DreINT0120532 @ danRer10
Intron Retention
Gene
ENSDARG00000058467 | prpf40a
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:ZFIN;Acc:ZDB-GENE-030131-274]
Coordinates
chr9:4748054-4751383:+
Coord C1 exon
chr9:4748054-4748115
Coord A exon
chr9:4748116-4751245
Coord C2 exon
chr9:4751246-4751383
Length
3130 bp
Sequences
Splice sites
5' ss Seq
TCTGTGAGT
5' ss Score
7
3' ss Seq
TACCACACGTCACCCTGCAGGGT
3' ss Score
6.34
Exon sequences
Seq C1 exon
AGAGAAGTTATAAGAAATCGAAGAAACACAAGAAGAAGGGAAAGAAAAGACGACATAAGTCT
Seq A exon
GTGAGTACAAACAACCTTGTCTTTTTTTTTTTCTTTTAAGCTTTTCATTTTACATCCAATTACTTCAAATGGTTGACTATGAACCTGATTATGTTGCTAAAAAGATTTAAATTTAATATATGTGTGAACAATGCATGAGTCAAAAGAAAATGTTTTCGACATTAAAAATAACAAAAATCATTCTACATTTTTGAGTAGCAATAATAATATTGCCAAAAAACAGGACATTAGAATGATTTCTGAGGGATTGTGTGATGCATCCTTGCGAGGCAAATCTTTTACCAAAAAAAAAAAAAAAATCCCAAATGCAAACTAGTTTTTAAGTTGTTAAGAGTGGCTGACTAGTATTGGTAAACTAGTAACATCAGAAAACAAGGCTAGCATAATAAAGACAGCTGATTGGGATTGACCGAGTTTATACAGCAAATGCCTTTCCATCTCCGATTCACACAACCAACCAATGAAAAAAAGTTTGCAAATTAAGGGATTTTTAGGGGTCTCGATATCATATAAAAATGTCTCTGATTTAAATGATATGATGCATTATTAAGCTTGTTTAATATGAATGTCCGACCTATAGAAACATTCCTAGAGTGTCAGTGGAAGTACAGTTACTCTTAAGTAAAAAAATGCTGGCTTCCACACAATTCCATCATGTTGTCCCAACACAAATCGATAAGGTTTACTTAATTGTTTTATGTTCATGTTTATGTTTGTAAAAACGATCAAGTTTTCTGAATAAAAACCATAAGAATTGTTTTACCAACTGATTTTAGCCTAATGACACTAATATACTAATATTAAACTCTTTTTATTTATCCTACAACATTGAGATAGTATTGTTTCGTGAGTTTAGTGTCAAGATTACCTATAGAATCTTGACTTGAGTGTATTGTTGTTTATTTTTTATTATATCTTGTTTTTCATGCGATACTACATAAATTGCATTAACACAGGCTGGTAAACCTGGAGTAATGGTGCTGAAAACCACAGGAATACATTTAATTTTTTATATAGTTAAGTGCACACAGCATGCCATATCATCTGATAATTGTAAGAAGTAATTCCAAAAAGCAACTGACTGTAATGCCACATATAACATCACAAAATAAGATGCATAAGCCTAGTTCAGTGACTCATCAGCCGGAATCAGCTGAGGTGAAGTTAGCTGTCACTCAAATGGCCACGCCCTTAATTATACAGACTTAATATAACCTAATATAAAGGAAATGGATGAGTTATAAAAAATTCACCCTCCTCACAGTTGTCATGAAGGGTAATAATAGCTATATGAACCAAAATTGTTCTTTGTACCAGGCTGTAAACACCCTTTTTTATGCTGTAAAGTTGACCATTCTAACAGTGGGGTCAATAGAAATTTGCTTCATATAGAGCCAGGACTAGCGGAATTTCGATGAATTACAGTTTCAGTTACTTCTGTGTTGTCTTCCCGAGGGAGAGTGTTAGGTTGCCGCTTGGTACAAATGCGTATGAAAAAGTATTGCTTTGTATATTGTTATAAGATGCTTTGTACAAGTGCGTATGAGAAGGCATTGCACATGTTTATTGCACAGTAGGGGAATATTAACTGTTCATGAGGTAGATGGCCTGGGGAAAGAAACTTTCGATGTGTCTGCCTGTTTTTGTGCTCTGTAGTGCCGACCAGACGGTAACAGTTCGAACAGGAAGTGTGCTGGGTGCGAGGCGTCCCGAGTGATTTTGCGAGCTCTTTTACTCACTCTGGAAGAGTACAGTTCTTGAAGTGTAGGAAGGGTAGTGCCAGTGATTCGGTTAGCAGTCCGGACTATTCGCTGTAGTCTAAGGAGGTCTGCTTTGGCAGCTGAGCCGAACCAGATGGTGTATGAAGTGCAGAGGATGGATTGGATGACAACTGAGTAGAACTGTACGAGCAGCTCCTGTGGGAGGTTGAACTTCCTCAGCTGATGAAGGAAGTACAGTCTCTGCTGGCCTTTCTTCACAATCATTGATTGCTAGACTGAAGATTCTCAGGGCGAGGGGGGCCAGATGTGAGTTTCTGCAGATTTTTTGTGATTCGAACATTTAGAAATGAAACTAAAGAGACGGTTGTTGTTTAATTTTATTGGTGATTCCTAATATGATATTTAATTGTAAGCTTGGGGAGCATTTTGGAGAATTTAATGGTTCCCCATTCAAACAGAATGTCTGAGCATACTGCCCAATAGGCGTTTCAAAGCTGGCCACTGAGTGAAATGACTTGCCTTAAAAGGACTTGCATAATAGATAAGAAAAATACTATGTGCTGGAATATCAAGTCAATTCCATGCGTGTTCAATAAGAAAAAGTCTGGAGAGTGTTTTCTTCAATGCCAAAAATATTAGTAATTTATTAGATACAAATTAATAATTAGATGACAGAGCTCTAGGCTACGTTACCCCAATGCAATACAAGAATTCAAGAGGTTCGCAACTAACTTGCATTTCCTGACAGCAGCATATATACACAACTGATATTAACAGGTGGAGTTTGGTGTAACGTCACTTATCATTCATTCTGCAGACCTTTGGCTCTTGTAACCCCCAGACATACTTCCTCTTTCCCCAACCCTTCTCTGCATACCAGAACTGAACAATTATGTGCATCTTCAATATATTTCACAACTTCTACAAAGATCATGCTCCTCCTTGTGGCATGTCCAGACAGAAGTCTGGAACAAACGCAAAATTTATTCTTACTCTGCTTTTTCCTCTGGTCAGCAGTTTTTCTAAGTATGCAGCACAGTAAAAAGAGGAAGTGTGTCTGGTCAAGATGTGTTGTAATACAATAAAAAAGATTAATTAATCTGTTAGTCTAAACATTTTTCTAATAAATAAAAACACAAAAGTAATACAAATGAATTCCTTTTCTCCAACATATGATTTGATTATTGGATAATTTGATAGTTGGAGCATTTTCCAAAATTTTTTCCTTCATGTTGAGAAAGAAACTCAAAAAGGTCTTAAAGTTGTATTTAGCCTATGGCTATTCCTGAAATGAGGTGCAATTCCTCATTTACTCTCATTAAGCACACATTAAGTTTTAATATTTCTAGTTTTACAAGGCTAATATAGGGTAATGAGCAATTTACGGAATACCACACGTCACCCTGCAG
Seq C2 exon
GGTTCCCCTGAGTCTGAAGGAGAGAGAGAGCGGAAAGGAAGAGAGAAGGACAAAGATAAAGAGAACGACAAATCCAGAGCCAAGCTGCGTGGAGAATCCAAACAGAAATCCCCCAAAAGAAAGAGTGCTAAAGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058467:ENSDART00000081326:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]