BtaINT0118343 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048151 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:43636427-43636802:+
Coord C1 exon
chr2:43636427-43636541
Coord A exon
chr2:43636542-43636710
Coord C2 exon
chr2:43636711-43636802
Length
169 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGA
5' ss Score
7.62
3' ss Seq
TTCTTTAGTTTTTTCATTAGGAT
3' ss Score
6.29
Exon sequences
Seq C1 exon
ATATTTTTAGATGAACTGCATGAACATGGACAACTGCATTCTATGTCATCTTGGATGGAATTGTATCCAACAATTAGTTCTGACATTAGATTCACTAATATGCTTGGTCAGCCGG
Seq A exon
GTGAGATTCTTCTTTTTCCTAAATTGTAGTTATAATAGTTGGAACGGGCCACAGGGAAGGGTGGTTGTGTTTGGGGCATGGGGTGTGCTTTCTTTTGTTTTATAAACAAAAAAGTAATTGCAGCTCTTTGATTAGAGCTAGCTTTTGACTTCTTTAGTTTTTTCATTAG
Seq C2 exon
GATCAACTGCACTTGACCTTTTCAAGTTTTATGTTGAGGATCTTAAAGCACGTTATCATGATGAAAAGAAGATAATAAAAGACATTCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048151:ENSBTAT00000064349:23
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:
PF0184614=FF=FE(67.9=100)
A:
NA
C2:
PF0184614=FF=PD(17.9=32.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTTTAGATGAACTGCATGAACATG
R:
ATCTTCTTTTCATCATGATAACGTGC
Band lengths:
186-355
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]