FB2025_05 , released December 11, 2025
Gene: Dmel\cliff
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General Information
Symbol
Dmel\cliff
Species
D. melanogaster
Name
clifford
Annotation Symbol
CG1603
Feature Type
protein_coding_gene
FlyBase ID
FBgn0033185
Gene Model Status
Current
Stock Availability
12 publicly available
Gene Summary
Chromatin-binding protein involved in the organization of active promoters and insulators (PubMed:38769058). Essential for the activity of heterochromatin promoters; primarily binds to specific motifs within promoters of housekeeping genes (PubMed:38769058). May also associate to a lesser extent with promoters in euchromatin (PubMed:38769058). Mediates recruitment of Cp190, a multifunctional protein involved in the recruitment of transcription complexes, the creation of open chromatin regions and the activity of insulators (PubMed:38769058). Cooperates with pita and su(Hw) to recruit Cp190 and regulate insulator function at the front-ultraabdominal (Fub) boundary (PubMed:38769058). May cooperate with other C2H2 zinc finger proteins, such as M1BP, to recruit CP190 to promoters (PubMed:38769058). May be involved in cellular organization and development of the eye (PubMed:37680216). (UniProt, Q1LZ24)
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
43D1-43D1
Sequence location
Recombination map
2-56
RefSeq locus
NT_033778 REGION:7513846..7516390
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 (12 terms)
Molecular Function (6 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
enables chromatin insulator sequence binding
inferred from direct assay
(Sokolov et al., 2024)
enables promoter-specific chromatin binding
inferred from direct assay
(Sokolov et al., 2024)
enables protein binding
inferred from physical interaction with UniProtKB:Q24478
(Sokolov et al., 2024)
enables sequence-specific DNA binding
inferred from direct assay
(Sokolov et al., 2024)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables DNA-binding transcription factor activity
inferred from biological aspect of ancestor with PANTHER:PTN008617116
(GO Reference Genome Project, 2011-)
enables sequence-specific DNA binding
inferred from sequence or structural similarity with UniProtKB:Q99592
(Gene Ontology Curators, 2002-)
enables transcription cis-regulatory region binding
inferred from biological aspect of ancestor with PANTHER:PTN008617116
(GO Reference Genome Project, 2011-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in positive regulation of transcription by RNA polymerase II
inferred from mutant phenotype
(Ashton-Beaucage et al., 2014)
inferred from direct assay
(Sokolov et al., 2024)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in chromatin organization
inferred from biological aspect of ancestor with PANTHER:PTN002812652
(GO Reference Genome Project, 2011-)
involved_in positive regulation of transcription by RNA polymerase II
inferred from sequence or structural similarity with UniProtKB:Q99592
(Gene Ontology Curators, 2002-)
involved_in regulation of DNA-templated transcription
inferred from biological aspect of ancestor with PANTHER:PTN008617116
(GO Reference Genome Project, 2011-)
Cellular Component (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
is_active_in chromatin
inferred from direct assay
(Sokolov et al., 2024)
located_in nucleoplasm
inferred from direct assay
(Sokolov et al., 2024)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN008617116
(GO Reference Genome Project, 2011-)
located_in nucleus
inferred from sequence or structural similarity with UniProtKB:Q99592
(Gene Ontology Curators, 2002-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
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).
Protein Function (UniProtKB)
Chromatin-binding protein involved in the organization of active promoters and insulators (PubMed:38769058). Essential for the activity of heterochromatin promoters; primarily binds to specific motifs within promoters of housekeeping genes (PubMed:38769058). May also associate to a lesser extent with promoters in euchromatin (PubMed:38769058). Mediates recruitment of Cp190, a multifunctional protein involved in the recruitment of transcription complexes, the creation of open chromatin regions and the activity of insulators (PubMed:38769058). Cooperates with pita and su(Hw) to recruit Cp190 and regulate insulator function at the front-ultraabdominal (Fub) boundary (PubMed:38769058). May cooperate with other C2H2 zinc finger proteins, such as M1BP, to recruit CP190 to promoters (PubMed:38769058). May be involved in cellular organization and development of the eye (PubMed:37680216).
(UniProt, Q1LZ24)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\cliff 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 Q1LZ24)

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

Gene model reviewed during 5.48

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

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
cliff-RA
FBtr0088979
NM_136446
2130
586
cliff-RB
FBtr0336925
NM_001273849
2368
586
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
cliff-PA
FBpp0088052
68.3
586
6.44
Q1LZ24
NP_610290
AAF59239
cliff-PB
FBpp0307862
68.3
586
6.44
Q1LZ24
NP_001260778
AGB93311
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

586 aa isoforms: cliff-PA, cliff-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts (via regions flanking MADF domain 1) with Cp190 (via regions between the BTB domain and first zinc finger domain); the interaction is probably direct and is essential for protein function.

