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Protein

Glycerophosphodiester phosphodiesterase domain-containing protein 3

Gene

GDPD3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi71 – 711Divalent metal cationSequence analysis
Metal bindingi73 – 731Divalent metal cationSequence analysis
Metal bindingi86 – 861Divalent metal cationSequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerophosphodiester phosphodiesterase domain-containing protein 3 (EC:3.1.-.-)
Gene namesi
Name:GDPD3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:28638. GDPD3.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 22CytoplasmicSequence analysis
Transmembranei3 – 2321HelicalSequence analysisAdd
BLAST
Topological domaini24 – 198175ExtracellularSequence analysisAdd
BLAST
Transmembranei199 – 22123HelicalSequence analysisAdd
BLAST
Topological domaini222 – 31897CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • integral component of membrane Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA142671741.

Polymorphism and mutation databases

BioMutaiGDPD3.
DMDMi226694188.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 318318Glycerophosphodiester phosphodiesterase domain-containing protein 3PRO_0000251936Add
BLAST

Proteomic databases

EPDiQ7L5L3.
MaxQBiQ7L5L3.
PaxDbiQ7L5L3.
PRIDEiQ7L5L3.

PTM databases

PhosphoSiteiQ7L5L3.

Expressioni

Gene expression databases

BgeeiQ7L5L3.
CleanExiHS_GDPD3.
ExpressionAtlasiQ7L5L3. baseline and differential.
GenevisibleiQ7L5L3. HS.

Organism-specific databases

HPAiHPA041148.
HPA041470.

Interactioni

Protein-protein interaction databases

BioGridi122571. 6 interactions.
STRINGi9606.ENSP00000384363.

Structurei

3D structure databases

ProteinModelPortaliQ7L5L3.
SMRiQ7L5L3. Positions 38-308.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini39 – 308270GP-PDEAdd
BLAST

Sequence similaritiesi

Contains 1 GP-PDE domain.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000046745.
HOGENOMiHOG000008170.
HOVERGENiHBG054611.
InParanoidiQ7L5L3.
OMAiRPHLLHT.
PhylomeDBiQ7L5L3.
TreeFamiTF328545.

Family and domain databases

Gene3Di3.20.20.190. 1 hit.
InterProiIPR004129. GlyceroP-diester-Pdiesterase.
IPR030395. GP_PDE_dom.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PANTHERiPTHR23344. PTHR23344. 1 hit.
PfamiPF03009. GDPD. 1 hit.
[Graphical view]
SUPFAMiSSF51695. SSF51695. 1 hit.
PROSITEiPS51704. GP_PDE. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q7L5L3-2) [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
MSLLLYYALP ALGSYAMLSI FFLRRPHLLH TPRAPTFRIR LGAHRGGSGE
60 70 80 90 100
LLENTMEAME NSMAQRSDLL ELDCQLTRDR VVVVSHDENL CRQSGLNRDV
110 120 130 140 150
GSLDFEDLPL YKEKLEVYFS PGHFAHGSDR RMVRLEDLFQ RFPRTPMSVE
160 170 180 190 200
IKGKNEELIR EIAGLVRRYD RNEITIWASE KSSVMKKCKA ANPEMPLSFT
210 220 230 240 250
ISRGFWVLLS YYLGLLPFIP IPEKFFFCFL PNIINRTYFP FSCSCLNQLL
260 270 280 290 300
AVVSKWLIMR KSLIRHLEER GVQVVFWCLN EESDFEAAFS VGATGVITDY
310
PTALRHYLDN HGPAARTS
Length:318
Mass (Da):36,596
Last modified:April 14, 2009 - v3
Checksum:i4BD2FF25CF0CA22E
GO
Isoform 2 (identifier: Q7L5L3-1) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-62: Missing.

Show »
Length:256
Mass (Da):29,624
Checksum:i93D3C82D78A7F0CC
GO

Sequence cautioni

The sequence AAH02714.2 differs from that shown. Reason: Erroneous initiation. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 6262Missing in isoform 2. 1 PublicationVSP_036888Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK026256 mRNA. Translation: BAB15414.1.
AC012645 Genomic DNA. No translation available.
BC002714 mRNA. Translation: AAH02714.2. Different initiation.
CCDSiCCDS10671.2. [Q7L5L3-2]
RefSeqiNP_077283.2. NM_024307.2. [Q7L5L3-2]
UniGeneiHs.289015.

Genome annotation databases

EnsembliENST00000406256; ENSP00000384363; ENSG00000102886. [Q7L5L3-2]
GeneIDi79153.
KEGGihsa:79153.
UCSCiuc002dwp.4. human. [Q7L5L3-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK026256 mRNA. Translation: BAB15414.1.
AC012645 Genomic DNA. No translation available.
BC002714 mRNA. Translation: AAH02714.2. Different initiation.
CCDSiCCDS10671.2. [Q7L5L3-2]
RefSeqiNP_077283.2. NM_024307.2. [Q7L5L3-2]
UniGeneiHs.289015.

3D structure databases

ProteinModelPortaliQ7L5L3.
SMRiQ7L5L3. Positions 38-308.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122571. 6 interactions.
STRINGi9606.ENSP00000384363.

PTM databases

PhosphoSiteiQ7L5L3.

Polymorphism and mutation databases

BioMutaiGDPD3.
DMDMi226694188.

Proteomic databases

EPDiQ7L5L3.
MaxQBiQ7L5L3.
PaxDbiQ7L5L3.
PRIDEiQ7L5L3.

Protocols and materials databases

DNASUi79153.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000406256; ENSP00000384363; ENSG00000102886. [Q7L5L3-2]
GeneIDi79153.
KEGGihsa:79153.
UCSCiuc002dwp.4. human. [Q7L5L3-2]

Organism-specific databases

CTDi79153.
GeneCardsiGDPD3.
HGNCiHGNC:28638. GDPD3.
HPAiHPA041148.
HPA041470.
MIMi616318. gene.
neXtProtiNX_Q7L5L3.
PharmGKBiPA142671741.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000046745.
HOGENOMiHOG000008170.
HOVERGENiHBG054611.
InParanoidiQ7L5L3.
OMAiRPHLLHT.
PhylomeDBiQ7L5L3.
TreeFamiTF328545.

Miscellaneous databases

GenomeRNAii79153.
NextBioi68072.
PROiQ7L5L3.
SOURCEiSearch...

Gene expression databases

BgeeiQ7L5L3.
CleanExiHS_GDPD3.
ExpressionAtlasiQ7L5L3. baseline and differential.
GenevisibleiQ7L5L3. HS.

Family and domain databases

Gene3Di3.20.20.190. 1 hit.
InterProiIPR004129. GlyceroP-diester-Pdiesterase.
IPR030395. GP_PDE_dom.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PANTHERiPTHR23344. PTHR23344. 1 hit.
PfamiPF03009. GDPD. 1 hit.
[Graphical view]
SUPFAMiSSF51695. SSF51695. 1 hit.
PROSITEiPS51704. GP_PDE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Small intestine.
  2. "The sequence and analysis of duplication-rich human chromosome 16."
    Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J.
    , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
    Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Placenta.

Entry informationi

Entry nameiGDPD3_HUMAN
AccessioniPrimary (citable) accession number: Q7L5L3
Secondary accession number(s): Q9H652
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: April 14, 2009
Last modified: March 16, 2016
This is version 99 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  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.