RnoINT0063966 @ rn6
Intron Retention
Gene
ENSRNOG00000017925 | Gapvd1
Description
GTPase activating protein and VPS9 domains 1 [Source:RGD Symbol;Acc:1307479]
Coordinates
chr3:13765755-13767690:-
Coord C1 exon
chr3:13767568-13767690
Coord A exon
chr3:13765882-13767567
Coord C2 exon
chr3:13765755-13765881
Length
1686 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAA
5' ss Score
5.07
3' ss Seq
TGGGGGCTGGTTTTGTTTAGAGG
3' ss Score
3.34
Exon sequences
Seq C1 exon
ACGAGCCCAGCCCTAGGCTCAGTGCACAAGCTCAGGTTGCGGAAGACATTCTGGACAAATACCGAAATGCCATTAAACGGACCAGCCCCAGTGAAGGAGCACTGGCAAATGATGAGAGTACAG
Seq A exon
GTGAAAATCACCATAGGTTTGGGCAGTGACAGCCACCTTAGAGATGAGCTAAGGCAGACTGACGCAGCCTGTAGAGCGGGGCGTCCGGAGGACGTCATAGCTTTTGTAAGCATGTTAGCTCAGTATATCCCTCTCTGCAGCTTCTCAGTAAACCTGGGCACCCTAGATGTTCAGATGGTTTAGGGTCATCTAATGAGGCTGGGGTGACAGTCCAGAGGACCTTGGTGCGTGTTTTAGTGAGAAGGGAATCCCCCCCCCCCTTTTTCTTTTTACTGTTTGGAGAAGTGAGATTTGATGTAGTTGTGGACTTTTAGCAGAGCTGTGGTGGCCAACTCAGGCTAAGGTACCCTTGTTGCTTGGTACTTCTTTTCTACAAGGCTCCCCCCCTCGGAATACTAACTACCTATCATAAAAATATGGAGTCCTCAAGACACATGAAGGGAAAGCAAACGCACGTAGAGCATGAGCAGCAGCTTGCTAAACCTGCCCCACGCCCTGCCCACAGAGCAGGACTACGAGCTGTTCCAAGGAGGGCAGGGGGGTTCTACCTCTCTGTTTTCTTTCTCAGGGTTAGGGTGGTAAGACAGACTCTCACTCTCAAGGGCAGGCTGTCCCCAAACTCAGAATCCTCCTGCCTGCCTCCCAAGGGCCAAATTTCAGCGCAGCAAAGGTTATTAAATTTGACAGTTACCAGCATTTTGTCATAATTTCCTAGACAGTATTTAAGAACATTTTATTCCTTTTGACTTAAAACTGTTTTTGTTTATTTGTTTGTTGTTTTTCTTTTTTTTTGAGACAGAGTCTCATGTAGCCCAGGCTTGTATCAAACTCACAGTAACACTTACTTCTTGATGTTTTTAAAGATGAATTGCATTTTGTGTGTGTGTCTTTTTGCCTGTGATAAGTGCAGTACATGTGTGTGGTAACCATAGAGGCTAGAAAACGGGGTTAGATCTCTGGAACTGTAGTTACACACAGTTGCTGGGCATAGTATGGGCACTGTGAACCAATCCTGGGTCCTCTGAAAGAGAAACCCTTGTCTAGGTCTCTAGCCCTTGACTTCTTGACTTCCTGTCTCCACTTCAGCTGTTAGGGGTGCATCTCCACCCCTATCTTACTTGGTGCTCAGGATGGGACCCGAGGACTCTCACACGCCAAGCGAGCCCTCTCTTGCGGAGCCCCATGCCCCTGACTATATGTGTGTATATTGTCTCGGATTGACTGACTAAAAGCATGACCAGTGTGGGAATCTTGGTTCTGGCCTCGGTGTGTTTGTGAGCTGGTCCCTGGCTAAGTCTTAGGTGTGAGAGGGCTTTGTTGAGGAGAATCAGGAGACGTGAGTGAGTGTCTGTTCCAGCATTTGGAGGAGTCCATGTCTAAAGAGAAATGGCCTTTTGAGGCTCTTACTTGTGTGGTTCAGGGATTCTGGACTTTATTAAGTTATACAATTGGATTCTTACAAGTCGGACACTGTGGCAAGAAGTACAGCTACTCTCTGCTCTAATGTCTGCCGTCTTGCCTTGGCTGTTGATCACCTCATTCTATGTCTGATATTCGTTTTCTTTTCCCAAGAACTCTTATCACAAGATAAACTGACTTTTGATTAAATTTCTCTGAATACCTGCTAGTACCTGACATTTCCATATTAACTGGGCTATCCTTTTCTTGGGGGCTGGTTTTGTTTAG
Seq C2 exon
AGGTCATGGGTGATGGTGAAAGTGCTCACGATTCTCCTCGTGAGGAGCTGCAGAACATGTCAGCTGACGACCTCCCAGACTCTGCGAGCCAAGCAGCTCACCCTCAGGACTCTGCCCTCTCTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017925:ENSRNOT00000066961:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.930
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CTAGGCTCAGTGCACAAGCTC
R:
CTGTAAGAGAGGGCAGAGTCCT
Band lengths:
238-1924
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]