(UniProt, Q1LZ24)
Domain

Possesses 2 MADF domains, the negatively charged MADF1 and the positively charged MADF2 (PubMed:38769058). Both MADF domains are essential for protein function (PubMed:38769058). MADF2 is important for recruitment to heterochromatin and may mediate interaction with other proteins (PubMed:38769058).

Possesses a C-terminal cluster of 6 C2H2-type zinc fingers (PubMed:38769058). This cluster of zinc fingers is essential for protein function and sufficient for recognition and binding of specific DNA motifs in chromatin (PubMed:38769058).

(UniProt, Q1LZ24)
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\cliff 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).

1.04

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 4 -- 6
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | ubiquitous
(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
is_active_in chromatin
inferred from direct assay
(Sokolov et al., 2024)
located_in nucleoplasm
inferred from direct assay
(Sokolov et al., 2024)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\cliff 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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 4 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of cliff
Transgenic constructs containing regulatory region of cliff
Aberrations (Deficiencies and Duplications) ( 9 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
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) (135)
Hsap\BCL6
1 of 14
Yes
Yes
0  
Hsap\GZF1
1 of 14
Yes
No
Hsap\HIC1
1 of 14
Yes
Yes
Hsap\MECOM
1 of 14
Yes
No
Hsap\MYNN
1 of 14
Yes
No
Hsap\PLAGL1
1 of 14
Yes
Yes
Hsap\PRDM1
1 of 14
Yes
No
Hsap\PRDM9
1 of 14
Yes
No
Hsap\REPIN1
1 of 14
Yes
No
Hsap\RREB1
1 of 14
Yes
No
1  
Hsap\SALL4
1 of 14
Yes
No
1  
Hsap\ZBTB17
1 of 14
Yes
Yes
Hsap\ZBTB24
1 of 14
Yes
No
1  
Hsap\ZBTB47
1 of 14
Yes
No
Hsap\ZBTB48
1 of 14
Yes
No
Hsap\ZEB2
1 of 14
Yes
No
Hsap\ZFP1
1 of 14
Yes
Yes
Hsap\ZFP3
1 of 14
Yes
No
Hsap\ZFP28
1 of 14
Yes
No
Hsap\ZFP62
1 of 14
Yes
No
Hsap\ZFP69B
1 of 14
Yes
No
Hsap\ZIK1
1 of 14
Yes
No
Hsap\ZIM3
1 of 14
Yes
Yes
Hsap\ZNF16
1 of 14
Yes
No
Hsap\ZNF28
1 of 14
Yes
No
Hsap\ZNF35
1 of 14
Yes
No
Hsap\ZNF45
1 of 14
Yes
No
Hsap\ZNF57
1 of 14
Yes
Yes
Hsap\ZNF66
1 of 14
Yes
No
Hsap\ZNF71
1 of 14
Yes
No
Hsap\ZNF75D
1 of 14
Yes
Yes
Hsap\ZNF83
1 of 14
Yes
No
Hsap\ZNF84
1 of 14
Yes
No
Hsap\ZNF91
1 of 14
Yes
No
Hsap\ZNF93
1 of 14
Yes
No
Hsap\ZNF112
1 of 14
Yes
No
Hsap\ZNF131
1 of 14
Yes
No
Hsap\ZNF154
1 of 14
Yes
Yes
Hsap\ZNF184
1 of 14
Yes
No
Hsap\ZNF189
1 of 14
Yes
No
Hsap\ZNF211
1 of 14
Yes
No
Hsap\ZNF214
1 of 14
Yes
No
Hsap\ZNF223
1 of 14
Yes
No
Hsap\ZNF225
1 of 14
Yes
No
Hsap\ZNF226
1 of 14
Yes
No
Hsap\ZNF229
1 of 14
Yes
No
Hsap\ZNF234
1 of 14
Yes
No
Hsap\ZNF256
1 of 14
Yes
No
Hsap\ZNF267
1 of 14
Yes
No
1  
Hsap\ZNF275
1 of 14
