FB2024_03 , released June 25, 2024
Gene: Dmel\seq
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General Information
Symbol
Dmel\seq
Species
D. melanogaster
Name
sequoia
Annotation Symbol
CG32904
Feature Type
protein_coding_gene
FlyBase ID
FBgn0028991
Gene Model Status
Current
Stock Availability
19 publicly available
Gene Summary
sequoia (seq) encodes a pan-neuronally expressed zinc-finger transcription factor that governs dendrite and axon outgrowth. It is necessary for the proper development of tracheal branches and dendritic branches of multidendritic neurons, as well as development of the R8 cell in eye development. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

vr5, l(2)vr5, l(2)49Fc

Key Links
Genomic Location
Cytogenetic map
49F4-49F7
Sequence location
Recombination map
2-68
RefSeq locus
NT_033778 REGION:13176553..13190086
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (11 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (9 terms)
Terms Based on Experimental Evidence (9 terms)
CV Term
Evidence
References
involved_in branching involved in open tracheal system development
inferred from mutant phenotype
(Araújo and Casanova, 2011)
involved_in dendrite morphogenesis
inferred from mutant phenotype
(Gao et al., 1999)
involved_in negative regulation of transcription by RNA polymerase II
inferred from mutant phenotype
(Araújo and Casanova, 2011)
involved_in neuron development
inferred from mutant phenotype
(Brenman et al., 2001)
involved_in R7 cell development
inferred from mutant phenotype
(Petrovic and Hummel, 2008)
involved_in R8 cell development
inferred from mutant phenotype
(Petrovic and Hummel, 2008)
involved_in sensory organ development
inferred from mutant phenotype
(Andrews et al., 2009)
involved_in terminal cell fate specification, open tracheal system
inferred from mutant phenotype
(Araújo and Casanova, 2011)
involved_in ventral cord development
inferred from high throughput mutant phenotype
(Bivik et al., 2015)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in dendrite morphogenesis
traceable author statement
(Grueber and Jan, 2004)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in nucleoplasm
inferred from high throughput direct assay
(Lye et al., 2014)
located_in nucleus
inferred from direct assay
(Araújo and Casanova, 2011)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
located_in nucleus
traceable author statement
(Gao and Bogert, 2003)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
sequoia (seq) encodes a pan-neuronally expressed zinc-finger transcription factor that governs dendrite and axon outgrowth. It is necessary for the proper development of tracheal branches and dendritic branches of multidendritic neurons, as well as development of the R8 cell in eye development. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
C2H2 ZINC FINGER TRANSCRIPTION FACTORS -
Zinc finger C2H2 transcription factors are sequence-specific DNA binding proteins that regulate transcription. They possess DNA-binding domains that are formed from repeated Cys2His2 zinc finger motifs. (Adapted from PMID:1835093, FBrf0220103 and FBrf0155739).
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
l(2)49Fc
Embryonic lethal.
Summary (Interactive Fly)

zinc finger - required for specification of a subset of neurons - functions in regulating dendrite and axon development - necessary for the proper development of tracheal branches and dendritic branches of multidendritic neurons, as well as development of the R8 cell in eye development

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\seq for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry A1Z995)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Complex/atypical overlap: Shares UTR sequences with upstream and downstream genes; shares portion of CDS with one isoform of upstream gene; for some isoforms internal coding exons correspond to UTR exons of other gene.

Genes with CDS overlap: minor isoform of Kdm4B appears to share coding sequence with seq (terminal coding exon of Kdm4B and initial coding exon of seq, 131 residues). Other Kdm4B isoforms are highly conserved; seq orthologs not found outside Drosophila.

Gene model reviewed during 5.47

Exons of Kdm4B, seq and CG17724 overlap.

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.43

Gene model reviewed during 5.53

Sequence Ontology: Class of Gene
gene_with_dicistronic_mRNA
(FlyBase Genome Annotators, 2012)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
seq-RA
FBtr0100501
NM_001032244
3599
882
seq-RB
FBtr0344198
NM_001299450
5631
873
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
seq-PA
FBpp0099939
96.5
882
5.55
A1Z995
NP_001027415
AAZ52808
seq-PB
FBpp0310607
95.7
873
5.79
A0A0B4LFA2
NP_001286379
AHN56177
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\seq using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

