BtaINT0126503 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018690 | RPAP3
Description
Bos taurus RNA polymerase II associated protein 3 (RPAP3), mRNA. [Source:RefSeq mRNA;Acc:NM_001101930]
Coordinates
chr5:32762426-32763503:+
Coord C1 exon
chr5:32762426-32762609
Coord A exon
chr5:32762610-32763362
Coord C2 exon
chr5:32763363-32763503
Length
753 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
GTGTTGTTTTCCCTCCCTAGAAT
3' ss Score
11.49
Exon sequences
Seq C1 exon
GGATTGGTTGGTCAAAACTCTGCACGCCGTAATGGCTTCAACAAGTAAAGCAATTGAATTACAACTGCAAGTGAAACAAAATGCAGAAGAGTTACAAGACTTTATGAGGGATTTAGAAAACTGGGAGAAAGATATTAAACAAAAGGATATGGAACTTAGAAGACAGAATGGTGTTCCTGAAGAG
Seq A exon
GTAAATTTCTTAACTGAATTCCTACTTTAGCATCCAGGGAAACTCTTCATTTATTTATTTTAAAGTAAATCACAGCCTTTAAAATGTTTTGTGGAAATGCTAATTAAAGAGATTTACTTTCTGCCAACATTTTGAAAAATTCTACTTTTAAAAGTCTTTGTAATAATTGTATTAACTATCAATAGGACATTTTTAAGGCTTAGTCCATAGGAAGACCATGTGATAATTCTTAAGGTAAATGAATAGCATCATAAAATAGGCTTGTATATATATCATATGTAATTATATACTTAATGATATATTAACATACAGTATTGCCCTAAACACAGAGAATACCTAGACTCAACCAGTTTTCTTAAGACAGTGCATTGAGATGTGGACAGCTTTTTCATACTGTTGGTAATGTGGAGGCAGTTTGGTGCCATTGTACTGTTGCTAAATCATTGTATTAAGGCTGAAGGTCAAGCGGTTTTTGAATTTTGAATTTAGGATTGCAAATTAAGTGTATAATTAAAATTTCTGGGTAATATTTTTCTTATGACTGAACAGTGTTCAGTATTTGTCAAAGGATGAATTAAAATTTTCAGGCATAGGTTTATCATTAGAAATGAATGAATTGGTATTTCTAACCACTTGAAAACTAAACTAAAATTACTTTTACTTGAAAATATCCTTCAGTGAGAGTTTTAAACATCACTAGTTACACAGGAAAGTAACAGAGCTGTCTCAAAATGTGTTGTTTTCCCTCCCTAG
Seq C2 exon
AATTTACCTCCTATTCGAAATGGGAATTTTAGGAAAAAGAAGAAAGGCAAAGTTAAAGAGTCATCTAAAAAAACCAAAGATGAAAACGCAAAAAACAGGATAAAATCTTATGATTATGAGGCATGGGCAAAACTTGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018690:ENSBTAT00000024878:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.647 A=NA C2=0.660
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGGTCAAAACTCTGCACGC
R:
ACATCAAGTTTTGCCCATGCC
Band lengths:
318-1071
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]