FB2021_01, released Feb 18, 2021

Gene: Dmel\Xpd

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General Information
Symbol
Dmel\Xpd
Species
D. melanogaster
Name
Xeroderma pigmentosum D
Annotation Symbol
CG9433
Feature Type
protein_coding_gene
FlyBase ID
FBgn0261850
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Snapshot
Xeroderma pigmentosum D (Xpd) encodes a DNA helicase that is a subunit of the basal transcription and DNA repair factor TFIIH. [Date last reviewed: 2019-03-21]
Other Summaries
Also Known As

DmXPD, l(2)SH2137, ERCC2

Key Links
Genomic Location
Cytogenetic map
57C4-57C7
Sequence location
2R:21,171,001..21,174,504 [+]
Recombination map

2-93

RefSeq locus
NT_033778 REGION:21171001..21174504
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
GO Summary Ribbons
Gene Ontology (GO) Annotations (26 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
enables 5'-3' DNA helicase activity
inferred from sequence or structural similarity with SGD:S000000973
(Reynaud et al., 1999)
enables ATP binding
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
enables damaged DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000158239
(assigned by GO_Central )
(Gaudet et al., 2011)
enables DNA helicase activity
inferred from biological aspect of ancestor with PANTHER:PTN000158192
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (15 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
involved_in cellular response to DNA damage stimulus
inferred from direct assay
(Reynaud et al., 1999)
involved_in negative regulation of G2/M transition of mitotic cell cycle
inferred from direct assay
(Chen et al., 2003)
involved_in regulation of chromosome segregation
inferred from mutant phenotype
(Li et al., 2010)
involved_in regulation of mitotic nuclear division
inferred from mutant phenotype
(Chen et al., 2003)
involved_in regulation of syncytial blastoderm mitotic cell cycle
inferred from mutant phenotype
(Stettler et al., 2015)
involved_in response to UV
inferred from direct assay
(Sandoval and Zurita, 2001, Reynaud et al., 1999)
inferred from mutant phenotype
(Stettler et al., 2015)
Terms Based on Predictions or Assertions (10 terms)
CV Term
Evidence
References
involved_in nucleotide-excision repair, DNA duplex unwinding
inferred from biological aspect of ancestor with PANTHER:PTN000158239
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in nucleotide-excision repair, DNA incision
inferred from biological aspect of ancestor with PANTHER:PTN000158239
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in nucleotide-excision repair
inferred from sequence or structural similarity with HGNC:3434
(Reynaud et al., 1999)
inferred from sequence or structural similarity with SGD:S000000973
(Reynaud et al., 1999)
involved_in positive regulation of mitotic recombination
inferred from biological aspect of ancestor with PANTHER:PTN000158239
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in promoter clearance from RNA polymerase II promoter
inferred from sequence or structural similarity with HGNC:3434
(Reynaud et al., 1999)
involved_in response to oxidative stress
inferred from biological aspect of ancestor with PANTHER:PTN000158239
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in response to UV
inferred from biological aspect of ancestor with PANTHER:PTN000158239
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in transcription by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN000158239
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in transcription initiation from RNA polymerase II promoter
inferred from sequence or structural similarity with HGNC:3434
(Aoyagi and Wassarman, 2000)
inferred from sequence or structural similarity with SGD:S000000973
(Aoyagi and Wassarman, 2000)
involved_in transcription open complex formation at RNA polymerase II promoter
inferred from sequence or structural similarity with HGNC:3434
(Reynaud et al., 1999)
Cellular Component (7 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Reynaud et al., 1999)
located_in nucleus
inferred from direct assay
(Aguilar-Fuentes et al., 2008, Fregoso et al., 2007, Reynaud et al., 1999)
located_in polytene chromosome interband
inferred from direct assay
(Reynaud et al., 1999)
located_in polytene chromosome puff
inferred from direct assay
(Reynaud et al., 1999)
located_in polytene chromosome
inferred from direct assay
(Herrera-Cruz et al., 2012)
part_of transcription factor TFIIH core complex
inferred from direct assay
(Aguilar-Fuentes et al., 2008)
part_of transcription factor TFIIH holo complex
(Stettler et al., 2015)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
located_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000158239
(assigned by GO_Central )
(Gaudet et al., 2011)
part_of transcription factor TFIIH core complex
inferred from sequence or structural similarity with HGNC:3434
(Reynaud et al., 1999)
part_of transcription factor TFIIH holo complex
inferred from sequence or structural similarity with SGD:S000000973
(Aoyagi and Wassarman, 2000, Reynaud et al., 1999)
inferred from sequence or structural similarity with HGNC:3434
(Aoyagi and Wassarman, 2000)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
TRANSCRIPTION FACTOR II H - CORE COMPLEX -
The general transcription factor complex Transcription factor II H (TFIIH) is required in RNA pol II transcription at initiation, promoter escape, early elongation steps and transcription re-initiation after polymerase pausing. TFIIH can be divided into two subcomplexes: core and cyclin-dependent protein kinase-activating kinase (CAK). The core complex contains an ATP-dependent DNA helicase activity required for promoter DNA opening and nucleotide excision repair (NER). (Adapted from PMID:25693126 and PMID:21592869).
CDK-ACTIVATING KINASE-XERODERMA PIGMENTOSUM D COMPLEX -
The cyclin-dependent kinase (CDK)-activating kinase-Xeroderma pigmentosum D (CAK-XPD) complex is a four-subunit kinase module. CAK-XPD has a role in the regulation of the cell cycle progression in mitosis, where XPD negatively regulates the cell cycle function of the CAK activity. (Adapted from FBrf0227236, FBrf0211947, FBrf0159708 and PMID:21592869).
RAD3/XPD-LIKE DNA HELICASES -
Rad3/XPD-like DNA helicases belong to helicase superfamily 2 and are named after the S. cerevisiae Rad3 and human XPD orthologous genes. They typically contain large inserts within the helicase core domains and feature diverse C-termini and N-termini. The XPD/Rad3 helicase is a component of transcription factor IIH, which functions in transcription initiation and nucleotide excision repair in eukaryotes, catalyzing DNA duplex opening localized to the transcription start site or site of DNA damage, respectively. XPD has a 5' to 3' polarity and the helicase activity is dependent on an iron-sulfur cluster binding domain. The XPD gene is the target of mutation in patients with xeroderma pigmentosum, trichothiodystrophy, and Cockayne's syndrome (Adapted from PMID:20456941 and PMID:18510925.)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Xpd 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
Comments on Gene Model