-0.71

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 3 -- 16
nervous system
(Brenman et al., 2001)
embryonic stage 4 -- 6
anlage in statu nascendi
(Fisher et al., 2012)
central brain anlage in statu nascendi
(Fisher et al., 2012)
dorsal ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)
ventral ectoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)
antennal anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)
dorsal head epidermis anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)
visual anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)
embryonic stage 7 -- 8
antennal anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)
central brain anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)
dorsal head epidermis anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)
visual anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)
ventral ectoderm
(Fisher et al., 2012)
ventral nerve cord primordium

Comment: reported as ventral nerve cord anlage

(Fisher et al., 2012)
embryonic stage 9 -- 10
antennal primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
central brain primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
visual primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

(Fisher et al., 2012)
ventral ectoderm
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
embryonic stage 11 -- 12
antennal primordium
(Fisher et al., 2012)
central brain primordium
(Fisher et al., 2012)
dorsal sensory complex primordium
(Fisher et al., 2012)
hypopharyngeal sense organ primordium
(Fisher et al., 2012)
labial sensory complex primordium
(Fisher et al., 2012)
labral sensory complex primordium
(Fisher et al., 2012)
maxillary sensory complex primordium
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
ventral sensory complex anlage
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic brain
(Fisher et al., 2012)
embryonic dorsal epidermis
(Fisher et al., 2012)
embryonic head epidermis
(Fisher et al., 2012)
embryonic/larval nervous system
(Fisher et al., 2012)
larval ventral nerve cord
(Fisher et al., 2012)
Additional Descriptive Data

Transcript is first detected in stage 3/4 embryos in the developing nervous system and remains present througout embryonic development.

(Brenman et al., 2001)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 3 -- 16
nervous system & neuron & thecogen cell
• nucleus
(Brenman et al., 2001)
embryonic stage 11 -- 15
embryonic/larval central nervous system
• nucleus
(Araújo and Casanova, 2011)
third instar larval stage
photoreceptor cell R7
(Petrovic and Hummel, 2008)
photoreceptor cell R8
(Petrovic and Hummel, 2008)
photoreceptor R7 precursor cell
(Kulkarni et al., 2016)
photoreceptor R8 precursor cell
(Kulkarni et al., 2016)
adult stage
head & neuron
• nucleus
(Brenman et al., 2001)
Additional Descriptive Data

The expression pattern of seq is highly dynamic in the eye disc in early differentiating R7 and R8 cells during the time of axon growth and medulla innervation. Expression in R8 tails off before expression in R7 is observed. By the time the R7 cell initiates axonal projection which is accompanied by a high level of seq, the axon of the neighboring R8 cell has already reached the medulla and seq expression has been turned off.

(Petrovic and Hummel, 2008)

Protein is detected in embryos from stage 3/4 on in the nuclei of neurons and sheath cells of the developing nervous system. Pan-neural nuclear protein is also detected in the adult head including the photoreceptor cells.

