BtaINT0118340 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048151 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:43629710-43630907:+
Coord C1 exon
chr2:43629710-43629818
Coord A exon
chr2:43629819-43630756
Coord C2 exon
chr2:43630757-43630907
Length
938 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTA
5' ss Score
7.04
3' ss Seq
CATACATTCATATTTTTTAGGAG
3' ss Score
9.29
Exon sequences
Seq C1 exon
AAAAGCAGAGCAAATGTTTGGAGAGATGGAAGTCTGGAATGCAATATCAGAACGTGATCGTCTTGAAATCTATGAAGATGTTTTATTCTTTCTTTCAAAAAAAGAAAAG
Seq A exon
GTATTATTCACTGTTAACAGTATTTATAGATTAAACAACATGTTTCTTGTTTAGGAGTTACTTTATAACATGTCCATTCTTGTTGGTTTATCTACTATATATGGTGCTGTAGATCTGTTTATTAGAAGTTAAGTTAAAAAATAGGTAGCTCTTGGATTTTCCTGGTGGTCCAGTGGTTAAGAATCCACCAGCCAATGCAGGGGACATGCTTTCAGTGCTTGTCAGGGAAGATCGCACATGCCACAGGCAACTAAGTCTTTGCCACAACTACTGAAGTAGCTAATACCTAGATTGTCATTAATTGCCTGTCTTCTGCCCACTTAGAAAATGCTTTTTTTTTTTTTAGCTTGTTTGAGTTTAGAAAATACTCAGTATTTTTCCTTACAAGGCATTAATTTATGATTATTTTAAAAGAACAGCAGTAATGTGTAATTGTTAAAATGTATTTGTATTAAAATGTATTTGTAGGGTAGTGTTTTTGAAATACTGTCCTGCAAATACATTTAGTTTTGCTCATGTCTATATTATTCACTAAGTTATATGTTATCCAGTCTTCCAGGAGACTTATAGAAATGTAAGTATTATTAACAAAAATTTGAACATCACTGAAAGTGGTTGAACACATTATCGTTTACCTGTTGTGTGATTTGTCTGCAGTAACTTTTGTTTGGATAGTGTCTACAATACATAGTTGTGGGAAGAGAGATTTTGTGAGGCGGAGAGGGAGTTCCAGGTTAGTCTTAGAAGAGAAGTTAAACAAATTGAAGGTAAGAGGGAAGCAGTTAGGCAAGAGTACTGAAAAGGTAAAGAGTGTTGATATTTAAAGCAAATGGATAGCATTTGAAATTTGGACATCAGAATGTGAAGAAACCTTTATTGATTGCATTTCATACATTATGCTTTATTTGAACGTTAAAACATACATTCATATTTTTTAG
Seq C2 exon
GAGCAAGCAAAGCAGTTGCGAAAGAGGAATTGGGAAGCCTTAAAAAACATACTTGACAACATGGCTAATGTGACATATTCTACTACTTGGTCTGAAGCCCAGCAGTATCTGATGGATAATCCAACTTTTGCAGAAGATGAGGAATTACAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048151:ENSBTAT00000064349:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(54.0=73.0)
A:
NA
C2:
PF0184614=FF=PU(75.0=82.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCAGAGCAAATGTTTGGAGAGA
R:
TCTGTAATTCCTCATCTTCTGCA
Band lengths:
257-1195
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]