FlyBase Gene Report: Dmel\HP6

General Information

Symbol

Dmel\HP6

Species

D. melanogaster

Name

Heterochromatin protein 6

Annotation Symbol

CG15636

Feature Type

protein_coding_gene

FlyBase ID

FBgn0031613

Gene Model Status

Current

Stock Availability

8 publicly available

Gene Summary

Heterochromatin protein 6 (HP6) encodes a chromo shadow domain protein involved in telomere capping. [Date last reviewed: 2019-09-19] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Interactive Fly

Also Known As

Umbrea

Key Links

Genomic Location

Cytogenetic map

25A1-25A1

Sequence location

2L:4,577,719..4,578,218 [-]

Recombination map

2-13

RefSeq locus

NT_033779 REGION:4577719..4578218

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (14 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables protein binding

inferred from physical interaction with UniProtKB:Q95RV2

(Joppich et al., 2009)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

enables chromatin binding

inferred from biological aspect of ancestor with PANTHER:PTN000517042

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity with FLYBASE:Su(var)205; FB:FBgn0003607

(Levine et al., 2012)

Biological Process (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in female meiotic nuclear division

inferred from mutant phenotype

(Mukai et al., 2007)

involved_in telomere capping

inferred from mutant phenotype

(Joppich et al., 2009)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in chromosome organization

inferred from sequence or structural similarity with FLYBASE:Su(var)205; FB:FBgn0003607

(Levine et al., 2012)

involved_in heterochromatin formation

inferred from biological aspect of ancestor with PANTHER:PTN000517042

(GO Reference Genome Project, 2011-)

Cellular Component (8 terms)

Terms Based on Experimental Evidence (6 terms)

CV Term

Evidence

References

located_in chromocenter

inferred from direct assay

(Joppich et al., 2009)

located_in chromosome, centromeric region

inferred from direct assay

(Ross et al., 2013)

located_in chromosome, telomeric region

inferred from direct assay

(Joppich et al., 2009)

located_in heterochromatin

inferred from direct assay

(Swenson et al., 2016)

located_in nucleolus

inferred from direct assay

(Joppich et al., 2009)

located_in nucleus

inferred from direct assay

(Ida et al., 2009, Greil et al., 2007)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

located_in chromatin

inferred from sequence or structural similarity with FLYBASE:Su(var)205; FB:FBgn0003607

(Levine et al., 2012)

located_in nucleus

inferred from electronic annotation with InterPro:IPR008251

(InterPro Project Members, 2004-)

is_active_in pericentric heterochromatin

inferred from biological aspect of ancestor with PANTHER:PTN000517042

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Heterochromatin protein 6 (HP6) encodes a chromo shadow domain protein involved in telomere capping. [Date last reviewed: 2019-09-19]

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\HP6 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 Q9VR09)

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 5.43

Gene model reviewed during 5.53

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

HP6-RA

FBtr0077444

NM_134998

500

106

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

HP6-PA

FBpp0077134

11.8

106

4.52

Q9VR09

NP_608842

AAF50999

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

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

Nucleotide / Polypeptide Records

UniProt

Q9VR09

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\HP6 using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

HP6_1

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).

4.34

Transcript Expression

RT-PCR

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

organism

Comment: highest in adult males

(Ida et al., 2009)

adult stage | male

testis

(Ida et al., 2009)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | male

testis | apical

(Ida et al., 2009)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in chromocenter

inferred from direct assay

(Joppich et al., 2009)

located_in chromosome, centromeric region

inferred from direct assay

(Ross et al., 2013)

located_in chromosome, telomeric region

inferred from direct assay

(Joppich et al., 2009)

located_in heterochromatin

inferred from direct assay

(Swenson et al., 2016)

located_in nucleolus

inferred from direct assay

(Joppich et al., 2009)

located_in nucleus

inferred from direct assay

(Ida et al., 2009, Greil et al., 2007)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\HP6 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\HP6

View exonic expression by tissue for Dmel\HP6

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

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

33661/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0031613

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0031613

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0031613

Flygut - An atlas of the Drosophila adult midgut

FBgn0031613

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 7 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 7 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of HP6

Transgenic constructs containing regulatory region of HP6

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(2L)Exel8011

(Ryder, 2004.4.26)

Inferred from location ( 2 )

