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Protein

Segmentation protein paired

Gene

prd

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Pair-rule protein expressed in a segmentally repeating pattern to define the polarity of embryonic segments. Capable of sequence-specific DNA-binding.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi213 – 27260HomeoboxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: UniProtKB
  • RNA polymerase II regulatory region sequence-specific DNA binding Source: FlyBase
  • transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding Source: FlyBase

GO - Biological processi

  • periodic partitioning by pair rule gene Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: FlyBase
  • regulation of transcription, DNA-templated Source: UniProtKB
  • transcription from RNA polymerase II promoter Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Pair-rule protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

SignaLinkiP06601.

Names & Taxonomyi

Protein namesi
Recommended name:
Segmentation protein paired
Gene namesi
Name:prd
ORF Names:CG6716
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 2L

Organism-specific databases

FlyBaseiFBgn0003145. prd.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 613613Segmentation protein pairedPRO_0000050167Add
BLAST

Proteomic databases

PaxDbiP06601.
PRIDEiP06601.

Expressioni

Gene expression databases

BgeeiP06601.
GenevisibleiP06601. DM.

Interactioni

Protein-protein interaction databases

BioGridi60680. 11 interactions.
DIPiDIP-22888N.
STRINGi7227.FBpp0079882.

Structurei

Secondary structure

1
613
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi29 – 313Combined sources
Beta strandi37 – 393Combined sources
Helixi46 – 5712Combined sources
Helixi62 – 698Combined sources
Helixi73 – 8614Combined sources
Helixi106 – 1127Combined sources
Turni113 – 1164Combined sources
Helixi122 – 13110Combined sources
Beta strandi133 – 1353Combined sources
Helixi143 – 1497Combined sources
Helixi222 – 23413Combined sources
Helixi240 – 25011Combined sources
Helixi254 – 27522Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FJLX-ray2.00A/B/C196-276[»]
1PDNX-ray2.50C27-154[»]
ProteinModelPortaliP06601.
SMRiP06601. Positions 28-150, 212-276.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06601.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini27 – 153127PairedPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi541 – 57636His/Pro-richAdd
BLAST

Sequence similaritiesi

Belongs to the paired homeobox family.Curated
Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation
Contains 1 paired domain.PROSITE-ProRule annotation

Keywords - Domaini

Homeobox, Paired box, Repeat

Phylogenomic databases

eggNOGiKOG0849. Eukaryota.
ENOG410XS01. LUCA.
GeneTreeiENSGT00680000099553.
InParanoidiP06601.
KOiK09381.
OMAiAAMHRPF.
OrthoDBiEOG7WT431.
PhylomeDBiP06601.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
1.10.10.60. 1 hit.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001523. Paired_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00292. PAX. 1 hit.
[Graphical view]
PRINTSiPR00027. PAIREDBOX.
SMARTiSM00389. HOX. 1 hit.
SM00351. PAX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 2 hits.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00034. PAIRED_1. 1 hit.
PS51057. PAIRED_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform B (identifier: P06601-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MTVTAFAAAM HRPFFNGYST MQDMNSGQGR VNQLGGVFIN GRPLPNNIRL
60 70 80 90 100
KIVEMAADGI RPCVISRQLR VSHGCVSKIL NRYQETGSIR PGVIGGSKPR
110 120 130 140 150
IATPEIENRI EEYKRSSPGM FSWEIREKLI REGVCDRSTA PSVSAISRLV
160 170 180 190 200
RGRDAPLDND MSSASGSPAG DGTKASSSCG SDVSGGHHNN GKPSDEDISD
210 220 230 240 250
CESEPGIALK RKQRRCRTTF SASQLDELER AFERTQYPDI YTREELAQRT
260 270 280 290 300
NLTEARIQVW FSNRRARLRK QHTSVSGGAP GGAAASVSHV AASSSLPSVV
310 320 330 340 350
SSVPSMAPLA MMPGSLDPAT VYQQQYDFYG SHANISVSAA APMASSNLSP
360 370 380 390 400
GITTTPPHHH QFYNPSANTA SYIMPGENGN TTPTGNIIVS SYETQLGSVY
410 420 430 440 450
GTETETHQTM PRNESPNESV SSAFGQLPPT PNSLSAVVSG AGVTSSSGAN
460 470 480 490 500
SGADPSQSLA NASAGSEELS AALKVESVDL IAASQSQLYG GWSSMQALRP
510 520 530 540 550
NAPLSPEDSL NSTSSTSQAL DVTAHQMFHP YQHTPQYASY PAPGHAHSHH
560 570 580 590 600
GHPHAPHPHA HPHPQYAGAH PHYPPPSSSA HFMPQNFNAA AFPSPSKVNY
610
TTMPPQPFYP SWY
Length:613
Mass (Da):65,497
Last modified:January 1, 1988 - v1
Checksum:i777772C6E704C1A2
GO
Isoform A (identifier: P06601-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-23: Missing.

