BtaINT0118330 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048151 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:43585376-43586829:+
Coord C1 exon
chr2:43585376-43585459
Coord A exon
chr2:43585460-43586697
Coord C2 exon
chr2:43586698-43586829
Length
1238 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
AAATTGTCCCTCTTTTTCAGATG
3' ss Score
10.46
Exon sequences
Seq C1 exon
ATGTGTAGCGGCAGTGGCCGCCGGCGGAGCAGTCTGAGCCCGACGATGAGGCCGGGGACGGGAGCCGAGCGTGGAGGCCTCATG
Seq A exon
GTGAGTGAAATGGAGAACCATCCTCCCTCGCGGGGTCTCGGGGACGGGGAGCGGAGATTGTCCGGCTCAAGCCTCTGCTCCAGCTCTTGGGTCTCTGCTGACGGCTTCCTGAGGAGACGGCCCTCGGTAAGGGAGCGGTGGGGCAGGGGGAAAGCGGCACAATGAAAAACGGAATCAGAGAGACAGGAAGCATTCTCCAAAAGGAGAAGAAGATCAGAGTGGACGAAGGAAGAGCTCGAGATGCTGGGATTTGTTCCGAGGGAGAGAAATGGAGAGCGGGGATGCACAAAGGAAAGGAAGTGGGACCCTGGAAGTTTTCAGTAGGTTCGGCCTAGGCAGATGCGCGGTGGAGGTGCTGGGCCCTGGGCGGGGTGAGCGTTTTGGAGAGGTAGGCTGGGTTAAGCAGGGAGGGGGAGGCGGAGACGGAGACTTTTTCCGTAGACTTTGTTAACAGAGTCTGCCAGAATCTTAACTAATAGTAGTGGTGTTCGCAGCGGGGGGATCGCTGGGAGAATTGTCAGCAGATAACTACCTGGTTTTACGACCTGGAACAATGGACACGTAAAGAAAGGAGTTGTCTTATAAAAAGCGCATTAAGGTGCCTAAATTAGTTGTTTACGTTTAGTGTTCGTAAATAACAGAGCTTAGTCTTTGGGGGGGGGGTATTTTTTTGCATAAGTTATTTTAGCTGTGTTAGAGATTCTATTAGGAAATAATATATTTGTTAGGAGTGAAATGTCCCCGGGTACCGACGCTGTCTTTTATAAGACCAGCCCTCATCTCAGTTAATTGGGTAAATTTTCAGCGTTCTAAAGCTTAAAATCAGCTTAGAAATGAACTTGATAATGTGACGTTATAAAATAAACATAGTTGGCTATCTTATATCTGTGAAGTAGGACAAAGTTGTGGTTTTCACCGTAACAGTTAAGCTGGCCTTCACATGCATTTCCTCCCAGTTTAGCAAGCCAACTGGCAATTGATTAAATCAGCATGCTCTTTAAAAAAACTATGAATTAGGTGTCCGGTACTGATTTTAATTTTTCCATTTTCTGAAATTTAGTCAAGTTCAAGCTTATAAACACTGGTGTAATTCTTTTATTTAAGAGAAGAAAGTATAAGTAATTGAGTCGAACATTAGCCAAATATTATGTCATGCACAAAACTGATTTGTAGGAATCAAATTTTTGAGAAGCATTTATTGAAACTTGGCAAATTTTTAAATTGTCCCTCTTTTTCAG
Seq C2 exon
ATGGGGCATCCTGGCATGCATTATGCCCCAATGGGAATGCATCCTATGGGTCAGAGAGCGAATATGCCTCCTGTACCTCATGGAATGATGCCACAAATGATGCCCCCAATGGGAGGACCACCAATGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048151:ENSBTAT00000064349:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.898
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGTGTAGCGGCAGTGGC
R:
TTGTCCCATTGGTGGTCCTCC
Band lengths:
216-1454
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]