAT00000027997:3
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:
PF032249=V-ATPase_H_N=FE(26.9=100),PF122313=Rif1_N=FE(8.9=100)
A:
NA
C2:
PF032249=V-ATPase_H_N=PD(21.8=60.5),PF122313=Rif1_N=FE(11.7=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:
ACTCACATTGCCAGTCAAAACTCA
R:
TTTGCCAACGACTTCAGTGGG
Band lengths:
222-1692
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]