RnoINT0162669 @ rn6
Intron Retention
Gene
ENSRNOG00000020485 | Vav3
Description
vav guanine nucleotide exchange factor 3 [Source:RGD Symbol;Acc:1565941]
Coordinates
chr2:212427056-212428715:+
Coord C1 exon
chr2:212427056-212427141
Coord A exon
chr2:212427142-212428582
Coord C2 exon
chr2:212428583-212428715
Length
1441 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCGT
5' ss Score
9.49
3' ss Seq
GCACTGTCTCTCCTTCACAGGCA
3' ss Score
10.85
Exon sequences
Seq C1 exon
AACCAGCCCGTTTTGCTCTTTGGGCGACCGCAGGGAGACGGTGAAATCCGAATAACCACACTGGACAAGCATACGAAACAAGAAAG
Seq A exon
GTGCGTGGCACACTGTGCACTCTCACAGTAGTAGCTGCTATCACAGCTATTCTAGGATGGGTGGCAGTGCGCGCAGGCCAGGGGGCGGCCAGTCACAGGTCCCTTACCTTCTTTAACGTATGTTCCATACATTACTTCTCTTTCTAGCCTGCACTCTGTTGATTCGCCTAAGATTTTAGGTGCTAGATAAAAATGTTAGGACATAAGATGCATCTCAGTCATGAAACGCCATCAGACAATTGCTGTAAAACCACGATCACCTTTTTAAAAAAGGCTCATTGAAAATTAACTGAAAATAATGGAATTCATCCTAGAAAGCAATGCGGAATGGGAACTACTTAATAATGTTTTTATTTAGGGAGATCTTTAGGCAGAGTCCTTGAATGTCCTAAGTACCCTTGGCCTTTTATTCTTTGTCACAACAGGTGATTGTCAGACAGATGCTTTTGTGGGGGATTTTCTGGACTCTTTGTAGAAGCAGAAGTCTGCCAGCAGGGGGCAGCATTGGCCCTTGTTTCCACCTTGATACCCTGACTCCTCAGGTAGCTCTCTGGAGCCACACGTTTGACTTTGAAGATGAGGAAAGTGTTTGAACACCAGGAATGTGTCCTTGTCACAATCACTGGCTAAGAATAAGTGTGTTAATCACTGAGAGTTTTAAAAAGCACATGTTTATTGGGGTTGGATGATAAGGTTAGAAGCTTCGTTTCCTTCCCCAATTAATGTTGCTTTTAATAAAAAAAAATTAGCACAGAAACTTAACCATCACCTTCCTGGCTTGCAGTTTCTCTTACACCCAAGCTACGCTTAAGGTGACCCATTAAATTGTGACACTGAACACAAGGAGTGAAGGCACAGGTTCTAAAGTTAGCCCGGGTGTGATCTATATCTGCCAGATCATCAGTGTAAGGTTTGGCAATTTACATACAACCCTCTGCCCCCGGCGTGGGTCTGCTCACCCAGGGTGAGAGTGGGGACCCCAGGAACTTACTTTATGTCCTGTTTGTGGAATGGGTGAACAGTTCTCAAGGCTTTTGATTGATAACTATTATGGTTATAGGCGATCTGTCCTGACTGAGTATTTTTCTGAGACTCTAGCATTTAAATAAAAAGAGAGCAATTATTCATGAGTAGCTTTATGGCTATCCCAGTGAATATTGACTCTAAAGTGTATGGACTGCTTTTCTAATGAGCCTTCCCTTTCTTTTTGTTAAAATGGGGGGAACTGGGGTGGAATGGCACCATTTCTCCTTCTGCATGGTGGTGAAGGACAGTGATGTTCCTGTGGGCCTGTATCCCTTATCGCTTTCACCGTGCAGCCCTGCCTGTGACCCTTAATGCAGGAGTACGCTTGGCTGGTGCAGTCTCGTCTTGCCAGGGAAAACGATACGTGCCCGTAAACCGTTGGCTGTCAGTCACCCGCACTGTCTCTCCTTCACAG
Seq C2 exon
GCATATCTTCTTATTCGATCTGGCAGTGATTGTCTGTAAAAGGAAAGGGGATAACTACGAGATGAAGGAAATAATAGATCTCCAGCAGTACAAGATCGCCAACAACCCTACCACGGATAAAGAGAATAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020485:ENSRNOT00000027813:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.103 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0063014=Filamin=PU(5.9=65.5),PF0016924=PH=PU(17.8=62.1)
A:
NA
C2:
PF0063014=Filamin=FE(13.7=100),PF0016924=PH=FE(43.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACCAGCCCGTTTTGCTCTTT
R:
TATTCTCTTTATCCGTGGTAGGGT
Band lengths:
214-1655
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]