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

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

HP6^GD4434

viable, with Scer\GAL4^pnr-MD237

HP6^GD4434

viable, with Scer\GAL4^tin.CΔ4

HP6^GD4434

Other Phenotypes

Allele

abnormal neuroanatomy | larval stage, with Scer\GAL4^insc-Mz1407

HP6^GD4434

visible, with Scer\GAL4^pnr-MD237

HP6^GD4434

Phenotype manifest in

Allele

chromosome, telomeric region, with Scer\GAL4^G61

HP6^GD4434

embryonic/larval salivary gland, with Scer\GAL4^G61

HP6^GD4434

eye, with Scer\GAL4^GMR.PS

HP6^UAS.cIa

ganglion mother cell | larval stage, with Scer\GAL4^insc-Mz1407

HP6^GD4434

larval neuroblast | larval stage, with Scer\GAL4^insc-Mz1407

HP6^GD4434

mesonotum, with Scer\GAL4^pnr-MD237

HP6^GD4434

polar body nucleus

HP6^36-5

trichogen cell, with Scer\GAL4^pnr-MD237

HP6^GD4434

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (17)

Hsap\CBX3

5 of 14

Yes

4 of 14

4 of 14

3 of 14

3 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (14)

Rnor\Cbx3

5 of 14

Yes

4 of 14

4 of 14

3 of 14

3 of 14

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (13)

Mmus\Cbx1

4 of 14

Yes

Mmus\Cbx3

4 of 14

Yes

Mmus\Cbx5

4 of 14

Yes

Mmus\Cbx7

3 of 14

Mmus\Mphosph8

3 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (14)

Xtro\cbx3

4 of 13

Yes

3 of 13

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Xtro\ucn3

1 of 13

Yes

Danio rerio (Zebrafish) (17)

Drer\cbx3b

5 of 14

Yes

4 of 14

4 of 14

4 of 14

3 of 14

3 of 14

3 of 14

Yes

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (12)

Cele\hpl-1

6 of 14

Yes

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Cele\W05F2.8

1 of 14

Anopheles gambiae (African malaria mosquito) (4)

Agam\AgaP_AGAP004723

5 of 12

Yes

Agam\AgaP_AGAP009444

5 of 12

Yes

Agam\AgaP_AGAP012013

2 of 12

Agam\AgaP_AGAP003597

1 of 12

Arabidopsis thaliana (thale-cress) (1)

Atha\TFL2

3 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (5)

Spom\chp1

3 of 12

Yes

Spom\chp2

3 of 12

Yes

Spom\swi6

3 of 12

Yes

Spom\clr4

1 of 12

Spom\hrp3

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:HP6. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (12)

6 of 13

6 of 13

5 of 13

5 of 13

rhi

5 of 13

CG8289

4 of 13

Oxp

4 of 13

3 of 13

2 of 13

1 of 13

1 of 13

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?

5 of 14

4 of 14

4 of 14

3 of 14

MPHOSPH8; M-phase phosphoprotein 8

3 of 14

611626

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

HP6 - CG34334

two hybrid

(Hu et al., 2017.6.13)

HP6 - HP4

anti bait coimmunoprecipitation, western blot, pull down, anti tag western blot, two hybrid

(Hu et al., 2017.6.13, Joppich et al., 2009)

HP6 - HP5

two hybrid

(Hu et al., 2017.6.13)

HP6 - Hmr

anti tag coimmunoprecipitation, peptide massfingerprinting, western blot

(Thomae et al., 2013)

HP6 - Jupiter

two hybrid

(Hu et al., 2017.6.13)

HP6 - Lhr

anti tag coimmunoprecipitation, western blot, two hybrid, peptide massfingerprinting

(Thomae et al., 2013, Brideau and Barbash, 2011)

HP6 - Msr-110

two hybrid

(Hu et al., 2017.6.13)

HP6 - Odj

two hybrid

(van Bemmel et al., 2013)

HP6 - Su(var)205

pull down, anti tag western blot, anti bait coimmunoprecipitation, western blot

(Joppich et al., 2009)

HP6 - XNP

two hybrid

(Hu et al., 2017.6.13)

HP6 - cav

pull down, anti tag western blot

(Joppich et al., 2009)

HP6 - dmt

two hybrid

(Hu et al., 2017.6.13)

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

suppressible

(Ida et al., 2009)

enhanceable

(Ida et al., 2009)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

59854

DroID - A comprehensive database of gene and protein interactions.

