RnoINT0118332 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38682146-38684296:-
Coord C1 exon
chr3:38684165-38684296
Coord A exon
chr3:38682941-38684164
Coord C2 exon
chr3:38682146-38682940
Length
1224 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
TATGTCAAATGTCTTTGCAGGGT
3' ss Score
8.95
Exon sequences
Seq C1 exon
GACTCTCCAGAATCAGATACTGAACGAGAGAAGGATAAAAAAGAAAAAGATCGGGAAAGTGAAAAAGACAGAAGTAGGCAGAGATCAGAATCAAAACACAAATCACCTAAGAAAAAGACTGGAAAGGATTCT
Seq A exon
GTAAGTACTGAAAATTGTTTCTTTCCTGAATTCAGAAAATCAAAAATGGATTCCCTCATAAAAACCTTGATGGTGCTTATAGGATAGGCTTTTTTTCTTAGTCTGCTAACAAAAAAGAAAGGAATACATTTTCTTCACTGCTTATCAAATAGATTTCTGGTACCATTTATTCATTCATTTCCTGCCTGTATTAGAAGGGAATGCTTCTAGGGATGAAATAAAAAGTAATAGATTTCTGTCGTCGTCATCCCCCCCCCCTGTTTTACACACACACACACACACACACAGACACAGACACAGACACCTTTTTAGAATATAAAATTTAGAAGGCTCAAATCAGGGTTTCTCTAGATAGCCATAGTAATGTTGCTCATAAATTCAGTTTCAAGAAGTAGCATCCCAACAACTAGTATAGACAGTCACGGGAAAACAGGAAATGGATTCATAAGTTATTATCACAGTGCTTGAGTCCTCTTGTGCACGACAGTGTCAGGACATACAGTAGCATCAGTTTCTTGGTTTTGCCATTTGTTGCACAGACTTGCTTTGTGCCCTCGGTGAAGAGAAGCCTTTCTACTTACAGCAGGATGTTCTGATCCATTGACAAGAGTGTTGCCGGGGATTGTTTTTTGTATTTTTGTTGAGTTTTTTGTTTTGTCTTGTTTTGGGATTTTTTTTTTTTAGCCTTCTTTGTTTCTTGTTTTTTAAATAATTTTCTACAATGTATTTTGATCATATTCAAACCCCCCCTTTTTTTTAATGTTTTGAATGAATCTGAGTCACAGCCTTCATGAAGAGTGAATCACTATACTTATTCCTTCTGTAGCAGTGGTTTAAACATCTCAGGAGCACTCCACTTTGAGGTTATATCTCAGATATAAGTCTTGTCTGTGTGTTTTTGAGCATAAGATTAGAGAACATATAGAGTCTAAGTCTAAAACTTAAATTGCTTTACAGGATTACCTAAAATCTATAAAATTAGCAAAAGCCATACAGCCTAGGAAGTGGGCACACACATGGCTTCCATTTTACCCTCTGATGACATCCAAGGGATGTTTAATAACCAACTGTTGGGTTTTAAGGCCAAACATCAGTTTGAAGTCCCTGTGAAATGTGTTTGTGTGGCTGAAATTCCATTTCTATTTTAGAATCTTTTTACGGTTTCAGTTTTTGTACCCTCTTCAGGATGAACTTCAATTGTAATTATGTCAAATGTCTTTGCAG
Seq C2 exon
GGTAACTGGGATACTTCTGGCAGTGAACTGAGTGAAGGGGAATTAGAAAAGCGCAGAAGAACCCTTTTGGAGCAACTGGACGATGATCAATAAATTATACCAAATATATGTTTATAGTATGATTTAAAGTCTAATTCAGACCAGGGATTATTTTAAGTCCAATTTACATAACACTGGGTTTTAATTGTGTCACAGGAAAAAAGTGCATTTATGTATTGTTATTGTGGACTTTATAAAAGCAAAGGAAATTGAAAATAACTTGATTCTGTCTCAAGAATCATATTTTCCTATGGTGATAACTGTCTCTCTGTGACCCTTTCATAGGGCACTACAGGATGGATTAAAAGTGGCAATTGAATGATAGCTGCAGACGTCTCTGCTTTGTTTTAAGTCAGGAGGTGACCTGATTTCCTTTATACAAGTTGGATTTTGAAGATACAATGACAATTTTTTGATAATGTAGTACAAAAAAAGCACCAGCAACCTATGAGAAGACTGCTTTTTTGTGCACTACTGAACTGGTTAAAGCCAACGTGAACTTTTCTGGTGAGCTCTTAAGAAATAGGTGTTTTTGATGGAAACTGGGTAGACCTCTAATGTAGTGGTGCCAATGAGCGCTGCTGTAATAAAGACACCATTATTTTTTATGGAACATCTGAACATTTTAAAAAGGCTCATGAGGGCATTATTTTGGGCATCTATTTTGAGGTGATGTTTTAAAATAGCTAACATCAAGTCAAATTGTAAATTAGTTTAAATATATTGCCTTAAGGACCTACTAAAGAATGTGCCACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:25
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
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACCTAAGAAAAAGACTGGAAAGGA
R:
TGAAAGGGTCACAGAGAGACAGT
Band lengths:
351-1575
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]