DmeINT0029123 @ dm6
Intron Retention
Gene
FBgn0028671 | Vha100-1
Description
The gene Vacuolar H[+] ATPase 100kD subunit 1 is referred to in FlyBase by the symbol DmelVha100-1 (CG1709, FBgn0028671). It is a protein_coding_gene from Dmel. It has 11 annotated transcripts and 11 polypeptides (5 unique). Gene sequence location is 3R:29131193..29137980. Its molecular function is described by: proton-transporting ATPase activity, rotational mechanism; ATPase binding; photoreceptor activity; calmodulin binding. It is involved in the biological process described with 7 unique terms, many of which group under: anatomical structure development; system development; response to stimulus; cellular metabolic process; ion transmembrane transport. 21 alleles are reported. The phenotypes of these alleles manifest in: cellular anatomical entity; vacuole; membrane-bounded organelle; organelle; cytoplasm. The phenotypic classes of alleles include: stress response defective; increased mortality during development; phenotype; sensory perception defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderately high expression. Peak expression observed within 00-06 hour embryonic stages.
Coordinates
chr3R:29133338-29135175:+
Coord C1 exon
chr3R:29133338-29133429
Coord A exon
chr3R:29133430-29135048
Coord C2 exon
chr3R:29135049-29135175
Length
1619 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAAT
5' ss Score
4.69
3' ss Seq
TGCTTCGTAATCCCCTCTAGCTT
3' ss Score
6.59
Exon sequences
Seq C1 exon
ATGGCCGACAACCAAAACGAGGACGAGCAGGCGCAGCTGCTGGGCGAGGAGGGTGTCCGGGCCAGCCAACCGGGCCAGAATTTGAAGCTTGG
Seq A exon
GTAAATATTGATGTGGACCTGGGAGCTGGGAGCACGGACGACGGACCACGACGGGAACAGGGGAAAACTAAACTCAGGCCAAGACCCACTCGCCTTCGCTCTCCTGCTCCTCTCACTCCTTGCTGTTTGTGTTCTACGCGTTCATGTCCTATCCATGTACCTTTGATGAGTGTTCCATGTTTTCCACGCGCTAGGCTATCGAATTGATTTCAAACATAAGCACATTGTCTACTTGTTTGCTCTGGTGTCGGTTTCCAAAACTATGCCTAATCCAATCCAACCTAATCCAATCCCATATCCCACATGCCCACAAATCCCAACAACCAACTTTCGGCGGCGGTTCTACTAACCACTTTCTAAGAGTTAACTCCAAGCTAACCTGTTTGTAAGTCGAGTCGAAATGACCTTTGCCCACCATTCACAATTTCTAGCAAGAAGGCGGCGTAAACCAAACGACCGAGTCGATGACCCGCGCCTTGATCACGGACGAGGCGCGCACCGCTGGTGCCTCCATGGGTCCCGTACAGCTCGGGTACGTATGCACCAGGACAGCTTCGAAAATGGGAAAGACGCACGCTCAGGCGTGGGCCGCAGTTCCGTCGGCAGGCAGATACTCTTTGGGCGAATAAGAGTGTACATAAAGGGATAAATTGTAATTTTAAATGGTGTACTTTTGGTTATCTTAACCCATTGGGTCTTACTTTTGTATATGTAATCTACTCTTTGTTCGATTTGTTTATACATATGTACATACCCAAAGATCCTATCTTTAGAAGTATCACATAAAGTAATCAGATTAGTGCCGCCCAGGGAGCTTTTGCCTTGCCCAATTTTTTTTAGCTCTTAACCAACGAAATGCCACACAAAATTATTGCTTACTGCCGCCAACGCCAAACTAATCAAACTCAGAACGCCAATGCAGCTGCGCCGTCACAGAGAAAGATTAACCGAACCATGTCCATTTATACCGTCCAGCTTGGAGTCCCCTGGAATTTCGAGCAATAATTTTCTGTGCAAGATCCCAAAATGACACATCGAATGCCACTAAATTAAACGTCGTTCTCTTCTTATGCTCCTCTCTTCCCCACACAAAAATGTCCAACCGAAAAATAATGTTGAAAATATAGTTACATGGAGAAATCAAACGAACGTGAGGATTATCTTCCATGGTTGGTACCCTGTCCCTTCAAAAAAAAAAAAGAAGAAAAAAACATGACTAGGTCAAACAATCAGTCAAACTCGTATCCATTAGCCAACGTACAGCGCTCATCAATCGTATTTGTATCCGTATTCGTATTCGATCGGTCAATCAGCTGTATATAGAAACATGTCATTAGCTTCGCTCGCCTCGCCTCGCCTCGCCTTGCCTCCCAGCACCGCCCCGCATCCCGTCCAGAACTCAGAGTGCCACCTAGAGTGCTAATGTGTCACCCATTCAACCGATCCCACCCAGTGCCTCATTCATCCCGATCCTCGCTCTCGTAACGCCTCGCGCGTCCATTGGTAACTTGTGCTTGAGAGTTTAGTTTTCCTTGTTTGTCGTAAATAACCGGAATGACATTGTTGGATAGCCCGTAGCGGAGATCTCTCACTAATAGCTGCTTCGTAATCCCCTCTAG
Seq C2 exon
CTTCGTGGCTGGCGTCATCCTGAGGGAGCGACTGCCGGCCTTCGAGCGGATGTTGTGGCGCGCCTGCAGGGGTAACGTCTTCCTGCGACAGGCGATGATTGAGACGCCGCTGGAGGATCCCACCAAT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0028671:FBtr0085379:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.438 A=NA C2=0.070
Domain overlap (PFAM):
C1:
PF0149614=V_ATPase_I=FE(3.8=100)
A:
NA
C2:
PF0149614=V_ATPase_I=FE(5.1=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0084743
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0084745, FBpp0084748, FBpp0084750
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:
CGACAACCAAAACGAGGACGA
R:
ATTGGTGGGATCCTCCAGC
Band lengths:
214-1833
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)