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

Gene model reviewed during 5.51

Sequence Ontology: Class of Gene
gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Xpd-RA
FBtr0071576
NM_166429
2797
769
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
RefSeq ID
GenBank
Xpd-PA
FBpp0071503
88.0
769
6.75
NP_726036
AAM70857
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)

783 (aa)

(Reynaud et al., 1999)
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
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Xpd 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
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 17
organism
(Reynaud et al., 1999)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 4
organism | ubiquitous
(Reynaud et al., 1999)
embryonic cortex
(Reynaud et al., 1999)
third instar larval stage
embryonic/larval salivary gland
(Reynaud et al., 1999)
embryonic/larval fat body
(Reynaud et al., 1999)
embryonic stage 6 -- 17
• nucleus
(Reynaud et al., 1999)
embryonic stage 5
• nucleus
(Reynaud et al., 1999)
embryonic stage 1 -- 3
organism | ubiquitous | uniform

Comment: maternally deposited

(Reynaud et al., 1999)
embryonic stage 5 -- 17
somatic cell
• nucleus
(Reynaud et al., 1999)
Additional Descriptive Data

Xpd protein is evenly distributed in the syncytial blastoderm embryo, and is not localized to the nucleus. At the cellular blastoderm stage, Xpd protein is mostly nuclear in somatic cells and is not found in pole cells. After the cellular blastoderm stage, Xpd protein is nuclear in both somatic and pole cells. In third instar larvae, Xpd protein is detected in the nuclei of tissues with polytene chromosomes. On the polytene chromosomes, Xpd protein is detected in interbands and are concentrated in specific zones of the puffs. Colocalization of Xpd protein with the protein detected with human anti-p62 antibody indicates that Xpd protein is part of the TFIIH RNA polymerase II transcription complex. Staining in salivary gland chromosomes increase following UV irradiation of larvae. Some cytoplasmic expression of Xpd is also detected in all developmental stages studied; in larval tissues, some cytoplasmic expression is detected in the fat body.

