BtaINT0118346 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048151 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:43637309-43637790:+
Coord C1 exon
chr2:43637309-43637446
Coord A exon
chr2:43637447-43637694
Coord C2 exon
chr2:43637695-43637790
Length
248 bp
Sequences
Splice sites
5' ss Seq
GATGTATGT
5' ss Score
6.31
3' ss Seq
TGCATATCTGAATTTTTCAGATC
3' ss Score
8.7
Exon sequences
Seq C1 exon
TTACTAGAAAAGGCAGAAGCCCGTGAACGTGAAAGAGAAAAAGAGGAGGCTCGGAAGATGAAACGAAAAGAATCTGCATTTAAGAGTATGTTGAAACAAGCTACTCCTCCAATAGAATTGGATGCTGTCTGGGAAGAT
Seq A exon
GTATGTATACTTACAAATTTTTTCCTTTACAGTTGAAAATAAAAATCTTTTTCTTTCTCATAGCTACAGAGATAAACTGAAGTTATTTGAAGATTGTGAACTCAGCTGTGATGGCATTTAGAAATACTGGAGGAATGGAAATAAAGACTGAGAGGGCTGGGCTGCCAGTTTTCACTTGCTGTTTTTTTAGTCATATTGGTATATTTTTCTCAGTTTTCATATTTTTATTGCATATCTGAATTTTTCAG
Seq C2 exon
ATCCGGGAGAGATTTGTAAAAGAGCCAGCATTTGAGGATATAACTCTAGAATCTGAAAGAAAACGAATATTTAAAGATTTTATGCATGTGCTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048151:ENSBTAT00000064349:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.543 A=NA C2=0.188
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(46.2=52.2)
A:
NA
C2:
PF0184614=FF=PD(50.0=81.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAAGCCCGTGAACGTGAAAG
R:
CTCAAGCACATGCATAAAATCTTTAA
Band lengths:
220-468
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]