Note: No experimental confirmation available.
Show »
Length:590
Mass (Da):62,920
Checksum:iD4B391B51DE7FF06
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti164 – 1641A → T.
Natural varianti220 – 2201F → I.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 2323Missing in isoform A. 1 PublicationVSP_007021Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M14548 Genomic DNA. Translation: AAB59221.1.
AE014134 Genomic DNA. Translation: AAN10801.1.
AE014134 Genomic DNA. Translation: AAF53160.1.
AY059447 mRNA. Translation: AAL13353.1.
PIRiA26062.
RefSeqiNP_523556.1. NM_078832.3. [P06601-2]
NP_723721.1. NM_164990.3. [P06601-1]
UniGeneiDm.2598.

Genome annotation databases

EnsemblMetazoaiFBtr0080298; FBpp0079882; FBgn0003145. [P06601-1]
GeneIDi34629.
KEGGidme:Dmel_CG6716.
UCSCiCG6716-RA. d. melanogaster. [P06601-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M14548 Genomic DNA. Translation: AAB59221.1.
AE014134 Genomic DNA. Translation: AAN10801.1.
AE014134 Genomic DNA. Translation: AAF53160.1.
AY059447 mRNA. Translation: AAL13353.1.
PIRiA26062.
RefSeqiNP_523556.1. NM_078832.3. [P06601-2]
NP_723721.1. NM_164990.3. [P06601-1]
UniGeneiDm.2598.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FJLX-ray2.00A/B/C196-276[»]
1PDNX-ray2.50C27-154[»]
ProteinModelPortaliP06601.
SMRiP06601. Positions 28-150, 212-276.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi60680. 11 interactions.
DIPiDIP-22888N.
STRINGi7227.FBpp0079882.

Proteomic databases

PaxDbiP06601.
PRIDEiP06601.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0080298; FBpp0079882; FBgn0003145. [P06601-1]
GeneIDi34629.
KEGGidme:Dmel_CG6716.
UCSCiCG6716-RA. d. melanogaster. [P06601-1]

Organism-specific databases

CTDi5548.
FlyBaseiFBgn0003145. prd.

Phylogenomic databases

eggNOGiKOG0849. Eukaryota.
ENOG410XS01. LUCA.
GeneTreeiENSGT00680000099553.
InParanoidiP06601.
KOiK09381.
OMAiAAMHRPF.
OrthoDBiEOG7WT431.
PhylomeDBiP06601.

Enzyme and pathway databases

SignaLinkiP06601.

Miscellaneous databases

EvolutionaryTraceiP06601.
GenomeRNAii34629.
PROiP06601.

Gene expression databases

BgeeiP06601.
GenevisibleiP06601. DM.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
1.10.10.60. 1 hit.
InterProiIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR001523. Paired_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00046. Homeobox. 1 hit.
PF00292. PAX. 1 hit.
[Graphical view]
PRINTSiPR00027. PAIREDBOX.
SMARTiSM00389. HOX. 1 hit.
SM00351. PAX. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 2 hits.
PROSITEiPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
PS00034. PAIRED_1. 1 hit.
PS51057. PAIRED_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structure of the segmentation gene paired and the Drosophila PRD gene set as part of a gene network."
    Frigerio G., Burri M., Bopp D., Baumgartner S., Noll M.
    Cell 47:735-746(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM B).
  2. "The genome sequence of Drosophila melanogaster."
    Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D.
    , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.
    Science 287:2185-2195(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Berkeley.
  3. Cited for: GENOME REANNOTATION, ALTERNATIVE SPLICING.
    Strain: Berkeley.
  4. "A Drosophila full-length cDNA resource."
    Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M., Celniker S.E.
    Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A).
    Strain: Berkeley.
    Tissue: Head.
  5. "Crystal structure of a paired domain-DNA complex at 2.5-A resolution reveals structural basis for Pax developmental mutations."
    Xu W., Rould M.A., Jun S., Desplan C., Pabo C.O.
    Cell 80:639-650(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 27-154.
  6. "High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA."
    Wilson D.S., Guenther B., Desplan C., Kuriyan J.
    Cell 82:709-719(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 196-276.

Entry informationi

Entry nameiPRD_DROME
AccessioniPrimary (citable) accession number: P06601
Secondary accession number(s): Q9VKB6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 1, 1988
Last modified: June 8, 2016
This is version 160 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.