BtaINT0118332 @ bosTau6
Intron Retention
Gene
ENSBTAG00000048151 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:43620867-43622923:+
Coord C1 exon
chr2:43620867-43620977
Coord A exon
chr2:43620978-43622802
Coord C2 exon
chr2:43622803-43622923
Length
1825 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
TTTATTTTTTTTCACTTCAGCAA
3' ss Score
7.61
Exon sequences
Seq C1 exon
AAATCAATGTGGACTGAACATAAATCACCTGATGGAAGGACCTACTACTACAATACTGAAACAAAACAGTCTACTTGGGAGAAACCAGATGATCTTAAAACTCCTGCTGAG
Seq A exon
GTAAAAGTTTGTTAGAGAGATTAAACAGTTTTCTTTTCTTTTTTTTATTTTAAGGGTTTTGGTATGTATTTGGCTTTCCAAAGAATCAGTTCAGTTCAGTTCAGTCACTCAGTTGTGTCCAACTCTTTGCGACCCCATGAATCGCAGCATGCCAGGCCTCCCTGTCCATCACCAACTCCCGGAGTTCACTCAGACTCACGTCCATCGAGTCAGTGATGCCATCCAGGCATCTCATCCTCTGTCGTCCCCTTCTCCTCCTGCCCCCAATCCCTCCCAGCATCAGAGTCTTTTCCAATGAGTCAACTCTTCACATGAGGTGGCCAAGTATTGGAGTTTCAGCTTCAGCATCAGTCCTTCCAATGAACACCCAGGACTGATCTCCTTTTGGATGAACTGGTTGGATCTCCTTGCAGTCCTAGGGACTCTCAAGAGTCTTCTCCAATACCACAATTCAAAAGCATCAATTCTTTGGCGCTTAGCTTTCTTCACAGTCCAACTCTCACATCCATACGTGAGGAATAGTACCACTTATATCAGAAAAGAATGCTGCAAAGGCATTCAGAGGAGAAAAGGGTTTGTACAGTCACACCAGTAAGAAAAAAGACAAAATTCATTCCTTTCTGTGAGCAAACCAAGTTTTTTGGTTTTGGTTTTTTGTTTTTTTTTTTTAACTGATTTTTACCCCTGCTCAGGAACTTTTGTCAGGTGGCTATCAATTAAAAGAAAAGTGACTTAAAGACTAAATTGGAAGGAAAAAAGTACTGTCTCTCCACTTGGTCTTTATCTTCCTCTTTATATCAAACCTGAGTGATTTCAGATGTCTTCTTCTGGGTGCTTATGTTTTTCCAATGAAGCTAGTGTCATGGAGATGAAGTTAAATTAACATACTTCCATCTTTTAGAATGGGAAATTATGTCTTTGAAAAATACAACCCCCACCTGAGTATGTATTATTTCATTTTATGTTGTAAACTATACAAATATGAAAGTAAGATTGAAGGAATAAACTGGGTAAGCAGTGTTCCATTTGGTTTAATTAGGAACTCTGGTGTTCTAAGTGAGAGTTGATCTGGCATTTCAAAGCTATATTTGAAAGTTTTTCCTAGTTGGCATCTTTTCTTATCCACACCCCCCGCCCCCCCCCCCCCGTTCTTAATTAAGAATTTGAAGAGGTAAAAAGTGTTTTTCAGGCCACCACAGTAATGATAGTATAGCAATATTTGGGAAGGGAATTTGGCAGATGATAAAATTTTTATTTATCCCATAGATATTTGCCCCAGACACTGATTAGATTTGTTTTCAATAGAATTCTCATCCCACCACCATAACAGGTTCTGTGTGTTGGGTTTTAAGTATTATTTAAACTGCTTCCTTACATGATGTAGTCACATAGGTTTGTGATAAATTGTTTGTGAAACTGAAATCTAAACATGACTAAATCAGATTTTGCTTTCTCTTAAATTTTTTTTTTCCTATTTGTATTAGTATTTGTGGAAAATGGATGGTAATTATTACCTGTGGTGAGTTGTAAATGGCAAGAGCATTCAAATCTGGATTTGAAAATCAGATAGACCTGGTTTTGAATCTTGTCTTTGCCCCTTAATAGGTACATTACCTTAGACAAACATAGTACATCCAAATAACTTAACATCTCTTATTTAGTAAGTATCCTGCAGTGGTTGTTTATATTGTCACCATCTTGCAAGGTTTAGAATTGTATGGGTTGATAATACCTAGTAAAATCAGTGATGTAAATGATGAAAACAGACTAAATCTATTACTGCTATCTGAAGTTTTTTTTTATTTTTTATTTTTTTTCACTTCAG
Seq C2 exon
CAACTTTTATCTAAATGCCCTTGGAAGGAGTACAAGTCTGACTCTGGAAAGCCTTATTATTACAATTCTCAAACAAAAGAATCTCGCTGGGCCAAACCTAAAGAACTTGAAGATCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000048151:ENSBTAT00000064349:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.743 A=NA C2=0.476
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(93.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=73.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCAATGTGGACTGAACATAAATCAC
R:
CTTCAAGATCTTCAAGTTCTTTAGGT
Band lengths:
230-2055
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]