DreINT0120523 @ 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
chr9:4738739-4740275:+
Coord C1 exon
chr9:4738739-4738872
Coord A exon
chr9:4738873-4740160
Coord C2 exon
chr9:4740161-4740275
Length
1288 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACT
5' ss Score
6.6
3' ss Seq
GAATGTTATTTGTGTTTCAGAAA
3' ss Score
7.76
Exon sequences
Seq C1 exon
ACATGGACAAGGAAGATGCGCTGATCTGTTTTGAGGAACACATCCGTGCTCTTGAGAAAGAGGAAGAAGATGAGAAGCAGAAAACTCTGCTGCGCGAGAGACGTCGACAGCGCAAGAACAGAGAGTCTTTTCAG
Seq A exon
GTGACTCACCTCCACACACACACACACACACACACGTGACTCCGTCTCATTCGTAATTTGCTTCCCGCGTCCAGGCCTATTGAAATCAAAACCTTTCAACTTAATTAATTGGAACTTGATGCTGGAATATCAGCAAATGCCAGTGTTGACAGATCGCCTGTTTGACCTAGTATGGAAAATCATCACGCTGTGATGCTAACAAAGAGAATGCTGAAGCAACTCTTGGCTTTATTGAGACTCTGAACTTCATTAACCCCAAATATTCATCATTCCTTCCTCAAGCAAATTTGTAAATATTAGATCTATTCAGCAATAATGTTAATTGCATTGGCATATTTAGCTGACGTTTTCCCAGCTTGTAGTAGTCGATCAAAAAGCTTTTTAGTTTCTTATGACTATACACTAGCAGTGGAATTTACTGCGATATGACGGGGCTTGATCATAATCAAGGGGCTTGTTCAAAGGTTGATCATAGTCTCTTCCAAAAAAAAGAAGAGTATCTTCTTCAACAGAAAAATTGATCACAGTTACAGCCAGCATCCCACAAAAAGCACTTCGAGCCTCATTTTGTGCATATCAAATCGCAAAATCCGAAAAGCCACACACCATATATTGTTGACTGCTTTGAATGGATAAATTTTTTTACCCATTTTTCCATATTAAAATATTATGGTGGGTCTTGAGATTGAATTACTTGGCTAGGTGGGTCCCTGAATAAAAAAGTTTGGGAATCCCTGGTATAAACAATGTGGCCAGCTACTTGTACCGAGAGAATGCCTTGCTACCATGGAGACATAAGAGACGGACTTCACCATAGTCACAACAGATGTTTGATAGTATGTTTTGGATCGGCCTCATCTGCTTGATACTTGATCCGGCCAAAAATCATCATTCAGCTCTATATCTGATATCTGATCCATAAACATTATACTAGATGGGAAATATTGCCATTATTTTATTGAACCTAATATTTGACTTTATCAGTGTGGTTTGAATAAAATGCTGCTCTTTAAACTTGTACTACAAAATCTGCATCTGACAATGCCACTTTACTGACAGTAGTATTGACTTTTTTTAATCAAATGTAACTAATTTTGCACCTATAGTTGTTTATTCTGTTTTGTTATGATTGGTAGTTATTACTGTTTTAATTACAAAATCAATTCGTCATAAAAGTGGAAACGTCTTAATCAGTATTGACATTGGTCAACATGAGAACTGTTTAACCTCTGATGAGTCACTGATTAGGAAAAAGAGTTCATGGTTGTGAATGTTATTTGTGTTTCAG
Seq C2 exon
AAATTCCTGGATGAGCTTCATGATCATGGGCAGCTGCACTCCATGTCTGCCTGGATGGAGATGTACCCAACCATCAGTGCCGATATTCGCTTCAGCAACATGCTGGGCCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058467:ENSDART00000081326:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.289 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(23.2=28.9),PF0184614=FF=PU(10.7=13.3)
A:
NA
C2:
PF0184614=FF=FE(67.9=100)
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:
ATGGACAAGGAAGATGCGCTG
R:
TTGCTGAAGCGAATATCGGCA
Band lengths:
230-1518
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]