(Reynaud et al., 1999)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Reynaud et al., 1999)
located_in nucleus
inferred from direct assay
(Aguilar-Fuentes et al., 2008, Fregoso et al., 2007, Reynaud et al., 1999)
located_in polytene chromosome interband
inferred from direct assay
(Reynaud et al., 1999)
located_in polytene chromosome puff
inferred from direct assay
(Reynaud et al., 1999)
located_in polytene chromosome
inferred from direct assay
(Herrera-Cruz et al., 2012)
part_of transcription factor TFIIH core complex
inferred from direct assay
(Aguilar-Fuentes et al., 2008)
part_of transcription factor TFIIH holo complex
(Stettler et al., 2015)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Xpd in GBrowse 2
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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
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 ( 34 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Xpd
Transgenic constructs containing regulatory region of Xpd
Aberrations (Deficiencies and Duplications) ( 2 )
Inferred from experimentation
Gene disrupted in
Df(2R)Exel6072
(Ryder, 2004.4.26)
Df(2R)Exel6073
(Ryder, 2004.4.26)
Inferred from location
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal
lethal, with XpdG602D
lethal, with XpdR616P
lethal, with XpdR616W
lethal, with XpdR658H
lethal, with XpdR683Q
lethal, with XpdSH2137
lethal (with Df(2R)K11)
lethal | recessive
lethal - all die during embryonic stage | maternal effect, with Scer\GAL4αTub84B.PL, XpdSH2137
lethal - all die during embryonic stage | maternal effect, with Scer\GAL4αTub84B.PL, XpdUAS.Tag:V5
lethal - all die during embryonic stage | partially | heat sensitive
partially lethal - majority die, with Scer\GAL4pnr-MD237
partially lethal - majority die | conditional, with XpdD234N
partially lethal - majority die | conditional, with XpdG47R
partially lethal - majority die | conditional, with XpdG675R
partially lethal - majority die | conditional, with XpdSH2137
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4tin.CΔ4
Other Phenotypes
Allele
abnormal mitotic cell cycle | embryonic cycle 10, with XpdG47R
abnormal mitotic cell cycle | embryonic cycle 10, with XpdG675R
abnormal mitotic cell cycle | embryonic cycle 10, with XpdR112H
abnormal mitotic cell cycle | embryonic cycle 10, with XpdR601L
abnormal mitotic cell cycle | embryonic cycle 10, with XpdR683W
abnormal mitotic cell cycle | embryonic cycle 10, with XpdR722W
abnormal mitotic cell cycle | embryonic cycle 10, with XpdSH2137
abnormal mitotic cell cycle | embryonic stage
abnormal mitotic cell cycle | embryonic stage | maternal effect, with Scer\GAL4αTub84B.PL, XpdSH2137
abnormal mitotic cell cycle | embryonic stage | maternal effect, with Scer\GAL4αTub84B.PL, XpdUAS.Tag:V5
radiation sensitive | embryonic stage, with XpdD234N
radiation sensitive | embryonic stage, with XpdG47R
radiation sensitive | embryonic stage, with XpdG675R
radiation sensitive | embryonic stage, with XpdSH2137
some die during embryonic stage | maternal effect, with Scer\GAL4αTub84B.PL, XpdSH2137
some die during embryonic stage | maternal effect, with Scer\GAL4αTub84B.PL, XpdUAS.Tag:V5
some die during embryonic stage | partially | heat sensitive
some die during pupal stage, with Scer\GAL4pnr-MD237
visible, with Scer\GAL4pnr-MD237
Phenotype manifest in
Allele
centrosome | embryonic cycle 10, with XpdG47R
centrosome | embryonic cycle 10, with XpdG675R
centrosome | embryonic cycle 10, with XpdR112H
centrosome | embryonic cycle 10, with XpdR683W
centrosome | embryonic cycle 10, with XpdSH2137
mitotic cell cycle | heat sensitive
nuclear chromosome | embryonic cycle 10, with XpdG47R
nuclear chromosome | embryonic cycle 10, with XpdG675R
nuclear chromosome | embryonic cycle 10, with XpdR112H
nuclear chromosome | embryonic cycle 10, with XpdR683W
nuclear chromosome | embryonic cycle 10, with XpdSH2137
trichogen cell, with Scer\GAL4pnr-MD237
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (6)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\ERCC2
14 of 15
Yes
Yes
Hsap\BRIP1
2 of 15
No
No
1  
Hsap\DDX11
2 of 15
No
No
Hsap\RTEL1
2 of 15
No
No
Hsap\LOC102725121
1 of 15
No
Yes
Hsap\MAP2K7
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Ercc2
15 of 15
Yes
Yes
Mmus\Brip1
2 of 15
No
No
Mmus\Ddx11
2 of 15
No
No
Mmus\Rtel1
1 of 15
No
No
Rattus norvegicus (Norway rat) (4)
Rnor\Ercc2
13 of 13
Yes
Yes
Rnor\Rtel1
2 of 13
No
No
Rnor\Brip1
1 of 13
No
No
Rnor\Ddx11
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\ercc2
9 of 12
Yes
Yes
Xtro\brip1
2 of 12
No
Yes
Xtro\ddx11
2 of 12
No
No
Xtro\rtel1
1 of 12
No
No
Danio rerio (Zebrafish) (4)