Yes
No
Hsap\ZNF282
1 of 14
Yes
No
Hsap\ZNF287
1 of 14
Yes
No
Hsap\ZNF322
1 of 14
Yes
No
Hsap\ZNF334
1 of 14
Yes
No
Hsap\ZNF347
1 of 14
Yes
No
Hsap\ZNF354B
1 of 14
Yes
No
Hsap\ZNF358
1 of 14
Yes
No
Hsap\ZNF391
1 of 14
Yes
Yes
Hsap\ZNF397
1 of 14
Yes
No
Hsap\ZNF408
1 of 14
Yes
No
Hsap\ZNF415
1 of 14
Yes
No
Hsap\ZNF417
1 of 14
Yes
No
Hsap\ZNF418
1 of 14
Yes
No
Hsap\ZNF430
1 of 14
Yes
No
Hsap\ZNF436
1 of 14
Yes
No
Hsap\ZNF454
1 of 14
Yes
No
Hsap\ZNF470
1 of 14
Yes
No
Hsap\ZNF483
1 of 14
Yes
Yes
Hsap\ZNF484
1 of 14
Yes
No
Hsap\ZNF490
1 of 14
Yes
Yes
Hsap\ZNF506
1 of 14
Yes
No
Hsap\ZNF530
1 of 14
Yes
No
Hsap\ZNF534
1 of 14
Yes
No
Hsap\ZNF544
1 of 14
Yes
No
Hsap\ZNF546
1 of 14
Yes
No
Hsap\ZNF549
1 of 14
Yes
No
Hsap\ZNF551
1 of 14
Yes
No
Hsap\ZNF557
1 of 14
Yes
No
Hsap\ZNF561
1 of 14
Yes
Yes
Hsap\ZNF567
1 of 14
Yes
No
Hsap\ZNF569
1 of 14
Yes
No
Hsap\ZNF577
1 of 14
Yes
No
Hsap\ZNF583
1 of 14
Yes
No
Hsap\ZNF586
1 of 14
Yes
No
Hsap\ZNF587
1 of 14
Yes
No
Hsap\ZNF594
1 of 14
Yes
No
Hsap\ZNF595
1 of 14
Yes
No
Hsap\ZNF600
1 of 14
Yes
No
Hsap\ZNF606
1 of 14
Yes
No
Hsap\ZNF613
1 of 14
Yes
No
Hsap\ZNF615
1 of 14
Yes
No
Hsap\ZNF616
1 of 14
Yes
No
Hsap\ZNF620
1 of 14
Yes
Yes
Hsap\ZNF624
1 of 14
Yes
No
Hsap\ZNF626
1 of 14
Yes
No
Hsap\ZNF629
1 of 14
Yes
No
Hsap\ZNF649
1 of 14
Yes
Yes
Hsap\ZNF658B
1 of 14
Yes
No
Hsap\ZNF658
1 of 14
Yes
No
Hsap\ZNF668
1 of 14
Yes
Yes
Hsap\ZNF674
1 of 14
Yes
No
Hsap\ZNF678
1 of 14
Yes
No
Hsap\ZNF680
1 of 14
Yes
No
Hsap\ZNF681
1 of 14
Yes
No
Hsap\ZNF682
1 of 14
Yes
No
Hsap\ZNF689
1 of 14
Yes
No
Hsap\ZNF710
1 of 14
Yes
No
Hsap\ZNF718
1 of 14
Yes
No
Hsap\ZNF721
1 of 14
Yes
No
Hsap\ZNF723
1 of 14
Yes
No
Hsap\ZNF726
1 of 14
Yes
No
Hsap\ZNF727
1 of 14
Yes
No
Hsap\ZNF736
1 of 14
Yes
No
Hsap\ZNF737
1 of 14
Yes
No
Hsap\ZNF746
1 of 14
Yes
No
3  
Hsap\ZNF761
1 of 14
Yes
No
Hsap\ZNF765-ZNF761
1 of 14
Yes
No
Hsap\ZNF768
1 of 14
Yes
No
Hsap\ZNF776
1 of 14
Yes
No
Hsap\ZNF777
1 of 14
Yes
No
Hsap\ZNF778
1 of 14
Yes
No
Hsap\ZNF782
1 of 14
Yes
No
Hsap\ZNF808
1 of 14
Yes
No
Hsap\ZNF829
1 of 14
Yes
No
Hsap\ZNF845
1 of 14
Yes
No
Hsap\ZNF846
1 of 14
Yes
No
Hsap\ZNF860
1 of 14
Yes
No
Hsap\ZNF875
1 of 14
Yes
No
Hsap\ZNF879
1 of 14
Yes
No
Hsap\ZNF880
1 of 14
Yes
No
Hsap\ZSCAN1
1 of 14
Yes
No
Hsap\ZSCAN10
1 of 14
Yes
No
Hsap\ZSCAN12
1 of 14
Yes
No
Hsap\ZSCAN22
1 of 14
Yes
No
Hsap\ZSCAN30
1 of 14
Yes
Yes
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) (14)
Rnor\Plagl1
1 of 14
Yes
Yes
Rnor\Prdm16
1 of 14
Yes
No
Rnor\Rreb1
1 of 14
Yes
No
Rnor\Zbtb48
1 of 14
Yes
No
Rnor\Zeb2
1 of 14
Yes
No
Rnor\Zfp1
1 of 14
Yes
No
Rnor\Zfp26
1 of 14
Yes
No
Rnor\Zfp62
1 of 14
Yes
No
Rnor\Zfp131
1 of 14
Yes
No
Rnor\Zfp180
1 of 14
Yes
No
Rnor\Zfp451
1 of 14
Yes
Yes
Rnor\Zfp560
1 of 14
Yes
No
Rnor\Zfp710
1 of 14
Yes
Yes
Rnor\Znf354b
1 of 14
Yes
Yes
Mus musculus (laboratory mouse) (32)
Mmus\2610021A01Rik
1 of 14