(Brenman et al., 2001)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nucleoplasm
inferred from high throughput direct assay
(Lye et al., 2014)
located_in nucleus
inferred from direct assay
(Araújo and Casanova, 2011)
Expression Deduced from Reporters
Reporter: PBac{681.P.FSVS-1}seqCPTI001516
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult brain cell body rind
(Knowles-Barley, 2011.8.24)
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\seq in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 26 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 12 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of seq
Transgenic constructs containing regulatory region of seq
Aberrations (Deficiencies and Duplications) ( 30 )
Inferred from experimentation ( 30 )
Gene disrupted in
Df(2R)BSC273
(Kahsai and Cook, 2018, Dean et al., 2013)
Df(2R)CX1
(Brenman et al., 2001)
Df(2R)Exel8057
(Dean et al., 2013, Andrews et al., 2009)
Df(2R)vg33
(Lasko and Pardue, 1988)
Df(2R)vg56
(Hao et al., 1995, Lasko and Pardue, 1988)
Df(2R)vg104
(Hao et al., 1995, Lasko and Pardue, 1988)
Df(2R)vg106
(Hao et al., 1995, Lasko and Pardue, 1988)
Df(2R)vg-B
(Brenman et al., 2001, Hao et al., 1995, Wu and Howe, 1995, Lasko and Pardue, 1988)
Df(2R)vg-P2
(Hao et al., 1995, Lasko and Pardue, 1988)
Gene not disrupted in
Df(2R)R7
(Lasko and Pardue, 1988)
Df(2R)Su(z)2-1.a6
(Wu and Howe, 1995)
Df(2R)Su(z)2-1.b8
(Wu and Howe, 1995)
Df(2R)Su(z)25
(Wu and Howe, 1995)
Df(2R)Su(z)3-1.iy
(Wu and Howe, 1995)
Df(2R)Su(z)3-1.jtg
(Wu and Howe, 1995)
Df(2R)trix
(Brenman et al., 2001)
Df(2R)vg62
(Wu and Howe, 1995, Lasko and Pardue, 1988)
Df(2R)vg79b3
(Lasko and Pardue, 1988)
Df(2R)vg79d8
(Lasko and Pardue, 1988)
Df(2R)vg81
(Lasko and Pardue, 1988)
Df(2R)vg83f15
(Lasko and Pardue, 1988)
Df(2R)vg107
(Lasko and Pardue, 1988)
Df(2R)vg120
(Lasko and Pardue, 1988)
Df(2R)vg124
(Lasko and Pardue, 1988)
Df(2R)vg133
(Lasko and Pardue, 1988)
Df(2R)vg135
(Lasko and Pardue, 1988)
Df(2R)vg136
(Hao et al., 1995, Lasko and Pardue, 1988)
Df(2R)vg-C
(Brenman et al., 2001, Lasko and Pardue, 1988)
Df(2R)vg-D
(Wu and Howe, 1995, Lasko and Pardue, 1988)
In(2LR)vg79a
(Lasko and Pardue, 1988)
Inferred from location ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal (with Df(2R)BSC273)
lethal (with seq9.17)
lethal (with seq22)
lethal (with seqEP728)
lethal (with seqvr5-5)
lethal (with seqvr5-48)
lethal | male limited, with Scer\GAL4Bx-MS1096
lethal | male limited | cold sensitive, with Scer\GAL4Bx-MS1096
lethal | recessive
lethal - all die during embryonic stage
lethal - all die during embryonic stage (with Df(2R)Exel8057)
lethal - all die during embryonic stage (with seqA41)
lethal - all die during embryonic stage (with seqU5)
lethal - all die during embryonic stage | recessive
Other Phenotypes
Allele
abnormal neuroanatomy
abnormal neuroanatomy | adult stage, with Scer\GAL4GMR.long
abnormal neuroanatomy | adult stage | somatic clone
abnormal neuroanatomy | pupal stage, with Scer\GAL4GMR.long
abnormal neuroanatomy | somatic clone | third instar larval stage
non-suppressor of variegation | dominant, with In(1)wm4
non-suppressor of variegation | dominant, with P{hsp26-pt-T}39C-5
some die during embryonic stage
some die during embryonic stage (with Df(2R)Exel8057)
some die during embryonic stage (with seqA41)
some die during embryonic stage (with seqU5)
some die during embryonic stage | recessive
visible | female limited, with Scer\GAL4Bx-MS1096
visible | female limited | cold sensitive, with Scer\GAL4Bx-MS1096
Phenotype manifest in
Allele
apterous-expressing neuron of the lateral cluster of the thorax | ectopic
apterous-expressing neuron of the lateral cluster of the thorax Ap4 | increased number
axon & embryonic central nervous system
axon | dorsal | embryonic stage
chaeta | somatic clone
chordotonal organ & neuron & embryo
dendrite | dorsal | embryonic stage
dendrite | embryonic stage | lateral
embryonic/larval ganglionic tracheal branch
embryonic/larval ganglionic tracheal branch, with Scer\GAL4elav-C155, Scer\GAL4sca-109-68