Drer\ercc2
14 of 15
Yes
Yes
Drer\brip1
2 of 15
No
No
Drer\ddx11
2 of 15
No
No
Drer\rtel1
2 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (5)
Cele\xpd-1
15 of 15
Yes
Yes
Cele\chl-1
2 of 15
No
No
Cele\Y54G2A.50
2 of 15
No
Yes
Cele\dog-1
1 of 15
No
No
Cele\rtel-1
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (7)
Atha\UVH6
9 of 9
Yes
Yes
Atha\AT1G09995
1 of 9
No
Yes
Atha\AT1G20720
1 of 9
No
No
Atha\AT1G20750
1 of 9
No
No
Atha\AT1G79890
1 of 9
No
No
Atha\AT1G79950
1 of 9
No
No
Atha\AT2G05635
1 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\RAD3
14 of 15
Yes
Yes
Scer\CHL1
1 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\rad15
11 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG091902R8 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00002371
Drosophila simulans
Dsim\GD11571
Drosophila sechellia
Dsec\GM15813
Drosophila erecta
Dere\GG22096
Drosophila yakuba
Dyak\GE12176
Drosophila ananassae
Dana\GF11940
Drosophila pseudoobscura pseudoobscura
Dpse\GA25100
Drosophila persimilis
Dper\GL10160
Drosophila willistoni
Dwil\GK21904
Drosophila virilis
Dvir\GJ20544
Drosophila mojavensis
Dmoj\GI20811
Drosophila grimshawi
Dgri\GH20727
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091501KI )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17008608
Glossina morsitans
Tsetse fly
Gmor\GMOY009347
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_12162
Mayetiola destructor
Hessian fly
Mdes\Mdes012334
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL000404
Anopheles darlingi
American malaria mosquito
Adar\ADAC008565
Anopheles gambiae
Malaria mosquito
Agam\AGAP002988
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ018703
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W01D3 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA007191
Danaus plexippus
Monarch butterfly
Dple\DPOGS215089-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL010535
Apis florea
Little honeybee
Aflo\3289410756
Apis mellifera
Western honey bee
Amel\Xpd
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP16405
Bombus terrestris
Buff-tailed bumblebee
Bter\15209166
Linepithema humile
Argentine ant
Lhum\LH12604
Linepithema humile
Argentine ant
Lhum\LH15800
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:000847
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG004274
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_07835
Tribolium castaneum
Red flour beetle
Tcas\TC002825
Pediculus humanus
Human body louse
Phum\PHUM583990
Rhodnius prolixus
Kissing bug
Rpro\RPRC011276
Cimex lectularius
Bed bug
Clec\CLEC005898
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI008186
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_04056
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X01B4 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR005040
Ixodes scapularis
Black-legged tick
Isca\ISCW000859
Stegodyphus mimosarum
African social velvet spider
Smim\KFM63527.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur02g06630
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_324413
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0262 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Ercc2-3
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_028740gn
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Ercc2_1
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Ercc2
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (2)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG4078
4 of 10
CG11403
4 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Model Summary Ribbon
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 8 )
Potential Models Based on Orthology ( 2 )
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
Disease Associations of Human Orthologs (via DIOPT v8.0 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?
ERCC2; ERCC excision repair 2, TFIIH core complex helicase subunit
14 of 15
126340
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
Summary of Genetic Interactions
esyN Network Diagram
esyN Network Key:
Suppression
Enhancement
View in Interactions Browser
Please look at the allele data for full details of the genetic interactions
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Xpd
suppressible
CycB
(Li et al., 2010)
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
crb
suppressible
Xpd
(Yeom et al., 2015)
Mms19
suppressible
Xpd
(Nag et al., 2018)
External Data
Linkouts
DroID - A comprehensive database of gene and protein interactions.
InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
MIST (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2R
Recombination map

