DreINT0120533 @ 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
chr9:4751246-4755652:+
Coord C1 exon
chr9:4751246-4751383
Coord A exon
chr9:4751384-4755036
Coord C2 exon
chr9:4755037-4755652
Length
3653 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TACATGTATGTGTTTGTCAGGGT
3' ss Score
5.8
Exon sequences
Seq C1 exon
GGTTCCCCTGAGTCTGAAGGAGAGAGAGAGCGGAAAGGAAGAGAGAAGGACAAAGATAAAGAGAACGACAAATCCAGAGCCAAGCTGCGTGGAGAATCCAAACAGAAATCCCCCAAAAGAAAGAGTGCTAAAGAAGAG
Seq A exon
GTGAGCACTCGTGTGTTGATGTTGCATTGTAGATATAGCAGTGTGCAAATATTCACATCACAAAATACACAATGTTGAATTGTGATTAGAATTAACCAGGAAGCAGTTCAGAATGAATCTATCTTTAAAAGCATGTGACTGAAATTTCAAGCTAACTTAAACCATTTTGGCACAAGTATTGATTAAATATGTGACTTTAAAGGGGAGCTGTTATGCAAAAATCCCTTTTATAAGGGGTTTAAGCACAGTTGTGTGACAGCATTGAGACAAAATAGCCAACCTAATTTTCATTCTTCAACATTATTTGGTGGCTGTTTTCAGCTGAAACTTCACACACTCTCTCAAGGGTTATCTGAAAGTTATTTTAGATCTTATTTCAGCACAATATTAATTGTGTTTTTATTACAGTAAATACTATACAGTGTTCTTTTACATTTGATCACATTGTTTGGTTACATTATCTTACTTCAGAATATCCAGAAAATCCTAACGCACTATTTCATTTGTATCTTTGTATTCATTTGTGCTCATCATTTGTTTATACTTTAAGGATGCTTTCACATCTTTAGTTCACTTCATTTGGTCCGGACCAAGGGCAATAAATGATACATTGTTGCATTTTCTGCCTTCTTTGGGTTGTTTTCACACCACACTGCTGGCTTTTTTCTGAACCAGTTGAAAAGAACCAAAATGTAGTCGAAATACAAAATTTGGTCTCTCTTACACAATGTGTCTTCTTTACAGTGGTCAAATTTATTAACTTACTAAGTAACGAACAAACGAATCATATTGTGACGATAACGAAGTTACTATATTAAAGCGTTACAGTATTAGCTACTGTCAAAAGCAATGCCGTTACAGTAACCCATTACTAGTATTCCGTTAATGCCCAACATTATTTATAATATACACATACTCTATAAAATTACCACAATGTTAGTCATGAGTTGGGCCTGACAGAATCTGTGCACATTTTTTGCTATTCCTGTGGAGAATTTAGTACACAATTTGTGGATTTATGCGTAATGATTTTGGAAGTATCATAACTAAAAACCTGATATATATATAAATAAAAAATAATACATTCTTAGCTTTTATTTAATGTGTTCAATGCAAATCCAATTAGATCCACTTATTTGGGAAACAAAGCCAGTCTCTTATATAATACATCTACTAAAAGACAGAAATTATTACTTAACAAACTGTATTGTAAATAAATCATATGAACATGTTAATATTACAATTATTATATCACAATAATATTAGGGAAATTAATTTAAAAACTGAATAAATGTAAATTTACACAAGTAAATACGTAGACTCAATTAGGGTTGGGCCGATAGACAATGCCATCGTCTATCGCCGATGGCCAATAGACAACATGATGCTGAGTCGGCATCGCCGATTCTCCGCCCCGCCCCCTTTCGCAAACCCACTCGTGAAAAATACACACTCAGGCCTGTTTACACTAATGCGTCTTAGTGTTCGTAGAACGAAAATGATCCACACCTTGTTTTACCTAGCATTTCTGAACAGCCCTCCGTCTGCTGAAAACGCACATCACGTGACCACACACACACTGTCATGCACTCGTCTGAGCTCCAGAGAGCAGTGCATGTCGGACAGTATGTCAAGGATGTACCGCTGGTTTGCGTTTCACCATAGTTGTTAAACGTGATATTCAGACATCCATAGTCTCCTGGAAGTTCCGTAAGTGTCCCGCAAATGCATAGAGACTCCCGGATGCCTGCAAACGACTCCCGGATGCCCGCAAACGAGTGATAATCTCCAGGAAATCGCTCCTCTCTCTCCCGGTCCTCAAATAGTTCGTGCACCCCTCACCACCGGATCCCTCCTCGCTCTTCAGACATGTCGTGCACACTCTGTCAAACACCGCCTCCTACATCGGGTCTGGATGCAGACCTGGTGCAGTGCAATCTGAGCTGCATCCAATGCTTTTTAATGGGCTCACCTAACCCCACCCCTAACCCTAGCCATCACAGTGACGTCACTCGCTCCATTTCAGTGCATTGTGTCTCACATTGCATCGCTGAGTAATGCATCATAAAGGCTGCATCCAGATACTATTGAAATTGGTCGTCATCGCCCAACCCTAAACTCGATGATCTAAAAATCTGTGGATTTCTGTGTGCGCAGATTTTTTGTGGGCCTAGTTAAGAGTTCTTTCCAAATAGTTATTGAAAGCAGACCTTTTATAGCCCTTTTTATAAGACGTAAAATAAGTCTCTGATGTGCCTAGAGTGGGTATGTGTGAAGTTTCAGCTCAAAATACCACACAGATCATCTTTTATAATTGCCCCTTTTAGGCTTTGATCCAAATTGTGCTGTTTTGTTGACTGTCACTTTACATTCAAATGAGATTGTGCTCTCAGTCCAACAACATTATGGAATCAGTCTGCCTAAAGAATGCTCCATATTTACAGCTGAAGCCAGCGCTTTACTTTTAGCATTGGAGTTTATAGAAAATGCCCAACAAAAGAAATCTATCATTTTTACAGACTCTAAATCATGCCTCCAAGTTATGGAATCTTCAAAGAATGATCATCTTTTGATTGATAATATTTGAACTAAAGTTCACCAACTACAAAATCAGTTTTATCACATCATTTTCTGCTGGGTTCCAGGACATGTCGGACTTTCAGGGAATGAGCGAGCTGATGCAGCTGCTAAAGATGCTTTTGAAGCAAGTAGTGAACAAATGGCAAATCCCTCCGTCAGAGATGAAACCTTTTATAAACGCTTACATTTTAAACAAGTGGCAAAAGGAATGGGATGCATTAGAAAACAATAAATTACACGAAATCCAACCTGAAATTTCACACAGAATTTTAAGACATTTTAAGAATCGATTTGATCAAGTAGTTTTTACCAGATGTCGTATTGGGCAAACGAGAATAACACATGGTTTTCTGCTCCAAGGTGAAAACCCTACTCAGTGTTTGTTCTGCAAAACTCCTCTTACTGTAAAACATATTTTACTGGACTGTACTGCTTTTACTGATTCCAGAAGGACTTTTTTATGAAAAGGACATTTTTAACAAAGTGAAACCAGAGAAGATTTTAGAATTTTTATCATGTATTAACACAAAAAAATCTTATTTAATTTGTTTTATTTTGTTTGTGGATTTTTAAATTGTATATTTATTGTTGAAAGATTCCTGCCATGAAAATAGCCTTGGTTGCTGACATGGCATTAAATAAAAAAAACAAAACAAAAATACATTACATTACATGTGCTCTCAGTCCTCTTATGAAAATGACCTTCAACAAGTACAGAGTGTAGACTCAAATGGCAGACAGCTGCTTCTCACTCAGGGCTGTCTATGCTAATGAGGGGGAGATCATCACTAATGGGCGGGGCTTTCCTCCTCTGATGACACGTACAAAGAGAGAATGCCAATCAAAGTGTTTCTGCAGACGGTTTCATCAAGTGCGATTTATAAAACAAAAGATTTCATACATTTTGATCATTAGAGGCTGGCTATTTTTACACACTGCTGCCATATAGAAGAGATTTTTGCATAGTAGGTCCCCTTTAATACATTAATATTGCAATATACAATCACAGACAAACCAAATGTTGTTTGAATATCTGAATAGATCATATCTGAATACATGTATGTGTTTGTCAG
Seq C2 exon
GGTGGATGGGATACGTCTGGCAGTGAACTGAGTGAAGGAGAGCTGGAGAAGAGGCGGCGCACACTTCTAGAGCAGCTGGATGCTCCGTAAATCCCTCTGTTTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTCCATCTCCGCCTCTCTCTCTTGCATTCCTGTAATGTTGTGTCCTCCTAGAGTTTGCTGGCAGAGTCTCTATCAGCATCTGAGCAGTGGATATTCAGATGAATCTCTGCGAGAGACACGGTTTGTCTGAACATCAGCACTCTTCTTCATCTGGGCACATGCTTGATTTTGTTTTTGTAAGATTATTTTCAGAGGTTGCAAGCGTTATGTTGCCTTTAACTGCAGAACCTTTTTTTAGGTAGTTGTAAATTTGTTATTGCCAATAGTTTTAAACATTACCGGAGGAAATTACCAAGCCTGAAGAAAACAAAGAACACACCTGATATTCAGCTTCAGATTAATCTGTACAATTGTATGTGGAAGCCATTTTTGGAAAGCAATGTTATTATCCGTATGAAAGTAAATCAAATATCTGCAGCATTGTTTTCAACTTGAATTTTGACAAATAAACTATGAAAAAAGGTTTCTTTGTTGCTTTATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058467:ENSDART00000081326:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
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]