FBgn0031613

MIST (genetic) - An integrated Molecular Interaction Database

33661

MIST (protein-protein) - An integrated Molecular Interaction Database

33661

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-13

Cytogenetic map

25A1-25A1

Sequence location

2L:4,577,719..4,578,218 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

25A1-25A1

Limits computationally determined from genome sequence between P{lacW}Tps1^k08903&P{EP}morgue^EP1184 and P{lacW}l(2)k10004^k10004&P{EP}CG3036^EP963

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-13

(FlyBase, 2016)

2-13.7

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

60096

y¹ sc^* v¹ sev²¹; P{TRiP.HMC05090}attP40

12747

w¹¹¹⁸; net¹ P{GT1}HP6^BG01429 dpy^BG01429/In(2LR)Gla, wg^Gla-1 PPO1^Bc

FlyORF

F002385

M{UAS-HP6.ORF.3xHA.GW}ZH-86Fb

NIG-Fly

HMJ24113

y¹ v¹; P{TRiP.HMJ24113}attP40/CyO

M2L-2141

y¹ w¹¹¹⁸; HP6^SK8 P{neoFRT}40A/CyO-Tb

2LG-1700

y² VhaAC39-1^cho-1 v¹; P{U6-HP6.NIG.sgRNA}attP40/CyO

VDRC

v13072

w¹¹¹⁸; P{GD4434}v13072

v13073

w¹¹¹⁸; P{GD4434}v13073/TM3

Genomic Clones (14)

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

cDNA Clones (10)

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

IP05759

Other clones

DPiM_IP05759

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.

FBgn0031613

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0031613

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Ross et al., 2013, Ida et al., 2009, Joppich et al., 2009)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Essential for viability.

(Chen et al., 2010)

DNA-protein interactions: genome-wide binding profile assayed for HP6 protein in Kc167 cells; see Chromatin_types_NKI collection report. Individual protein-binding experiments listed under "Samples" at GEO_GSE22069 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22069).

(Filion et al., 2010)

Umbrea forms discrete dots in heterochromatin.

(Hiatt et al., 2007)

Umbrea contains a chromo shadow domain.

(Hiatt et al., 2007)

Relationship to Other Genes

Source for database merge of

Additional comments

The HP6 gene may have been derived from the HP1b gene, but as the region of similarity between the two genes does not span an exon-exon junction in the parental gene, retroposition cannot necessarily be inferred.

(Zhang et al., 2011)

Umbrea is the result of a duplication of HP1b.

(Hiatt et al., 2007)

Nomenclature History

Source for database identify of

Source for identity of: Umbrea CG15636

(Hiatt and Malik, 2007.2.25)

Source for identity of: HP6 Umbrea

(Greil et al., 2007)

Nomenclature comments

Etymology

"Umbrea" is the "goddess of shadows". This gene encodes an HP1-like protein, and while HP1s have a chromo and a shadow domain, "Umbrea" only has a shadow domain, which is important for its new function.

(Hiatt and Malik, 2007.2.25)

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG15636

(National Institute of Genetics Fly Stocks, 2023-, National Institute of Genetics Fly Stocks, 2022-, Kwon et al., 2016, Hosono et al., 2015, Chen et al., 2012, Levine et al., 2012, Zhang et al., 2011, Chen et al., 2010, Chen et al., 2010, Zhang et al., 2010, Ida et al., 2009, Perkins et al., 2009, Doheny et al., 2008, Greil et al., 2007, Hiatt and Malik, 2007.2.25, Mukai et al., 2007)

UMB

(Levine et al., 2012)

UMBREA

(Levine and Malik, 2013)

Umbrea

(Ross et al., 2013, Thomae et al., 2013, Hiatt and Malik, 2007.2.25, Hiatt et al., 2007)

umbrea

(Joppich et al., 2009)

Name Synonyms

CG15636

Heterochromatin protein 6

(John et al., 2016)

Umbrea

(Levine et al., 2012, Levine et al., 2012, Shevelyov et al., 2009, Brideau and Barbash, 2008, Hiatt and Malik, 2007.2.25, Hiatt et al., 2007)

Secondary FlyBase IDs

Datasets (1)

Study focus (1)

Experimental Role

Project

Project Type

Title

transgene_used

FBGSE22069

genome binding

Protein profiling reveals five principal chromatin types in Drosophila cells.

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 29 )

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.

33661

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

BH023736

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.

Q9VR09

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Q9VR09

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.