2-93

Cytogenetic map
57C4-57C7
Sequence location
2R:21,171,001..21,174,504 [+]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
57C4-57C7
Left limit from in situ hybridisation (FBrf0157097) Right limit from in situ hybridisation (FBrf0157097); Limits computationally determined from genome sequence between P{EP}CG4266EP2258 and P{EP}CG30394EP962&P{lacW}domk08108
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
57C4-57C6
(Oh et al., 2003)
57C6-57C7
(Brodsky, 1999.3.2)
57C5-57C9
(determined by in situ hybridisation)
(Reynaud et al., 1999, Zurita et al., 1998)
Experimentally Determined Recombination Data
Location

2-93

(FlyBase, 2016)

2-100.3

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (9)
Genomic Clones (13)
 

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

cDNA Clones (170)
 

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 GBrowse 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
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
     

    polyclonal

    (Aguilar-Fuentes et al., 2006, Reynaud et al., 1999)
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of

    Source for identity of: Xpd CG9433

    (Kodira, 1999.11)
    Source for database merge of

    Source for merge of: Xpd l(2)SH2137

    (Li et al., 2010)
    Additional comments
    Other Comments

    Xpd regulates the Cdk-activating-kinase (CAK) complex activity and mitotic progression.

    (Chen et al., 2003)

    1 allele of l(2)SH2137 recovered in a P-insertion screen.

    (Oh et al., 2003)

    Gene is involved in pre-replication DNA repair of UV and AA lesions.

    (de Buendia, 1998)
    Origin and Etymology
    Discoverer
    Etymology

    Named "Xpd" after the human ortholog.

    (FlyBase, 2009-)
    Identification
    External Crossreferences and Linkouts ( 76 )
    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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
    Other crossreferences
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    FlyMine - An integrated database for Drosophila genomics
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    InterPro - A database of protein families, domains and functional sites
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (14)
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (75)