RnoINT0020984 @ rn6
Intron Retention
Gene
ENSRNOG00000006839 | Arl5a
Description
ADP-ribosylation factor like GTPase 5A [Source:RGD Symbol;Acc:621327]
Coordinates
chr3:37936871-37938697:-
Coord C1 exon
chr3:37938550-37938697
Coord A exon
chr3:37936955-37938549
Coord C2 exon
chr3:37936871-37936954
Length
1595 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
TTTTTTTGTAATTATTTTAGTTT
3' ss Score
8.16
Exon sequences
Seq C1 exon
TTCCATGAATGAAGTTGTACATACATCTCCTACAATAGGAAGCAATGTGGAAGAGATTGTGGTTAATAATACACGTTTCCTGATGTGGGATATTGGTGGCCAAGAATCCCTTCGTTCTTCCTGGAACACTTATTATACTAACACAGAG
Seq A exon
GTAACATTCCTAATGCTACTGTTTACATGAATGTCTGAGTCCTTGAGAAGCATTTGGCTTTGAGTCATTACAGTCTTTAAAAAGGAGCAGCATTTTGATTTTCGAGTGTGAGCCTAGTAGTTTTCCATTCCTTGTTTCCAAACCTTAACTCCATTCATCATCTGGTCTCTGTAGGGAGAGCTGGTGGGTGATCAGGCAGTCAGGTTGTTTGGTCCAGTAGCTACTCTTAAATGTCTTGCATTTCATGATTTCTGATTGCATTTCCTTCTTGCTGTTCATATGTGTCTAAGTGGGAGAAATCCCAGCCAAGTGAAAGGACTCCTCTGTGGTTTGAGTCCTAGCCAGTTTTTGCCGAGTATTTTCTTTTATGCAGTATAGTTGCAGTTGAAGAAATCTTTTAATTATAAAGCATTTTAGATATAATCATATGGTTTTATTTACATGTTTTGTTCCATGAGAATATTTCAAACCTATGACATTTAAATTCATCATCTAGGCCTATAAGTTGAAAGATTGAACCAGTTGTTTTTTTAGTGTGTATTATAAGGCCTTAAAAATACTCTGCACATACATATGTAAGGCTGATATTTAAATCATTAATGATACTACCAAGTGTCTCGTGGCCTGGCCCCAGCACTCCATTAGCATTTCGTCCTGTGATTGGAGGAATTGTATGTATGGCTTATAAAGGTCAATGTCAGACCCCCATACACAGTGCTGCAGGCATTAAATTGTGTCAGCCTTGAAAAGGGTTGATTCAAATGCCATCTAAAGTCTTCTGCCAGCAGACTACCCAGTGAAATGTTGTAGTTGCTGCAAACTAAGGAACAAAAGGCTAAAAACTATAGCATTTTATTTGGGAATTATTATCTAGTCCTAAAAATAAAAATGCAGTGTGTTTCGGTAACAGGTAATGTGAGCGATATAAGTATAGTAACTGAACATTTCCGTCTTCTTTGTGATGCTCTTGGTTAGTGCAGTGGGGTCTGCCCACCCCAGAAGCCACTGTTTGACCATGTGTTCATTACAGAGCTGTGCTTGCAGATAGCAGATGCTCTGGGCACAAGGAAGTACTTCTTTTATATGCCAGTTGATACCTTCAATTTGTTAATTTCTTTATCTGTCACATTGTCCTACCACACATACCGTTCTGGGTTTCAAAGAATAGTCGTAGTGATTGCCTGGAAGTAATTTACACTGGGACCTAAAGTGTTGGGGTTGGTTTTTGGTTTGGTTGGTTTTTTTGTTTGAAATAGTGTTATGGTGTAAATACAGGGATATAGGGATGTAGGCCTATTAGTGTTCATACAGTAGTTTTGAGAAGAAAAATGTTCTATTTTTATTAGAGTGTTAGCATAATATTCTTGGCTTTTGTTTTTTCTTTTAAAAACTAGTAAATGTATTTGAATTAGAAATGAGTCAGATCCTTAAGCTTTATAGCAAGTATGCTACGTATCCCTGGTTCTCTTACCATACAATAGATTTTATGTCTTAATATAAGTGTCATGTAATTAAATGCATAAGCACCTAATGAATTTTCAGATACCAAATTCTGTAAGTCACTAATGATCTTTTTTTTTTTGTAATTATTTTAG
Seq C2 exon
TTTGTAATAGTTGTGGTGGACAGCACAGACAGAGAAAGAATTTCTGTAACTAGAGAAGAGCTCTACAAAATGCTAGCCCACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006839:ENSRNOT00000009181:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002516=Arf=FE(28.5=100)
A:
NA
C2:
PF0002516=Arf=FE(15.7=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:
TCCATGAATGAAGTTGTACATACATC
R:
TCGTGGGCTAGCATTTTGTAGA
Band lengths:
230-1825
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]