embryonic/larval ganglionic tracheal branch (with seqC022)
embryonic/larval ganglionic tracheal branch (with seqZ1241)
embryonic central nervous system & axon
embryonic peripheral nervous system & axon
embryonic peripheral nervous system & multidendritic dendrite | ectopic
embryonic peripheral nervous system & multidendritic neuron
embryonic peripheral nervous system & multidendritic neuron | supernumerary
embryonic peripheral nervous system & sensory neuron
growth cone | pupal stage, with Scer\GAL4GMR.long
medulla layer M1 | adult stage | somatic clone
medulla layer M2 | adult stage | somatic clone
medulla layer M3 | adult stage, with Scer\GAL4GMR.long
medulla layer M3 | adult stage | somatic clone
medulla layer M3 | pupal stage, with Scer\GAL4GMR.long
medulla layer M6 | adult stage, with Scer\GAL4GMR.long
medulla layer M6 | adult stage | somatic clone
medulla layer M6 | pupal stage, with Scer\GAL4GMR.long
mesothoracic tergum & adult peripheral nervous system & sensory neuron | somatic clone
motor neuron & axon & embryo
multidendritic neuron & dendrite & embryo
photoreceptor cell & axon | somatic clone
photoreceptor cell R7 | adult stage | somatic clone
photoreceptor cell R7 | pupal stage, with Scer\GAL4GMR.long
photoreceptor cell R8 | adult stage, with Scer\GAL4GMR.long
photoreceptor cell R8 | adult stage | somatic clone
photoreceptor cell R8 | pupal stage, with Scer\GAL4GMR.long
presumptive embryonic/larval peripheral nervous system | dorsal
scutellum & adult peripheral nervous system & sensory neuron | somatic clone
tormogen cell | somatic clone
wing | female limited, with Scer\GAL4Bx-MS1096
wing | female limited | cold sensitive, with Scer\GAL4Bx-MS1096
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (15)
Hsap\BRPF1
1 of 14
Yes
No
Hsap\BRPF3
1 of 14
Yes
No
Hsap\BTBD18
1 of 14
Yes
No
Hsap\JADE1
1 of 14
Yes
No
1  
Hsap\JADE2
1 of 14
Yes
No
Hsap\JADE3
1 of 14
Yes
No
Hsap\KDM4A
1 of 14
Yes
No
Hsap\KDM4B
1 of 14
Yes
No
1  
Hsap\KDM4C
1 of 14
Yes
No
Hsap\KDM4D
1 of 14
Yes
No
Hsap\KDM4E
1 of 14
Yes
No
Hsap\LIMCH1
1 of 14
Yes
No
Hsap\MLLT6
1 of 14
Yes
No
Hsap\MLLT10
1 of 14
Yes
No
2  
Hsap\PHF14
1 of 14
Yes
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (13)
Rnor\Brd1
1 of 14
Yes
No
Rnor\Brpf1
1 of 14
Yes
No
Rnor\Brpf3
1 of 14
Yes
No
Rnor\Btbd18
1 of 14
Yes
No
Rnor\Jade1
1 of 14
Yes
No
Rnor\Jade2
1 of 14
Yes
No
Rnor\Kdm4a
1 of 14
Yes
No
Rnor\Kdm4b
1 of 14
Yes
No
Rnor\Kdm4c
1 of 14
Yes
No
Rnor\Kdm4d
1 of 14
Yes
No
Rnor\Limch1
1 of 14
Yes
No
Rnor\Mllt10
1 of 14
Yes
No
Rnor\Phf14
1 of 14
Yes
No
Mus musculus (laboratory mouse) (15)
Mmus\Brd1
1 of 14
Yes
No
Mmus\Brpf1
1 of 14
Yes
No
Mmus\Brpf3
1 of 14
Yes
No
Mmus\Btbd18
1 of 14
Yes
No
Mmus\Jade1
1 of 14
Yes
No
Mmus\Jade2
1 of 14
Yes
No
Mmus\Jade3
1 of 14
Yes
No
Mmus\Kdm4a
1 of 14
Yes
No
Mmus\Kdm4b
1 of 14
Yes
No
Mmus\Kdm4c
1 of 14
Yes
No
Mmus\Kdm4d
1 of 14
Yes
No
Mmus\Limch1
1 of 14
Yes
No
Mmus\Mllt6
1 of 14
Yes
No
Mmus\Mllt10
1 of 14
Yes
No
Mmus\Phf14
1 of 14
Yes
No
Xenopus tropicalis (Western clawed frog) (6)
Xtro\btbd18
1 of 13
Yes
No
Xtro\faf2
1 of 13
Yes
No
Xtro\gabarapl1
1 of 13
Yes
No
Xtro\gtf3c5
1 of 13
Yes
No
Xtro\limch1
1 of 13
Yes
Yes
Xtro\phldb1
1 of 13
Yes
No
Danio rerio (Zebrafish) (12)
Drer\brd1a
1 of 14
Yes
No
Drer\brd1b
1 of 14
Yes
No
Drer\brpf3b
1 of 14
Yes
No
Drer\jade1
1 of 14
Yes
No
Drer\jade2
1 of 14
Yes
No
Drer\jade3
1 of 14
Yes
No
Drer\kdm4aa
1 of 14
Yes
No
Drer\kdm4ab
1 of 14
Yes
No
Drer\kdm4c
1 of 14
Yes
No
Drer\limch1a
1 of 14
Yes
Yes
Drer\limch1b
1 of 14
Yes
Yes
Drer\mllt10
1 of 14
Yes
No
Caenorhabditis elegans (Nematode, roundworm) (3)
Cele\jmjd-2
1 of 14
Yes
No
Cele\lin-49
1 of 14
Yes
No
Cele\phf-14
1 of 14
Yes
No
Anopheles gambiae (African malaria mosquito) (31)
Agam\AgaP_AGAP000080
1 of 12
Yes
No
Agam\AgaP_AGAP000585
1 of 12
Yes
No
Agam\AgaP_AGAP000754
1 of 12
Yes
No
Agam\AgaP_AGAP001073
1 of 12
Yes
No
Agam\AgaP_AGAP001480
1 of 12
Yes
No
Agam\AgaP_AGAP001646
1 of 12
Yes
No
Agam\AgaP_AGAP002163
1 of 12
Yes
No
Agam\AgaP_AGAP002297
1 of 12
Yes
No
Agam\AgaP_AGAP003189
