DmeINT0031801 @ dm6
Intron Retention
Gene
FBgn0005558 | ey
Description
The gene eyeless is referred to in FlyBase by the symbol Dmeley (CG1464, FBgn0005558). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (4 unique). Gene sequence location is 4:697689..721173. Its molecular function is described by: RNA polymerase II cis-regulatory region sequence-specific DNA binding; RNA polymerase II regulatory region sequence-specific DNA binding; sequence-specific DNA binding; DNA-binding transcription factor activity, RNA polymerase II-specific; protein binding. It is involved in the biological process described with 19 unique terms, many of which group under: growth; sensory system development; post-embryonic development; sensory organ morphogenesis; cellular response to stimulus. 86 alleles are reported. The phenotypes of these alleles manifest in: medulla; cellular anatomical entity; eye disc; hemolymph; visual system. The phenotypic classes of alleles include: increased mortality during development; increased cell death; phenotype; visible. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of very low expression. Peak expression observed within 06-12 hour embryonic stages.
Coordinates
chr4:710917-712673:+
Coord C1 exon
chr4:710917-711082
Coord A exon
chr4:711083-712492
Coord C2 exon
chr4:712493-712673
Length
1410 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGA
5' ss Score
8.24
3' ss Seq
AATGATGGATTTATTTTTAGGTA
3' ss Score
7.56
Exon sequences
Seq C1 exon
GTCACAGTGGAGTAAATCAGCTGGGTGGCGTTTTTGTTGGAGGAAGGCCTTTGCCAGATTCAACACGGCAAAAAATTGTCGAACTGGCACATTCTGGAGCTCGGCCATGTGATATTTCTCGAATTCTGCAAGTATCAAATGGATGTGTGAGCAAAATTCTCGGGAG
Seq A exon
GTAGGACCATTTCCGTATATTTCTTAATTCTTAATACGTTTTGAAAATGATATGTCTTGGTGTAGACAATGGTGTACAGGGTTTAAACATTCATATTGTTTAGATTTTATTTTCTACTATTTCTCAAAAATGTTCTAACTAGTCATACTCTCTCTAAGAAGTACAACAACGCAAAAATATTGGTCATAAGCTTAAGCTCTCGAAGATTATAAATTTATTTATTAAATTTAAGATTATAATTTATTTTAACAATATAATGAAGCTATTGTTGATCAAGACACTGATACCTATGTATGCGGCAACTAAAACTGATCTTCTTAAATTATTTCAGTTTTTATTGTGGGCTTGTTACGTTAAGACTAGACGAAGTTTTATCCTTATAGTTTTTATCCTAGGGTGAATTCTAACCGATTATGATTGTAAATTCTAGGTTTTTAATGTGCAACATTTAATTTTTGCAATTTTAGTTTTTTTTAATTATTGATGTCCTACCATGCCGAAACCCAGTCGGGGTGGTCACGGTGGTGGTGGCGCTTAAGTCTCCTTTTGACTCTAGTTCGAGGGGCAGCACTGATAGTTCTGCACTGACTGGCCAGGCTGTTTGGGTGCGCATTAAGTCGTTCCATATATTTTTCGGGGATGTTCTGGAGCTTCTCTCCGAGTTTGGGGGTCTTGAGATCGCGTTCGAGAAATTCTTCTTAGGGTCTTCGTCTGTAGAGCCCGGATCTTATTTAGGCGACTTTTTGCAGCAATGGCGTGCGAGTATATCTGAATCCCGTAGAACAGGCTGGGGCCAATGTGGACTTGCAGTCAAGCGACAGTTTGTTGTGTGGAGCAATAAGCCAGGCCATTCGAGCTACCTTCCTATAGAGGGTTATACCAAGGTATTTATTCGCCTGGTGGTTGTGGATCGTTTTACCATTAAGGCAGATACCCGGACAACTACCTGTCACATTGGCACACTTTTCAGCTCCAGTTCCGGTTCTCAGCCCATTCATCCAGTTATTAGACCAAGGGAGCAGACATTATACTTGTGTTTTTCGCACAGTAGCATCGTCAGCTTAGGTGGCTATGGGGACATTTTCTTTCTCTACTCCTGTGACTGGTGTGTGAGTAGGCATGTCCGAAGCAAAGACTGAGTATAGGATGGGGCCTATTTATCAGAACTAAAAAAACACCCGACGCACCATTCAGAAGATTCTACATCTTATTGTCTGGAGTCCAAGAATTAAATGGGCAAGGACTAATAATATTAAACAGATAGCATGCCTTCGCTAGACGTAAGATCTACTTCCAGCTTTCCTACGAATATATACCAAGTAGATTGCAAATTGCAAAGGAACTTAATGTTTCATTATATATCAAGTTTATTTGTTGAAATAAAAATTATAATGATGGATTTATTTTTAG
Seq C2 exon
GTATTATGAAACAGGAAGCATACGACCACGTGCTATCGGAGGATCCAAGCCACGTGTGGCCACAGCCGAAGTCGTTAGCAAAATTTCGCAGTACAAACGCGAGTGTCCTAGCATATTTGCTTGGGAAATTCGGGATAGATTACTTCAGGAGAACGTTTGTACTAACGATAATATACCAAGT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0005558:FBtr0089236:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.225 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(44.0=98.2)
A:
NA
C2:
PF0029213=PAX=FE(48.0=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0088300
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0099809, FBpp0099810
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:
GTGGAGTAAATCAGCTGGGTGG
R:
CGTTAGTACAAACGTTCTCCTGA
Band lengths:
327-1737
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)