Yes
No
Mmus\2610044O15Rik8
1 of 14
Yes
No
Mmus\Gm4724
1 of 14
Yes
No
Mmus\Gm5141
1 of 14
Yes
No
Mmus\Gm14443
1 of 14
Yes
No
Mmus\Prdm13
1 of 14
Yes
No
Mmus\Prdm16
1 of 14
Yes
No
Mmus\Rreb1
1 of 14
Yes
No
Mmus\Zbtb48
1 of 14
Yes
No
Mmus\Zeb2
1 of 14
Yes
No
1  
Mmus\Zfp1
1 of 14
Yes
Yes
Mmus\Zfp26
1 of 14
Yes
No
Mmus\Zfp61
1 of 14
Yes
No
Mmus\Zfp62
1 of 14
Yes
No
Mmus\Zfp93
1 of 14
Yes
No
Mmus\Zfp114
1 of 14
Yes
Yes
Mmus\Zfp131
1 of 14
Yes
No
Mmus\Zfp275
1 of 14
Yes
Yes
Mmus\Zfp287
1 of 14
Yes
Yes
Mmus\Zfp300
1 of 14
Yes
No
Mmus\Zfp354b
1 of 14
Yes
Yes
Mmus\Zfp456
1 of 14
Yes
Yes
Mmus\Zfp560
1 of 14
Yes
Yes
Mmus\Zfp710
1 of 14
Yes
Yes
Mmus\Zfp800
1 of 14
Yes
No
Mmus\Zfp808
1 of 14
Yes
No
Mmus\Zfp934
1 of 14
Yes
No
Mmus\Zfp966
1 of 14
Yes
No
Mmus\Zfp967
1 of 14
Yes
No
Mmus\Zfp968
1 of 14
Yes
No
Mmus\Zfp969
1 of 14
Yes
No
Mmus\Zscan22
1 of 14
Yes
No
Xenopus tropicalis (Western clawed frog) (30)
Xtro\e4f1
1 of 13
Yes
Yes
Xtro\hic2
1 of 13
Yes
Yes
Xtro\LOC496795
1 of 13
Yes
No
Xtro\LOC100489584
1 of 13
Yes
No
Xtro\LOC100493797
1 of 13
Yes
No
Xtro\LOC101732550
1 of 13
Yes
No
Xtro\LOC101733242
1 of 13
Yes
No
Xtro\LOC105947126
1 of 13
Yes
No
Xtro\LOC105947706
1 of 13
Yes
No
Xtro\LOC108648854
1 of 13
Yes
No
Xtro\parp6
1 of 13
Yes
Yes
Xtro\prdm1
1 of 13
Yes
No
Xtro\sall4
1 of 13
Yes
No
Xtro\siah3
1 of 13
Yes
No
Xtro\XB5795368
1 of 13
Yes
No
Xtro\zbtb11
1 of 13
Yes
No
Xtro\zbtb43
1 of 13
Yes
No
Xtro\zeb2
1 of 13
Yes
No
Xtro\zfp2
1 of 13
Yes
No
Xtro\znf180
1 of 13
Yes
No
Xtro\znf229
1 of 13
Yes
No
Xtro\znf420
1 of 13
Yes
No
Xtro\znf423
1 of 13
Yes
No
Xtro\znf521
1 of 13
Yes
No
Xtro\znf574
1 of 13
Yes
No
Xtro\znf605
1 of 13
Yes
No
Xtro\znf628
1 of 13
Yes
No
Xtro\znf665
1 of 13
Yes
No
Xtro\znf850
1 of 13
Yes
No
Xtro\znf883l
1 of 13
Yes
No
Danio rerio (Zebrafish) (36)
Drer\ctcf
1 of 14
Yes
No
Drer\im:7141269
1 of 14
Yes
No
Drer\LOC797319
1 of 14
Yes
No
Drer\LOC100148466
1 of 14
Yes
No
Drer\LOC100330321
1 of 14
Yes
No
Drer\LOC100534672
1 of 14
Yes
Yes
Drer\LOC100536922
1 of 14
Yes
No
Drer\LOC101884367
1 of 14
Yes
No
Drer\LOC101886309
1 of 14
Yes
No
Drer\LOC103910773
1 of 14
Yes
No
Drer\LOC103910897
1 of 14
Yes
No
Drer\LOC108182171
1 of 14
Yes
No
Drer\LOC108182318
1 of 14
Yes
No
Drer\LOC108183930
1 of 14
Yes
No
Drer\sall4
1 of 14
Yes
No
Drer\si:cabz01069020.1
1 of 14
Yes
No
Drer\si:ch73-120g24.5
1 of 14
Yes
Yes
Drer\si:ch73-266f23.4
1 of 14
Yes
Yes
Drer\si:ch211-142b24.6
1 of 14
Yes
Yes
Drer\si:ch211-229l10.11
1 of 14
Yes
No
Drer\zbtb18
1 of 14
Yes
Yes
Drer\zbtb48
1 of 14
Yes
No
Drer\zeb1a
1 of 14
Yes
No
Drer\zeb2b
1 of 14
Yes
No
Drer\zgc:113518
1 of 14
Yes
Yes
Drer\zgc:171673
1 of 14
Yes
No
Drer\zgc:171727
1 of 14
Yes
Yes
Drer\zgc:173615
1 of 14
Yes
No
Drer\zgc:174624
1 of 14
Yes
No
Drer\znf648
1 of 14
Yes
Yes
Drer\znf800a
1 of 14
Yes
No
Drer\znf1010
1 of 14
Yes
Yes
Drer\znf1023
1 of 14
Yes
