DmeINT0032475 @ dm6
Intron Retention
Gene
FBgn0001185 | her
Description
The gene hermaphrodite is referred to in FlyBase by the symbol Dmelher (CG4694, FBgn0001185). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is 2L:16677185..16679691. Its molecular function is described by: DNA binding; nucleic acid binding. It is involved in the biological process described with 6 unique terms, many of which group under: developmental process involved in reproduction; reproduction; developmental process; reproductive process; sex determination. 20 alleles are reported. The phenotypes of these alleles manifest in: somatic cell; developing material anatomical entity; abdomen; ganglion mother cell; neuroblast. The phenotypic classes of alleles include: increased mortality during development; fertile; phenotype; partially lethal. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 00-12 hour embryonic stages.
Coordinates
chr2L:16678318-16679383:+
Coord C1 exon
chr2L:16678318-16678581
Coord A exon
chr2L:16678582-16678642
Coord C2 exon
chr2L:16678643-16679383
Length
61 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGA
5' ss Score
5.46
3' ss Seq
CAATGTTTTTATCACTAAAGGCT
3' ss Score
3.39
Exon sequences
Seq C1 exon
GCTGTCAACGTTGATGGCCAGTTGCGATGGTTCCAGTCAATAGATCCACCGCCGGGAGCTCCAACAAAATTGGAGCTGCCCATAAAGAGCACTTCAATTTCTGTCCAGCAGCAAATGGACGAATTAGACGATGAGTTGGCCATGTCCCTTGCCGAAGAAGATCAGCAGGATGAGTTTCTTGTGCCAATGCTGAGCGGAGAGGAACCAGTTAAAATAAAACAATCATCGCTGACCGATCTGGCTTGGAGTTGGAGTACGCCGGAT
Seq A exon
GTAAGAAAGAACTATAAACGAAAAAAACGAACTTTTCCTAACAATGTTTTTATCACTAAAG
Seq C2 exon
GCTGTACATCACATAAGTCCCAAAGCGGAACTCAAGAAGGACCTTAAAGCTGGCGATGCAGATACAGATTTTCCAGATTGGTGGGATGATGGCAAGTACACAAAGATGCAAAAGAACCAAACATTTGCAAAGCACTCAAAGAAGCCGTCGCAGGAGAATGTGCAACGCATCCTGCGCATCATCTATGACATTTACTACAAACCCTTCAAGGAAGATCGCAAGCAGTTCGAGGCATTTCAAATTAAGGACTCCTGGCTGTGCGCGACTCGAATGACTCGCATGCAGATAATCAAGGACATGTACTCTAAACAGGGCACGTTAAGTCAAACTTGATGATAAAAAATGTATCATCCCTTTGGTATTTGTATAAGAATACCATTAAGTTGTTTACTATTTAAAGTGTAAAGTAAACGAATTAAGAAAATCCCAAGTACTTTAAAACTAGTTAATTAACCTTTAATTTAAGCCCAAAAACAAGTATAGGAGTAGTTTAAAAAAGAAAGAATACTATAGTCGAGATCCCCGACTATCATATAACCGTTACTCAGCTAGTGTGAATGCGAACGCGAAATTTAATCCTCTGGGATATTAATAAATATTGTATAATGTGAAAAAATTTAAAAAAAATTCAAACGTGTGGGCGTGACCGGTTTGGCGGCTTTAGGGCGTTGGAATGGGCGTGGCAAAAAGTTTTTTGGCAAATCGATAGAAATTTAAGCGACTAATAAAATTATGAAAAAT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0001185:FBtr0080883:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.432 A=NA C2=0.145
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0080440
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0307137
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:
CAATGCTGAGCGGAGAGGAAC
R:
TCTGCATCGCCAGCTTTAAGG
Band lengths:
142-203
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)