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Q925I7

- PDGFD_MOUSE

UniProt

Q925I7 - PDGFD_MOUSE

Protein

Platelet-derived growth factor D

Gene

Pdgfd

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 93 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      Previous versions | rss
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    Functioni

    Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Plays an important role in wound healing By similarity. Has oncogenic potential and can induce tumor formation. Induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix.By similarity3 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei247 – 2482CleavageSequence Analysis
    Sitei249 – 2502CleavageSequence Analysis

    GO - Molecular functioni

    1. platelet-derived growth factor receptor binding Source: MGI

    GO - Biological processi

    1. cellular process Source: MGI
    2. cellular response to amino acid stimulus Source: MGI
    3. multicellular organismal development Source: UniProtKB-KW
    4. platelet-derived growth factor receptor signaling pathway Source: InterPro
    5. positive regulation of cell division Source: UniProtKB-KW
    6. regulation of peptidyl-tyrosine phosphorylation Source: MGI

    Keywords - Molecular functioni

    Developmental protein, Growth factor, Mitogen

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Platelet-derived growth factor D
    Short name:
    PDGF-D
    Alternative name(s):
    Spinal cord-derived growth factor B
    Short name:
    SCDGF-B
    Cleaved into the following 2 chains:
    Platelet-derived growth factor D, receptor-binding form
    Short name:
    PDGFD receptor-binding form
    Gene namesi
    Name:Pdgfd
    Synonyms:Scdgfb
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 9

    Organism-specific databases

    MGIiMGI:1919035. Pdgfd.

    Subcellular locationi

    Secreted By similarity
    Note: Released by platelets upon wounding.By similarity

    GO - Cellular componenti

    1. extracellular space Source: MGI
    2. membrane Source: InterPro

    Keywords - Cellular componenti

    Secreted

    Pathology & Biotechi

    Keywords - Diseasei

    Proto-oncogene

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2323Sequence AnalysisAdd
    BLAST
    Chaini24 – 370347Platelet-derived growth factor D, latent formPRO_0000250190Add
    BLAST
    Chaini250 – 370121Platelet-derived growth factor D, receptor-binding formSequence AnalysisPRO_0000250191Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi109 ↔ 131PROSITE-ProRule annotation
    Glycosylationi276 – 2761N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi296 – 296InterchainPROSITE-ProRule annotation
    Disulfide bondi302 ↔ 360PROSITE-ProRule annotation
    Disulfide bondi306 ↔ 362PROSITE-ProRule annotation

    Post-translational modificationi

    Activated by proteolytic cleavage. Proteolytic removal of the N-terminal CUB domain releasing the core domain is necessary for unmasking the receptor-binding epitopes of the core domain. Cleavage after Arg-247 or Arg-249 by urokinase plasminogen activator gives rise to the active form By similarity.By similarity

    Keywords - PTMi

    Cleavage on pair of basic residues, Disulfide bond, Glycoprotein

    Proteomic databases

    PaxDbiQ925I7.
    PRIDEiQ925I7.

    PTM databases

    PhosphoSiteiQ925I7.

    Expressioni

    Tissue specificityi

    Expressed at high levels in developing heart, lung, kidney and some muscle derivatives. Moderately expressed in liver, brain and testis. In the kidney, localized to glomerular mesangial cells and vascular smooth muscle cells. Up-regulated in areas of renal fibrosis. In mice with unilateral ureteral obstruction, expressed in interstitial cells at day 4, with an increased to maximal expression at day 14.4 Publications

    Gene expression databases

    BgeeiQ925I7.
    CleanExiMM_PDGFD.
    GenevestigatoriQ925I7.

    Interactioni

    Subunit structurei

    Homodimer; disulfide-linked. Interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB By similarity.By similarity

    Protein-protein interaction databases

    STRINGi10090.ENSMUSP00000056240.

    Structurei

    3D structure databases

    ProteinModelPortaliQ925I7.
    SMRiQ925I7. Positions 62-206.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini52 – 170119CUBPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the PDGF/VEGF growth factor family.Curated
    Contains 1 CUB domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiNOG148355.
    GeneTreeiENSGT00390000005171.
    HOGENOMiHOG000261610.
    HOVERGENiHBG057324.
    InParanoidiQ925I7.
    KOiK05450.
    OMAiHYRGRSY.
    OrthoDBiEOG7VB2FN.
    PhylomeDBiQ925I7.
    TreeFamiTF332130.