No
Drer\znf1040
1 of 14
Yes
No
Drer\znf1043
1 of 14
Yes
No
Drer\znf1113
1 of 14
Yes
No
Caenorhabditis elegans (Nematode, roundworm) (5)
Cele\mnm-2
2 of 14
Yes
Yes
Cele\pag-3
1 of 14
No
No
Cele\pat-9
1 of 14
No
Yes
Cele\scrt-1
1 of 14
No
No
Cele\Y17G7B.22
1 of 14
No
No
Anopheles gambiae (African malaria mosquito) (22)
Agam\AgaP_AGAP000286
1 of 12
Yes
Yes
Agam\AgaP_AGAP001132
1 of 12
Yes
No
Agam\AgaP_AGAP002163
1 of 12
Yes
No
Agam\AgaP_AGAP002165
1 of 12
Yes
No
Agam\AgaP_AGAP003111
1 of 12
Yes
No
Agam\AgaP_AGAP003991
1 of 12
Yes
No
Agam\AgaP_AGAP004269
1 of 12
Yes
No
Agam\AgaP_AGAP004580
1 of 12
Yes
Yes
Agam\AgaP_AGAP004651
1 of 12
Yes
No
Agam\AgaP_AGAP004667
1 of 12
Yes
No
Agam\AgaP_AGAP005659
1 of 12
Yes
Yes
Agam\AgaP_AGAP006701
1 of 12
Yes
No
Agam\AgaP_AGAP006758
1 of 12
Yes
No
Agam\AgaP_AGAP007389
1 of 12
Yes
No
Agam\AgaP_AGAP008232
1 of 12
Yes
No
Agam\AgaP_AGAP008722
1 of 12
Yes
Yes
Agam\AgaP_AGAP009068
1 of 12
Yes
No
Agam\AgaP_AGAP009096
1 of 12
Yes
No
Agam\AgaP_AGAP009662
1 of 12
Yes
No
Agam\AgaP_AGAP009764
1 of 12
Yes
Yes
Agam\AgaP_AGAP010751
1 of 12
Yes
No
Agam\AgaP_AGAP012410
1 of 12
Yes
No
Arabidopsis thaliana (thale-cress) (1)
Atha\YY1
1 of 13
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\AZF1
1 of 13
Yes
No
Scer\ZAP1
1 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:cliff. 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) (43)
az2
4 of 13
CG1602
4 of 13
rgr
3 of 13
CG1529
2 of 13
MTF-1
2 of 13
Blimp-1
1 of 13
Cf2
1 of 13
CG2116
1 of 13
CG4730
1 of 13
CG4820
1 of 13
CG6654
1 of 13
CG6813
1 of 13
CG8944
1 of 13
CG10543
1 of 13
CG10654
1 of 13
CG11906
1 of 13
CG12236
1 of 13
CG15269
1 of 13
CG17803
1 of 13
CG18764
1 of 13
CG30020
1 of 13
CG42726
1 of 13
CTCF
1 of 13
esg
1 of 13
Imzf
1 of 13
Kah
1 of 13
Meics
1 of 13
Nnk
1 of 13
Odj
1 of 13
pad
1 of 13
Paris
1 of 13
Phs
1 of 13
scrape
1 of 13
scrt
1 of 13
sna
1 of 13
sqz
1 of 13
su(Hw)
1 of 13
trabl
1 of 13
wdn
1 of 13
wor
1 of 13
Zaf1
1 of 13
ZIPIC
1 of 13
zld
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
    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
    cliff - AIF
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - Ask1
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - Bcs1
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - CG10494
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - CG1513
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - CG33523
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - CG8478
    two hybrid array
    (Shokri et al., 2019)
    cliff - CG9205
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - Cp190
    two hybrid, anti bait coimmunoprecipitation, anti tag western blot
    (Sokolov et al., 2024)
    cliff - Ets65A
    two hybrid array
    (Shokri et al., 2019)
    cliff - GAPcenA
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - RanGAP