1 of 12
Yes
No
Agam\AgaP_AGAP003286
1 of 12
Yes
No
Agam\AgaP_AGAP003439
1 of 12
Yes
No
Agam\AgaP_AGAP003537
1 of 12
Yes
No
Agam\AgaP_AGAP003685
1 of 12
Yes
No
Agam\AgaP_AGAP005244
1 of 12
Yes
No
Agam\AgaP_AGAP005245
1 of 12
Yes
No
Agam\AgaP_AGAP005747
1 of 12
Yes
No
Agam\AgaP_AGAP005748
1 of 12
Yes
No
Agam\AgaP_AGAP006018
1 of 12
Yes
No
Agam\AgaP_AGAP006454
1 of 12
Yes
No
Agam\AgaP_AGAP006770
1 of 12
Yes
No
Agam\AgaP_AGAP006776
1 of 12
Yes
No
Agam\AgaP_AGAP007617
1 of 12
Yes
No
Agam\AgaP_AGAP008031
1 of 12
Yes
No
Agam\AgaP_AGAP008506
1 of 12
Yes
No
Agam\AgaP_AGAP008959
1 of 12
Yes
No
Agam\AgaP_AGAP010063
1 of 12
Yes
No
Agam\AgaP_AGAP010355
1 of 12
Yes
No
Agam\AgaP_AGAP011180
1 of 12
Yes
No
Agam\AgaP_AGAP011247
1 of 12
Yes
No
Agam\AgaP_AGAP011583
1 of 12
Yes
No
Agam\AgaP_AGAP013477
1 of 12
Yes
No
Arabidopsis thaliana (thale-cress) (6)
Atha\AT1G20670
1 of 13
Yes
No
Atha\AT1G76380
1 of 13
Yes
No
Atha\AT1G77800
1 of 13
Yes
No
Atha\AT3G14740
1 of 13
Yes
No
Atha\AT4G08455
1 of 13
Yes
No
Atha\AT5G55040
1 of 13
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (4)
Scer\GIS1
1 of 13
Yes
No
Scer\NTO1
1 of 13
Yes
No
Scer\RPH1
1 of 13
Yes
No
Scer\SNT2
1 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (3)
Spom\jmj3
1 of 12
Yes
No
Spom\nto1
1 of 12
Yes
No
Spom\snt2
1 of 12
Yes
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:seq. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (28)
ttk
2 of 13
ab
1 of 13
bab1
1 of 13
bab2
1 of 13
Br140
1 of 13
br
1 of 13
BtbVII
1 of 13
CG3726
1 of 13
CG6118
1 of 13
CG6765
1 of 13
CG8924
1 of 13
CG12236
1 of 13
CG15439
1 of 13
CG32121
1 of 13
CG34376
1 of 13
chinmo
1 of 13
fru
1 of 13
her
1 of 13
Kdm4A
1 of 13
Kdm4B
1 of 13
lolal
1 of 13
lola
1 of 13
lov
1 of 13
mamo
1 of 13
pre-lola-G
1 of 13
psq
1 of 13
rno
1 of 13
Trl
1 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    esyN Network Diagram
    Show neighbor-neighbor interactions:
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Other Interaction Browsers
    View in FlyBase Interactions Browser   View in MIST tool (external link)
    Please see the Physical Interaction reports below for full details
    protein-protein
    Physical Interaction
    Assay
    References
    seq - Atg8a
    pull down, autoradiography
    (Jacomin et al., 2020)
    seq - CG13287
    two hybrid array
    (Shokri et al., 2019)
    seq - Mad
    two hybrid array
    (Shokri et al., 2019)
    seq - Ubx
    bimolecular fluorescence complementation, fluorescence microscopy
    (Bischof et al., 2018)
    seq - abd-A
    bimolecular fluorescence complementation, fluorescence microscopy
    (Bischof et al., 2018)
    RNA-protein
    Physical Interaction
    Assay
    References
    seq - stau
    anti bait coimmunoprecipitation, partial DNA sequence identification by hybridization
    (Laver et al., 2013)
    Summary of Genetic Interactions
    esyN Network Diagram
    Show/hide secondary interactors 
    (data from AllianceMine provided by esyN)
    esyN Network Key:
    Suppression
    Enhancement
    Other Interaction Browsers
    View in FlyBase Interactions Browser   View in MIST tool (external link)
    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    seq
    suppressible
    bnl
    (Araújo and Casanova, 2011)
    seq
    suppressible
    CadN
    (Petrovic and Hummel, 2008)
    seq
    suppressible
    ham
    (Andrews et al., 2009)
    seq
    suppressible
    pnt
    (Araújo and Casanova, 2011)
    seq
    suppressible
    sv
    (Andrews et al., 2009)
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    trio
    enhanceable
    seq
    (Dean et al., 2013)
    External Data
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-68
    Cytogenetic map
    49F4-49F7
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    49F4-49F7
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    49C-50D
    (Gao et al., 1999)
    Determined by deficiency mapping (details unspecified).
    (Gao et al., 1999)
    Experimentally Determined Recombination Data
    Location

