BtaINT0118337 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048151 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:43628309-43628872:+
Coord C1 exon
chr2:43628309-43628373
Coord A exon
chr2:43628374-43628707
Coord C2 exon
chr2:43628708-43628872
Length
334 bp
Sequences
Splice sites
5' ss Seq
TAGGTAATA
5' ss Score
6.84
3' ss Seq
ATGATTTTTTTTTTGTTTAGTGC
3' ss Score
7.53
Exon sequences
Seq C1 exon
CGTGTACCATCTAATGCTTCATGGGAGCAAGCTATGAAAATGATCATTAATGATCCACGATATAG
Seq A exon
GTAATACTTTGGTTTTTTGATTACTTTGAGCAAAGCAAGCCTAGAGAATTTAAATTGTGTCAAATAATGTAAATTTTTATTCCCATTGATCTTCTTGTTATTTTGGATACCAATAATAGAGTTGCTTTATATCTGATAAGAACCAAAAGTTAAAAAGGTTTGTCACACAATGTGGGCACCCTTTTATAGATAGTAGAATTAATTTTTAAAGGAGAAATTATTTTCTGTTCAGTAACTTACTGAAATTTTCTTAATTTGTGAATGAAATTATTTTTTCAAGACACTAACATTTGATCATCTTCATTTACTCTTACATGATTTTTTTTTTGTTTAG
Seq C2 exon
TGCTTTAGCAAAGTTGAGTGAAAAAAAGCAGGCCTTTAATGCTTATAAAGTCCAAACAGAGAAAGAAGAAAAAGAAGAAGCAAGATCCAAATACAAAGAGGCTAAGGAATCCTTTCAGCGTTTTCTTGAGAATCATGAAAAAATGACTTCCACAACTAGATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048151:ENSBTAT00000064349:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.318 A=NA C2=0.357
Domain overlap (PFAM):
C1:
PF0184614=FF=FE(42.0=100)
A:
NA
C2:
PF0184614=FF=PD(30.0=26.8),PF0184614=FF=PU(44.0=39.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGTACCATCTAATGCTTCATGG
R:
TTGTATCTAGTTGTGGAAGTCATTTT
Band lengths:
230-564
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]