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - Rel
    two hybrid array
    (Shokri et al., 2019)
    cliff - Sk2
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - az2
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - cert
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - cnc
    two hybrid array
    (Shokri et al., 2019)
    cliff - dco
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - l(2)k01209
    experimental knowledge based
    (Guruharsha et al., 2011)
    cliff - rdgB
    experimental knowledge based
    (Guruharsha et al., 2011)
    Summary of Genetic Interactions
    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
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Ras85D
    suppressible
    cliff
    (Ashton-Beaucage et al., 2014)
    External Data
    Subunit Structure (UniProtKB)
    Interacts (via regions flanking MADF domain 1) with Cp190 (via regions between the BTB domain and first zinc finger domain); the interaction is probably direct and is essential for protein function.
    (UniProt, Q1LZ24 )
    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
    FlyBase
    External Links
    External Data
    Linkouts
    Class of Gene
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2R
    Recombination map
    2-56
    Cytogenetic map
    43D1-43D1
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    43D1-43D1
    Limits computationally determined from genome sequence between P{lacW}cosk16101 and P{EP}CG1600EP398
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    2-56

    (FlyBase, 2016)

    2-56.7

    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (12)
    Genomic Clones (16)
     

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

    cDNA Clones (36)
     

    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
     
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
        Other Comments
        Relationship to Other Genes
        Source for database merge of
        Additional comments
        Nomenclature History
        Source for database identify of

        Source for identity of: cliff CG1603

        (Nowaskie et al., 2023)
        Nomenclature comments
        Etymology

        Named 'clifford' since the observed overgrowth of red-pigmented mutant tissue in eye clones was reminiscent of "Clifford the Big Red Dog".

        (Nowaskie et al., 2023)
        Synonyms and Secondary IDs (3)
        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/Swiss-Prot - Manually annotated and reviewed 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
        Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
        Flygut - An atlas of the Drosophila adult midgut
        MIST (protein-protein) - An integrated Molecular Interaction Database
        References (39)