DmeINT0029115 @ dm6
Intron Retention
Gene
FBgn0035103 | Vdup1
Description
The gene Vitamin D3 up-regulated protein 1 is referred to in FlyBase by the symbol DmelVdup1 (CG7047, FBgn0035103). It is a protein_coding_gene from Dmel. It has 6 annotated transcripts and 6 polypeptides (1 unique). Gene sequence location is 3L:176306..178963. Its molecular function is unknown. It is involved in the biological process described with: negative regulation of gene expression; protein transport. 3 alleles are reported. No phenotypic data is available. The phenotypic class of alleles includes: viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of very low expression. Peak expression observed within 06-24 hour embryonic stages, at stages throughout the pupal period.
Coordinates
chr3L:177382-178305:-
Coord C1 exon
chr3L:178022-178305
Coord A exon
chr3L:177874-178021
Coord C2 exon
chr3L:177382-177873
Length
148 bp
Sequences
Splice sites
5' ss Seq
GCCGTATGT
5' ss Score
6.35
3' ss Seq
TTTCGTTGGTTTTTCCTTAGGCG
3' ss Score
8.56
Exon sequences
Seq C1 exon
GAATCATCAACATTGTCACCAGTGCACCAAACAGGCTTGCCGACAGTCGCAGTTGCAGCTTACGCTTTTGGTAAAGATGTACATACTGGAGTTTTGCCCAAATTTGTAGGCGCGGGCGTGACACGCCCGACATGCTTCATGCGCCGACCTTGCAGTTGATGCTTAAGTGTTCGGGGCTTTCGTGCTGCATAGTTGTGCACGCAGCCATCTCTTGGCCGTACGAAACTGGTTTTGTTTCCTTTGCCCGCCTAGATGCTACCCACATAAATATGCAAACAAGCGCC
Seq A exon
GTATGTATGTGAGACCGTAGTCCGTAGTACATGGTCTCAGACCTAGCCAGCTATGACGGATAAGTTGTCATTAACCATAATGACGCGTGCGGAGCGGGTCAAATATTTGGCAACCGTGTTCTAACGAATTTCGTTGGTTTTTCCTTAG
Seq C2 exon
GCGTACGAATGAAATCGGCAACAAAACAGAGGCACGATGCCGCGCAAGTTGCTTAAATTCCTTATCATCTTCGACAACACTTCCCTCCTGTACTTCCCGGGCCAGTTTCTCTCCGGACGGGTTCTAATCGAATTGCAGGATGAGACGCCTGCTTTGGGACTTCATTTCCATGTGGTAGGCGAAGGGGTCGTGCGCAACGGGCGGCGACAGGAGCGGACATACGATAAGGAGAACTATATCGACTTTCGGATGCGACTTCTGGGGGACGTAGACCAAGGAGGTCCAGCTATACTCTCGCCAGGAATTCACAGCTTCCCCTTCAAACTCGGCTTGCCACTGGGTCTTCCATCTACATTTCTCGGTCGGTACGGCTGGATTCAGTTCTACTGCAAGGCGGCGCTCCGCGAGAACAATGGCATTATCCATAAGAACCACCAGGTCTTCATTGTGATGAATCCCATCGACCTAAACCTTGAAAAGCCCATCTTAGCA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0035103:FBtr0072536:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0033924=Arrestin_N=WD(100=90.8)
A:
NA
C2:
PF0033924=Arrestin_N=WD(100=90.8)
Main Inclusion Isoform:
FBpp0291104
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0072433, FBpp0072434, FBpp0072435, FBpp0306194
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:
TAAGTGTTCGGGGCTTTCGTG
R:
TTCGATTAGAACCCGTCCGGA
Band lengths:
253-401
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)