RnoINT0063973 @ rn6
Intron Retention
Gene
ENSRNOG00000017925 | Gapvd1
Description
GTPase activating protein and VPS9 domains 1 [Source:RGD Symbol;Acc:1307479]
Coordinates
chr3:13753748-13755056:-
Coord C1 exon
chr3:13754984-13755056
Coord A exon
chr3:13753946-13754983
Coord C2 exon
chr3:13753748-13753945
Length
1038 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATG
5' ss Score
8.73
3' ss Seq
TTGTCTGCCATCCCGCTCAGGTC
3' ss Score
8.35
Exon sequences
Seq C1 exon
GGTTCTGCATGAACACATCCAGAGATTATCTAAAGTAGTGACTGCAAACCACAGAGCTCTGCAGATCCCAGAG
Seq A exon
GTAATGTGGGCTTGCGTGTAGGTGGGTGGTGGTGCACCTGGAGAGTTAGCACTTCAGCAGGGCCCCGGGGGCCCGAGACGGAAGCAAGCACTGTTTTCCCAGGCGTTCCCAGGGAACTTCCAAGATGTAACTTCCTCTGTGTAGAGGACCATGGTGGAGGAGTGGGGCGAGCCGGTCGTAGGGTACCCCTTAAAGTAGCTCTGCTCCCAAACCCAGCTTCTGCCCCAGCTCTGCCCTCCTGGGCAGTGTGCTGCCACTGCACACCTTTAGGCTGGGCTTCCATTTCTGATGCAAACAAGAACTGTTCCAGAAGAAACGCTCAGTCTGTGTGGCCTCAGGACAGGTGCTTTCTCGGCACAGTGCCAGCTCTGTGAGATTTCTGTTTGCTAAAAATTCCTTATGATGAAACATTGAGCACTGCAGGGTTTTACATTTTCTTTGGTATGGGTTTTTTGTTGCTTGATGTTTGTTTGTTTGTTTGTTTGTTTGAGACAGCTCCCCCTACACACACACACACACACACACACACACACACACACACACACACACACACACACACGAGCGCGCGCACAGGGTCTCTACCTCAAGAGTAGAGACAGATTCTGTCCTCACTGACCTCAATCTTGCTATGTTGCCGACGCTGGCCTTAACCCCCTGACCCTCCTGCCTTGATCCCCAAGTGCTATGATCCCAAGCTTTCGCCACCGTCCTGGGCTTTTGTTCCTGAGGAAACACTGCAGCAAAGACCAGTAGTGGTGTGTCCATTGCCTTCTTGCTGCCGCTTGTCTGTGCTTTTGAACTCCACTAACTGGAAAGTCTCGTCCCAGCCTTGTAAGGGACTCACAGGGAGGTTGCGAGCTCCAGGCTCTGTGGCAGACCACCTCTGCCTCATGGCTAGGCTGCTATGTTTTGAGATAGGGTTTATCTTAGATGGCCGGGAAGGAAGTGGTCCCGGTCAGTTTGCTGGGGTGGGTCCTGTGGCTGCTGTGGAGACTGCTGCTGGGTTCATGATGTGATGTTGTCTGCCATCCCGCTCAG
Seq C2 exon
GTCTATCTTCGTGAGGCACCGTGGCCATCTGCACAGTCAGAAATCAGGACTATTAGTGCTTACAAGACGCCCCGGGACAAAGTGCAGTGCATCCTGAGAATGTGCTCCACTATCATGAACCTCCTGAGTCTGGCCAATGAGGACTCTGTCCCCGGGGCAGATGACTTTGTCCCCGTGTTGGTGTTTGTGTTGATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017925:ENSRNOT00000066961:25
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:
NO
A:
NA
C2:
PF0220413=VPS9=PU(56.3=87.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGCATGAACACATCCAGAGA
R:
CAACACAAACACCAACACGGG
Band lengths:
262-1300
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]