DmeINT0000685 @ dm6
Intron Retention
Gene
FBgn0261238 | Alh
Description
The gene Alhambra is referred to in FlyBase by the symbol DmelAlh (CG1070, FBgn0261238). It is a protein_coding_gene from Dmel. It has 14 annotated transcripts and 14 polypeptides (13 unique). Gene sequence location is 3R:7094596..7124185. Its molecular function is described by: DNA-binding transcription factor activity. It is involved in the biological process described with: larval somatic muscle development; regulation of transcription, DNA-templated; haltere development; molting cycle, chitin-based cuticle; instar larval development. 88 alleles are reported. The phenotypes of these alleles manifest in: embryonic/larval somatic muscle; wing; larva; embryonic/larval nervous system; RP2 motor neuron. The phenotypic classes of alleles include: phenotype; fertile; courtship behavior defective; viable. 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 00-18 hour embryonic stages, at stages throughout the pupal period, in adult female stages.
Coordinates
chr3R:7118958-7120882:-
Coord C1 exon
chr3R:7119462-7120882
Coord A exon
chr3R:7119049-7119461
Coord C2 exon
chr3R:7118958-7119048
Length
413 bp
Sequences
Splice sites
5' ss Seq
TAGGTGGGG
5' ss Score
3.33
3' ss Seq
TTTTTCGGTTGTTTCTGTAGCTT
3' ss Score
9.08
Exon sequences
Seq C1 exon
AAAAAGGGCGGCAACGTCAAAACAATACCTCCATATAAACCCATTCAACATGACACCTCTTCCGATTCGTGTTCGTCGCCCGAGAAGGAGATCGATTCAACCATGAACTCCGCGACAACTTCGGCCACAATCATAAAGATTACCAGCAGCAGTGGCAGTGCTGGTGGCAGCAGCAATGTTTTGAATGCAAGCTCCAGTGCTGGAATCTCTGCTGGAAGCAGCAGTGGGAGTGGCGTATCATCTTCCGCAAAGCAGCGCAAGAGCAATGCATCAAGTAAATCATCTAGCAGCAGTAGCAGTAGCTCGTCATCCTCAACAGGAGGGGCTCCCAACCCCTCCTCGAGTTCTGTGCATTCGGGAAGTGCTAGCAATATGACAGGAGGAGGAAGTGTACTACCAGGGAGTAGCAACATCGGCAACATTAGCAATAGTTTAAACAATAATCTGCCCGGAGGCAGTTCGTCCACCAGCAGTGCTGGAAACGTGCCTGGTGGAAGTGGGGGAATTATATCAGCTTCGAGCGGTGGTGCTACGCAATCGACAAGCAGTCAATCGTCAACAGCACCAGGAACCACCAAATCATCGGCCAGCAGTTCGAGCAGTAGTAGCAACAGCTACAAGGAGAAACATAGCAAAAGCTTAAGCAAATCCACATCCAGCAAGGACAAGGATGGAAAAGATAGCTCTACCAATTCAGCGAATAACAATTTCACAAATTCATCTGCATCATCAACATCTTCCAACTCCTCGTCGACACGAGAGAAATCCTCATCAAAGCTTTCTAAGAACAAAGACTCCAATCAAGTACCCAGTGCCACCAGCAGCTTAAGCACAACGAGCAGTATCAACACCCAGCCCAGTTCGTCGACTTCAACTGCTACAGCTGGATCGGGCGGTACTGGGACTCATGTGAGCAGTTCGGCTGCCAGTGGACTTAACTCAGCTCCTTCCACAACCAATGAGCATTCAAATCATGCCCACACCCTTAGCACAAATGGAACCGGAGCCGGAAGCGCAGCCGGAAAGTTGCAATCAGTCAGTAATCTGAGCAACAGTAGTTCTGGTTTTGGATCGGATCTGCGATCAGTCAGCACATCCTCAAGCTCCACTGTGAACGACTCCACCGGAGGATTCGGTAGTAATTCGAATTCAGAAAGGGAGAATTTGTCAGGCGCTGGATCGTCGGCAAGCAACATGCCTGGAACAATAGCTCCTGGTACTGGTGGCGTATCTTCCAGTGCGGCCACTAATCTAAGCACCAATAAGGGAGGCTCTTCGTCATCGACGGCGAATAGCCTTACATCTACGAGCACTTCCTCAGGCAGCTCCTCTAACTCGTCATCGAAAAAACGAAAAGCGGATTCTGCTAAGTCCACTAGCAGTATTTCCACCTCTGGCTCCGCTCTGGAGGATAACAATAG
Seq A exon
GTGGGGAACGAGAAACGCAAAGAAAAGGTCTTTTACAATTTACATTTTTCAAAATTTGGTAGTTACTTAGTTTACGCCTGATTTTAAAGAAACAAATGGGACTGTGTTGCACATCTATGATTTGCAAAATTGTTAATTTATCGAACACCCGGTGTAGACAACTCTTTTATTTTGTTATTCTAAATAAATTGTAATAATTAGAACATAATGTATATTAAACAGTGCCCAATGTTACTGAGAAACCAGACTTTTTAAATATGTTTTTGTAATTTCATTGAAAAAGGCAACTTTTGGAATCCGTTTCGTTTATTAGAGAATATACTAATACTAAAATAACCCCGTATAAGACCTTTTTCTACTGAAACAATGTATAGAAAAAATCACACTAATATATTTTTCGGTTGTTTCTGTAG
Seq C2 exon
CTTAATATCCCGCTATGATATCAAAGATGTTCAAGTTGCACTGACGCCTCTAACAGATTTTGAGAAGGAAATCGAGAAGAGCTCCAAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0261238:FBtr0081612:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.939 A=NA C2=0.710
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0306738
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0081129, FBpp0081130
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:
GAGAATTTGTCAGGCGCTGGA
R:
CCTCTTGGAGCTCTTCTCGAT
Band lengths:
354-767
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)