RnoINT0118337 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38701909-38703298:-
Coord C1 exon
chr3:38703245-38703298
Coord A exon
chr3:38701934-38703244
Coord C2 exon
chr3:38701909-38701933
Length
1311 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
TTTTCTGTTTTCTTTAATAGCCA
3' ss Score
9.65
Exon sequences
Seq C1 exon
GATACCAGAATACCATTGTTGCTGGAGGTCTTATTACAAAATCAAACCTGCATG
Seq A exon
GTGAGCTGCTTTGATAATTCATTTTCTGTTATATTTAACATTTAGAGTATGTCACTAATTTTCACTAACCATGAATGGATAAATCTGCAGTGAAAGACATTAATTCAAACAATTACTTCTGTATAAAAGTTATATTATAAATGAGCTTAAAGTGTTTAAAATTTTGTCTTGGTATTTTAAATAAACATGGACGTTGAACAGGTTTACATACAAACTTTTAGTATCCCTCAGAATGTTGGTGCATGCAGGGGACATGTGATTAAGCTTAATCATGATAGTAAGTTGATCTGAAGTTGATCTTAAGACAGTTATTTTGTCAACATATCTGCTTACACTTAATACTGACTTTGGTTTAGTATCATGAAACAGTATTTTTTTCTGAAAGTTAAATGAATATATAAATTATATAGTTATATATTTTATAGAAAGAAAGATTACTCATTACCATTCAAAATTTACAAAACTCAGGCCATAAAATAACACTCTGTAATGTGATTACTTTACTCTTCTTGAAATAGAATCCTTTATTAAATTGATGAGATCAGCTAGGTAAAGGTTATAGGAAAGTGGCAGAACTTTATATCATATTAGTTATGATTACTTTTTATGTGGATATTTTTCCATCTTAAAATAGATTTTCAGAAATATTTTCCTTATAGAGTCATAGTTGTTAAAATGTTGTTACATACATGGAGCCCCTCATTCTCTAGGGATACAAAGTTAAAGAACGTGTTTTACCATCAAATTAAAGTTTATCTGAGCCTAGAGTGCAAACAAATACTGAGTATTTAAATCTTTAAATCTCTGTTTAATTGTCTGAGTAGGAGCTTATAATTATTTTATCACTAGAATCACAAATTGCTCTTCAACAGAGTATCAAGCTCATTTCTGATATGACTGCAAATGGTTGGTTTGCATAGCTGCTTATCTGGTTATCAGTGCTAATGTGAAAAATGGGCCAGAAATTTCATGAGTTCAATATCAATTTAAATTTAGTGTCTTTTAAAAAGTAGTCTCATCCCTGGAGACAATACTTTTGTATTCCTAAATTATAAATCTTTTCAGAGTGTGATTACATGGCCAGTAGCCTTTGGAAAAGATTGCTAACTAATCAAAATTGCTGTTGTAAAAAGTTTCATTGTTGTATTGAGGCTTTGAAACTAAAGTAAGCACTTGCTCTTTAAAGCAAGTTTTTATTGTCAGATGGTAAATTAAATGATGAAATTATGGTACTTTCCTCTTCTTTTAGAGTTTGTTTTCAGTGGCTATATTTAAGAAACTACTTGATAACTTTTCTGTTTTCTTTAATAG
Seq C2 exon
CCATGATCAAAGCAGAAGAAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.123 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
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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]