Special

DmeINT0029108 @ dm6

Intron Retention

Gene
Description
The gene Vav guanine nucleotide exchange factor is referred to in FlyBase by the symbol DmelVav (CG7893, FBgn0040068). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (3 unique). Gene sequence location is X:19261820..19273280. Its molecular function is described by: Ras guanyl-nucleotide exchange factor activity; Rac guanyl-nucleotide exchange factor activity. It is involved in the biological process described with 20 unique terms, many of which group under: embryo development ending in birth or egg hatching; regulation of adherens junction organization; epithelial cell migration; protein phosphorylation; positive regulation of catalytic activity. 17 alleles are reported. The phenotypes of these alleles manifest in: eye-antennal disc; embryonic/larval dorsal branch; midline crossing tract; longitudinal connective; dorsal closure embryo. The phenotypic classes of alleles include: increased mortality during development; some die during pupal stage; phenotype; immune response defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages.
Coordinates
chrX:19269257-19269651:+
Coord C1 exon
chrX:19269257-19269365
Coord A exon
chrX:19269366-19269483
Coord C2 exon
chrX:19269484-19269651
Length
118 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAA
5' ss Score
6.68
3' ss Seq
TGTTCTTCCTTCCCCTCTAGACC
3' ss Score
12
Exon sequences
Seq C1 exon
TACCACCGACAATATTGCATGCAATGGAACCGGTTACGACCACACCAACACAAAAGAGGAGGAGGTGTACCAAGACCTGTGCGCCCTGCACAGGACGAGTAGAAGCCAG
Seq A exon
GTAGAATTGCGTACCAAACCGCCTGTCCATGCATGAGACACTTCGGTGGCCCCGTCACTTAGGCCGGAATCGTGTCCGTACTAACTCCCTGCTCTCCATGTTCTTCCTTCCCCTCTAG
Seq C2 exon
ACCGCCTCGTCGACGAGCTTTGAGCAGCGCGACTATGTCATCCGCGAGCTGATCGACACGGAGTCCAATTACCTGGACGTTCTCACTGCGCTGAAGACCAAGTTTATGGGTCCGCTGGAGCGGCATCTCAACCAGGACGAGCTGCGTCTCATATTCCCGCGCATCAGA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0040068:FBtr0074677:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.189 A=NA C2=0.000
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
PF0062115=RhoGEF=PU(24.4=76.8)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0112228


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0074448, FBpp0074449
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCATGCAATGGAACCGGTTA
R:
GGGAATATGAGACGCAGCTCG
Band lengths:
252-370
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Neural diversity
  • Neurogenesis
  • Neuronal activity
  • Splicing factor regulation (brain)
  • Splicing factor regulation (SL2)