    Family and domain databases

    Gene3Di2.10.90.10. 1 hit.
    2.60.120.290. 1 hit.
    InterProiIPR000859. CUB_dom.
    IPR029034. Cystine-knot_cytokine.
    IPR000072. PDGF/VEGF_dom.
    IPR027123. PDGFD.
    [Graphical view]
    PANTHERiPTHR10127:SF13. PTHR10127:SF13. 1 hit.
    PfamiPF00431. CUB. 1 hit.
    PF00341. PDGF. 1 hit.
    [Graphical view]
    SMARTiSM00042. CUB. 1 hit.
    SM00141. PDGF. 1 hit.
    [Graphical view]
    SUPFAMiSSF49854. SSF49854. 1 hit.
    SSF57501. SSF57501. 1 hit.
    PROSITEiPS01180. CUB. 1 hit.
    PS50278. PDGF_2. 1 hit.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q925I7-1) [UniParc]FASTAAdd to Basket

    Also known as: Long

    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

    MQRLVLVSIL LCANFSCYPD TFATPQRASI KALRNANLRR DESNHLTDLY    50
    QREENIQVTS NGHVQSPRFP NSYPRNLLLT WWLRSQEKTR IQLSFDHQFG 100
    LEEAENDICR YDFVEVEEVS ESSTVVRGRW CGHKEIPPRI TSRTNQIKIT 150
    FKSDDYFVAK PGFKIYYSFV EDFQPEAASE TNWESVTSSF SGVSYHSPSI 200
    TDPTLTADAL DKTVAEFDTV EDLLKHFNPV SWQDDLENLY LDTPHYRGRS 250
    YHDRKSKVDL DRLNDDVKRY SCTPRNHSVN LREELKLTNA VFFPRCLLVQ 300
    RCGGNCGCGT VNWKSCTCSS GKTVKKYHEV LKFEPGHFKR RGKAKNMALV 350
    DIQLDHHERC DCICSSRPPR 370
    Length:370
    Mass (Da):42,809
    Last modified:December 1, 2001 - v1
    Checksum:i9E80B4CF6813BFBE
    GO
    Isoform 2 (identifier: Q925I7-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         42-47: Missing.

    Show »
    Length:364
    Mass (Da):42,127
    Checksum:i4273B8715A7DBC97
    GO
    Isoform 3 (identifier: Q925I7-3) [UniParc]FASTAAdd to Basket

    Also known as: Short

    The sequence of this isoform differs from the canonical sequence as follows:
         258-261: VDLD → GIEV
         262-370: Missing.

    Show »
    Length:261
    Mass (Da):30,289
    Checksum:i3AA92B3236B16809
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti173 – 1731F → S in AAH30896. (PubMed:15489334)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei42 – 476Missing in isoform 2. 1 PublicationVSP_020616
    Alternative sequencei258 – 2614VDLD → GIEV in isoform 3. 2 PublicationsVSP_020617
    Alternative sequencei262 – 370109Missing in isoform 3. 2 PublicationsVSP_020618Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF335583 mRNA. Translation: AAK38839.1.
    AK003359 mRNA. Translation: BAB22735.2.
    AK141551 mRNA. Translation: BAE24732.1.
    BC030896 mRNA. Translation: AAH30896.1.
    CCDSiCCDS22801.1. [Q925I7-1]
    RefSeqiNP_082200.1. NM_027924.2. [Q925I7-1]
    XP_006509948.1. XM_006509885.1. [Q925I7-2]
    XP_006509949.1. XM_006509886.1. [Q925I7-3]
    UniGeneiMm.390122.

    Genome annotation databases

    EnsembliENSMUST00000058692; ENSMUSP00000056240; ENSMUSG00000032006. [Q925I7-2]
    ENSMUST00000168039; ENSMUSP00000128388; ENSMUSG00000032006. [Q925I7-1]
    GeneIDi71785.
    KEGGimmu:71785.
    UCSCiuc009oby.1. mouse. [Q925I7-1]
    uc009obz.1. mouse. [Q925I7-2]
    uc012gnq.1. mouse. [Q925I7-3]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF335583 mRNA. Translation: AAK38839.1 .
    AK003359 mRNA. Translation: BAB22735.2 .
    AK141551 mRNA. Translation: BAE24732.1 .
    BC030896 mRNA. Translation: AAH30896.1 .
    CCDSi CCDS22801.1. [Q925I7-1 ]
    RefSeqi NP_082200.1. NM_027924.2. [Q925I7-1 ]
    XP_006509948.1. XM_006509885.1. [Q925I7-2 ]
    XP_006509949.1. XM_006509886.1. [Q925I7-3 ]
    UniGenei Mm.390122.

    3D structure databases

    ProteinModelPortali Q925I7.
    SMRi Q925I7. Positions 62-206.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10090.ENSMUSP00000056240.

    PTM databases

    PhosphoSitei Q925I7.