    2-68

    (FlyBase, 2016)

    2-71.6

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (19)
    Genomic Clones (15)
     

    Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

    cDNA Clones (66)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequenced
    BDGP DGC clones
    Other clones
      Drosophila Genomics Resource Center cDNA clones

      For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

      cDNA Clones, End Sequenced (ESTs)
      BDGP DGC clones
      Other clones
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      Antibody Information
      Laboratory Generated Antibodies
       

      polyclonal

      (Brenman et al., 2001)
      Commercially Available Antibodies
       
      Cell Line Information
      Publicly Available Cell Lines
       
        Other Stable Cell Lines
         
          Other Comments

          dsRNA has been made from templates generated with primers directed against this gene. seq RNAi results in overextension of ddaD and ddaE dendrites.

          (Parrish et al., 2006)

          seq mutants affect the cell fate decision of a small subset of neurons but have global effects on axon and dendrite morphologies of most and possibly all neurons.

          (Brenman et al., 2001)

          seq has a function in dendritic development.

          (Gao et al., 1999)
          Relationship to Other Genes
          Source for database merge of

          Source for merge of: seq l(2)49Fc

          (Brenman et al., 2001)
          Additional comments

          Annotation CG4037 split into CG33182, CG32904 (seq) and CG17724 in release 3 of the genome annotation.

          (FlyBase Genome Annotators, 2002-2003)

          One or more of the processed transcripts for this gene share(s) untranslated sequences with a transcript of an adjacent gene, but encode(s) a single open reading frame (ORF). The non-overlapping ORFs that share untranslated sequences are represented by seq and CG17724.

          (FlyBase Genome Annotators, 2002-2003)
          Nomenclature History
          Source for database identify of
          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (14)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 34 )
          Sequence Crossreferences
          NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
          GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
          GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
          RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
          UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
          UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
          Other crossreferences
          AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
          BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
          DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
          EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
          FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
          FlyMine - An integrated database for Drosophila genomics
          InterPro - A database of protein families, domains and functional sites
          KEGG Genes - Molecular building blocks of life in the genomic space.
          MARRVEL_MODEL - MARRVEL (model organism gene)
          Linkouts
          BioGRID - A database of protein and genetic interactions.
          Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
          DroID - A comprehensive database of gene and protein interactions.
          DRSC - Results frm RNAi screens
          Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
          FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          Flygut - An atlas of the Drosophila adult midgut
          iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
          Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
          MIST (protein-protein) - An integrated Molecular Interaction Database
          References (87)