RnoINT0118339 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140967282-140968206:+
Coord C1 exon
chr7:140967282-140967368
Coord A exon
chr7:140967369-140968062
Coord C2 exon
chr7:140968063-140968206
Length
694 bp
Sequences
Splice sites
5' ss Seq
TTCGTAAGT
5' ss Score
9.77
3' ss Seq
TTTTCTTTCCTCATTTCCAGATG
3' ss Score
12.87
Exon sequences
Seq C1 exon
CAACAGTCGGTTCCCGATTCTGGTCCCCGGCCCCCAGCAGCGCCTGCCCCCTTCCCACCGGGGCCCCCCATGATGCCACCACCCTTC
Seq A exon
GTAAGTTTTATGTGTTTCCCTGGGCTTGGCTTTTCCAGCCTGCACCCTCAGTCCCTCCCTACCACTGCCATGTTGTCAGGAAGGACCTGTTTCACACCCTTTTGCTGCCTTTGGAAGATGGGTGGTGTTGAGCACTAGGGCGGGGGAGAGCTGCTTTTAAGCTCTAGTCTGTACAGTGACAATACTCCTTTTTCATTTTGTCCTTGGGATACTAGGGGCTGGAGGTCGGAGAAATGGAAGGGGAAGACTTTCCGTAGAGTGAGGCCTGGAGAGGCTCCTTTCTTTTTCATTGTTCCTTACTGTGCTTATAAAAGCCTCTGACTTTGGGCTGGAATAGCATTGGTGGCCATGAGTCAGAAAGGGATGGAGGCAAGAGACTAGGGTCCTTGCCTTGTCCCTTCACCTGCAGGTGTCAGGGGAGTGCCGGCTCTGTTTCCTTGCCCTGTCCTCTCCCTTCCTCACTTGTTAGGAAGCTGTTTGCTTGCCATCATGCCTGAGAACTCCTGGGTTATCTGTCTTTCTCAGTAGTGAGGGGGGAGACAGTCTTATGCCTTTTACTTCTCAATGGAAAGTCTTGGAATCACCTCTAGGCCAGGATGAGGGCTGGGTAGTTCCTGAGGTAGGTGGTCCTGAGATGGGATCCTATCTAAGACAGTATCCTCTGTTTAGTTTCTTTTTCTTTCCTCATTTCCAG
Seq C2 exon
ATGCCCCCTCCAGGGCTCCCACCTCCTTTTCCTCCGATGGGGCTCCCCCCTATGAGTCAGAGACCTCCAGCCATCCCCCCCATGCCACCTGGCATATTGCCCCCAATGCTTCCACCAATGGGGGCACCGCCTCCACTTACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:1
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=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:
GGTTCCCGATTCTGGTCCCC
R:
CTGTGTAAGTGGAGGCGGTG
Band lengths:
223-917
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]