BtaINT0125050 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021020 | RIF1
Description
replication timing regulatory factor 1 [Source:HGNC Symbol;Acc:HGNC:23207]
Coordinates
chr2:44768676-44773943:-
Coord C1 exon
chr2:44770725-44773943
Coord A exon
chr2:44768823-44770724
Coord C2 exon
chr2:44768676-44768822
Length
1902 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
CATGACTTAAATGTTTTCAGGTT
3' ss Score
7.66
Exon sequences
Seq C1 exon
GAGGAACAAAAGGAGAATGACATTGTCGTTCCTCAACATGTCATGGAAAACTGCGGTATGGATGAACATCTTGAAAAGGCTTCCCTTTTGAATAATGAGTGTGGTTCTATTGAGGAAACCAGTCCAAAAATACTGAGCAGTAATAATGATGCCAGAAAAAAAGCTTTAATTGCTTCAAATAAACCAACAGAATGTGCATCTACTACAGAAAATCCATCTGGTGTCAGCAGTAGCTCGGTTTCTATTGCCACCATTTCTGGAGCTCCCTTACAGCCTACAAGTCGAAGGCAATCCTTTATTACTTTGGAAAAGTTTGATGGTTCAGAAAATAGACCTTTTAGTCCATCACCCTTGAATAATATGTCATCAACTGTAATAGTGAAAAGTAACCAGGAAGGCATGGGTAAAACAGATAATCCATCAAAAGCAAAGAAGAGAGAAGTGGCTCTTTCCAAATCTGACTCTGAAAAAATAACACATGGGACTAAGAGATCAAGCCGAAGGTCGAGTAAATCTGAACCAATAGGGAGTAAAAAGTCTAAACCCTTAATGAGATCTGAACAAGAGAAAAGTACTCAAGAATCTGTTGATGGCACAGTAGCCTTAGAAAATAACCCACCTGGCTTGCTTAATCAGACAGAATGTGTGTTAGATAATCAGGTTCATCTCTCTGAATCTACAGTGGAGTTTGAGGATACAATGCTTGAATCAACAGTGGAGAATACTGTATTAGAAAACAATACTGTAGAAGAGAGAACCTTAGAAGTTAACTTGGAATCCAAAGAAAACACACCCCCAGCCATAATAACGGATCAGACAGTAAATGAGGATAGTCATATTCAGGTAACTCCAAATCAGAAAACCCTTAGGCGATCTTTAAGGCGACGTTCAGAAACAGCAGAACCAACCACTGATAGCCAAGATAAAGAAAATAATCATCAAAAAAGGGAAAGACGTAAAGAAGAAGAAAAGACTCCGCAGAAGAGTCCGTTACATGTAAAAGATGATGTTTTACCTAAGCAAAAATTGATTTCTGAACAAAGTGTACAGGGAAACTTAGTTGACAAAGGAAATAATTTACATGAGAAGGCTTTTGGGGAGACCAGTGCTAATGCTGAAATTGATGAAAATAGAAGAAAGCCAGATCTTGAGAATACTAAATCTGAAGGAGATGGTGTGCCGGACATTGCAGATAAATCCTCTGAGAAACCAGTAAGGGGACGAACACGATACCAAACAAGAAGAGCATCCCAGGGTTTACTTTCCAGCATTGAAAACTCAGAATCTGATAGTTCTGAGGCAAAAGAAGAAGGTTCTAAAAAGAAAAGATCTGGAAAATGGAAGAACAAAAGCAGTGACAATGTTGACATGGAAGATCAAGAAGAGAAAATGGTAAAACAGGAATGTATAAAAATTGAAAATCAGGCACATGATTATAAAGGGAATCCTGAAGTAGACAAAGATATAAAATCTCAAATCTGTGAAAAAGGAGATGAAAGTACTACTGTAAGTCTTCAAGATTCTACCGTATCTCCAGATTTATTACAAGTTTATGATGATGTATTGAATACTTCTGAGGGAGAAAGTAAAAGTAACAAAGATGCAGACCATTCCTTTTCAAATCCTTCTGTACCAGAATCAAATCTAAGGACTAGAAATGCCAGTAAGAGGTTACATAAGCGAGATTCTATAGAAAATAGCATGGGGGAATCCTCAAAAATAGGGACATCAGACATTTCTTTGCTTTCTGAAAAAACTCTTCAGACAGTAGAATGCCAGCACAAGAGAAGTAGGAGGGTGAGGCGATCTAAAGGTTGTGATTGTTGTGGAGAAAAATCACAGTCTCAGGAAAAGTCATTTACTGGGTTAAAGGATACAGAAAATTACGATGTAAAAGTCAGTGAAACAAAAAAGACAGATGGGGAAACACCTGTATCTATTTCAGAAACTTCGAAAGCTGATCTGTCCTCGGAGGTTAAACTTTTAGATGAGCATCATAGTGTGAATTTTCATTTGGATCTCAAGGAAGAGAATGATACTACTAATGATTCATTAATTATATCTGAAACTGAGTTAAAAGAAAATACTACTCAAAGCTTTCTTCCTTCTGAAATGGTAAAATTTAAAGAAACTTCTCGTAGGGATTCTGAGGAAGCAATATCTCTAGAAACCCAGGAGCCATCTAATAAGAAATGTAAAACTGTTGACCCACATTTAGATGTTTCCAAAGATATTTCACTGAAATGTTTTTCTTTGGAGACTAAAGAAGAAAAGTCAGAGGCCACTTCAAAAGAGAAATTGAGTACAGAGAACATTGTTATTGTTGAATCAAATGCAGAATCAAATCCAGAAGTAGATGCTATGGAATTGAATGTAGAAAATGATCAGTCTGAAGCTGGCTTCTCTGAACAAAAGAATGTCAAAACTGGTATTCCAGGGAAAGAAGTAACAGAGGAAAACAGTGAAAGAATGGATACACCTGAAAAACTGAAAGCCAATGAAGCAGTAACTGAGGAATTTAATTCAGCTACTGATTATTCGGATACTCCGACATCTGTAAAAGTGAATGCTCAGGTAGAGATCTCTGAACAAATAGCGGTTGGGGAGCTAGGTGGAGGAAGTGATGAATCTGATCCAGGCTCATCTGAAGAAATGAACGCTGAAATGAAAAATTGTGAAAAAACAGCGGTTTGTGAGGTGACTACTGAATCTGACCACGTCACTGAAACCGAAGACGAAGATGTAACTACCACGGCTTCTCTGCCTATAGAAGTTGAAACAAAGGAATTAGATGTAGAAGTCAATAACTTTGTTCCCGACACACTTGAGATGATCACTGAAGAAGGAAAGGTTGACCCTAACAAAACTGAAACGAATACTGAACCTAATAAATTGGAGGAAACACAGTTAGATGACAATCAGATGGTAGTGGAAAGTAATGAAACTTTACCGGAAGTTCACCATACTTCAGAGAAAGTAGAGGAGATAGCACAACCTCTGACATCTGAAACAGATATTTCTGGACTAATATCAGAAGACAGTAATACATCTCCTCAAAAATCGAAGGATATTGATCCTTTACTCATGTCAGCAAACGAGAGTCCTAGTGGCATGCACACACGTTGTGTGTGGTCTCCTTTGGCTTCTCCATCCACCAGCATTTTAAAGAGAGGACTAAAAAGACCCCAAGAAGATGAAATCTCGTCACCTGTCCACAAG
Seq A exon
GTAGGGGGATGGATGCTGAATGTTCATGAGTCCAAGGTTAATTGGGATAGTTTGGCCACTTGCTGACACTTGGTAAATGATGGGATATTGGGCGTACATGACCATTCGTTATGAATATATGCTATGACAGGGAAGAGGGCAGGCAGAAGGTGGACGTTGAGAAAAAGACTGAAGCCCTTTAGGTATTCCTTTATTTCAGGACCTGGTGTCTGTCGCTCAGTTGTGCTCGACTCTTTGCGATCCCATGGACTGCAGCCTGCCAGGCTCCTCTGTCCATGGGATTTTCCAGGCAGGTATACTAGAGTGGTTTGCCATTTCCTTCTCCAGGGGATCTTTCTGAACCAGGGATCAAACCTGGGTGCCTTGCACTGCAGGTGGATTCTTTACTGACTGAGCTACCAGGGAAGCCTAACACTTAGCTATAAATCTTTATACAACCATCACCATTTTTCACATTTTGCAAAATTGATAATCTCTCATGGTGATTTTTTCTCTGCTATATAATACACAAGGAAACACTTAGAAACCAATAAAGGAGCTTTAGTTAGTACTTACTGTGTACTAGGACATTATCCTGTCTGTTTCACATGTCTTTATATAAACTTAGACCTTTAACAATTAAAAATTTCTTTAGGCTATGCCTTCATTAATTTCTGCGTATGATTTCATTTGTAATTAATCTTGTTAATGCCCCCATCTTCTTCACTACATTTTAATTCTTGTAGTTTGTACACATATGGATTACCTATGTATCTGCTTTAGTCTCTGACCCTGTGACTTGCACATAGTTTAGAAAGGAAAAGTTGCATGTGCTTTACATAGCTCCACTTGTCCTCTATAACTATTTTATAAAGGTACTGTGTGGGCATTCCTTAATTTTGAAATTGGACCTACCATTTACTGTGGAATATATGTGTTTATGTATACAAACATGTATATATAGATAAAATCATACTGACACGTAATTTTGCCTTTAGCCAGCACATTGTGAAAACTTTCCCCAAATATACTAAAAATTTTTAAATTGAGAGTTCAAAGATTAGTTCTTAGGAAAACTTAACACTTGAGGGTTTTTAGTTTGGTCTTGCTTTGCTTTTGAGTCTTTTACCTTTTTTTTTTTTTTAATCTTAGGTTTAAATAGGTCATAGAAGTTCTTGAAAAATTTATGAAGATGAAATGATGTCTTCAGTATACTTTAGATTATTAATGCCAGTTAACTGTAGTCATGTTTTGTTTGATAGTAGCTCGTTTAATTTTTATTTACATATGATAGTTTTCTATAGCAGATATTTATAGAAAGTTCCCAATATTTTGGGAATAAGACATTTATATACATATTATGGTTTTGCATGCCCCGTTGGATACTTTTACCAGACAGCTGAGTAGCTGAATAAAGAGTTTAGAAAAGGCCAAAATAACTTCAAGCTGGGCTAAGCTTTTGTTTTTTGTTTTTGTTTTAACAAAAAATCTCACCCATTGCTGTGACTCTGTTACCCTCAAAGAATTAAGAACTGAGATTATTAAGGTATACCAAAGGCCAGTTAGTACTGTCTCTGCCTCTTTACCTCGTTCTTTATGGTTTGTAGTAAGCCTATGAGATTAGTAGAAATTTGTATACTTTTAACTGTCACATGCAATTTCATCAAGTTTCTGCTACTATCCTTTCATTCTCCTCGTTGCTGTACTTTGTATTAGACCATGGATACTTGGAATGACCCTTGGTCTTGAGTAATAGTTGTGAAAACAATCACCAGGAACAACTGCAAGTATGTGCAGTTGGCTTCTAGTAAGATAAATTAGGCCTCCAAACATACATGCTATTTTTGGCTGACCTTATAATGAGAGTTTATGGTATTTTTTTAAAACTTTTTAAAAATAAAAACATGACTTAAATGTTTTCAG
Seq C2 exon
GTTCGCCGTGTCTCCTTTGCAGATCCTATATACCAAGCAGGATTGGCAGATGACATTGATAGGCGATGCTCTATTGTTAGGTGCCATTCTTCAAATAGTTCTCTCATGGTAAAAAGTGTTAAAACTTCACCTACTGTGCAATCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021020:ENSBTAT00000027997:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.922 A=NA C2=0.214
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TGGAGGAAACACAGTTAGATGACA
R:
GGATCTGCAAAGGAGACACGG
Band lengths:
352-2254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]