    Proteomic databases

    PaxDbi Q925I7.
    PRIDEi Q925I7.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000058692 ; ENSMUSP00000056240 ; ENSMUSG00000032006 . [Q925I7-2 ]
    ENSMUST00000168039 ; ENSMUSP00000128388 ; ENSMUSG00000032006 . [Q925I7-1 ]
    GeneIDi 71785.
    KEGGi mmu:71785.
    UCSCi uc009oby.1. mouse. [Q925I7-1 ]
    uc009obz.1. mouse. [Q925I7-2 ]
    uc012gnq.1. mouse. [Q925I7-3 ]

    Organism-specific databases

    CTDi 80310.
    MGIi MGI:1919035. Pdgfd.

    Phylogenomic databases

    eggNOGi NOG148355.
    GeneTreei ENSGT00390000005171.
    HOGENOMi HOG000261610.
    HOVERGENi HBG057324.
    InParanoidi Q925I7.
    KOi K05450.
    OMAi HYRGRSY.
    OrthoDBi EOG7VB2FN.
    PhylomeDBi Q925I7.
    TreeFami TF332130.

    Miscellaneous databases

    NextBioi 334516.
    PROi Q925I7.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q925I7.
    CleanExi MM_PDGFD.
    Genevestigatori Q925I7.

    Family and domain databases

    Gene3Di 2.10.90.10. 1 hit.
    2.60.120.290. 1 hit.
    InterProi IPR000859. CUB_dom.
    IPR029034. Cystine-knot_cytokine.
    IPR000072. PDGF/VEGF_dom.
    IPR027123. PDGFD.
    [Graphical view ]
    PANTHERi PTHR10127:SF13. PTHR10127:SF13. 1 hit.
    Pfami PF00431. CUB. 1 hit.
    PF00341. PDGF. 1 hit.
    [Graphical view ]
    SMARTi SM00042. CUB. 1 hit.
    SM00141. PDGF. 1 hit.
    [Graphical view ]
    SUPFAMi SSF49854. SSF49854. 1 hit.
    SSF57501. SSF57501. 1 hit.
    PROSITEi PS01180. CUB. 1 hit.
    PS50278. PDGF_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Strain: BALB/c.
    2. "A novel murine PDGF-D splicing variant results in significant differences in peptide expression and function."
      Zhuo Y., Hoyle G.W., Zhang J., Morris G., Lasky J.A.
      Biochem. Biophys. Res. Commun. 308:126-132(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 3), TISSUE SPECIFICITY.
    3. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
      Strain: C57BL/6J.
      Tissue: Hippocampus.
    4. "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 3).
      Strain: FVB/N.
      Tissue: Mammary gland.
    5. "PDGF-D is a specific, protease-activated ligand for the PDGF beta-receptor."
      Bergsten E., Uutela M., Li X., Pietras K., Oestman A., Heldin C.-H., Alitalo K., Eriksson U.
      Nat. Cell Biol. 3:512-516(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY.
    6. "Platelet-derived growth factor D: tumorigenicity in mice and dysregulated expression in human cancer."
      LaRochelle W.J., Jeffers M., Corvalan J.R.F., Jia X.-C., Feng X., Vanegas S., Vickroy J.D., Yang X.-D., Chen F., Gazit G., Mayotte J., Macaluso J., Rittman B., Wu F., Dhanabal M., Herrmann J., Lichenstein H.S.
      Cancer Res. 62:2468-2473(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    7. Cited for: REVIEW.
    8. "Exogenous PDGF-D is a potent mesangial cell mitogen and causes a severe mesangial proliferative glomerulopathy."
      Hudkins K.L., Gilbertson D.G., Carling M., Taneda S., Hughes S.D., Holdren M.S., Palmer T.E., Topouzis S., Haran A.C., Feldhaus A.L., Alpers C.E.
      J. Am. Soc. Nephrol. 15:286-298(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY.
    9. "Obstructive uropathy in mice and humans: potential role for PDGF-D in the progression of tubulointerstitial injury."
      Taneda S., Hudkins K.L., Topouzis S., Gilbertson D.G., Ophascharoensuk V., Truong L., Johnson R.J., Alpers C.E.
      J. Am. Soc. Nephrol. 14:2544-2555(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY.
    10. "PDGF-D induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis."
      Uutela M., Wirzenius M., Paavonen K., Rajantie I., He Y., Karpanen T., Lohela M., Wiig H., Salven P., Pajusola K., Eriksson U., Alitalo K.
      Blood 104:3198-3204(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiPDGFD_MOUSE
    AccessioniPrimary (citable) accession number: Q925I7
    Secondary accession number(s): Q3URF6, Q8K2L3, Q9D1L8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 19, 2006
    Last sequence update: December 1, 2001
    Last modified: October 1, 2014
    This is version 93 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3