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Q925I7 (PDGFD_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 89. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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:

  1. Platelet-derived growth factor D, latent form
    Short name=PDGFD latent form
  2. Platelet-derived growth factor D, receptor-binding form
    Short name=PDGFD receptor-binding form
Gene names
Name:Pdgfd
Synonyms:Scdgfb
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length370 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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. Ref.6 Ref.8 Ref.10

Subunit structure

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

Subcellular location

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

Tissue specificity

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. Ref.2 Ref.5 Ref.8 Ref.9

Post-translational modification

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.

Sequence similarities

Belongs to the PDGF/VEGF growth factor family.

Contains 1 CUB domain.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q925I7-1)

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.
Isoform 2 (identifier: Q925I7-2)

The sequence of this isoform differs from the canonical sequence as follows:
     42-47: Missing.
Isoform 3 (identifier: Q925I7-3)

Also known as: Short;

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2323 Potential
Chain24 – 370347Platelet-derived growth factor D, latent form
PRO_0000250190
Chain250 – 370121Platelet-derived growth factor D, receptor-binding form Potential
PRO_0000250191

Regions

Domain52 – 170119CUB

Sites

Site247 – 2482Cleavage Potential
Site249 – 2502Cleavage Potential

Amino acid modifications

Glycosylation2761N-linked (GlcNAc...) Potential
Disulfide bond109 ↔ 131 By similarity
Disulfide bond296Interchain By similarity
Disulfide bond302 ↔ 360 By similarity
Disulfide bond306 ↔ 362 By similarity

Natural variations

Alternative sequence42 – 476Missing in isoform 2.
VSP_020616
Alternative sequence258 – 2614VDLD → GIEV in isoform 3.
VSP_020617
Alternative sequence262 – 370109Missing in isoform 3.
VSP_020618

Experimental info

Sequence conflict1731F → S in AAH30896. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Long) [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: 9E80B4CF6813BFBE

FASTA37042,809
        10         20         30         40         50         60 
MQRLVLVSIL LCANFSCYPD TFATPQRASI KALRNANLRR DESNHLTDLY QREENIQVTS 

        70         80         90        100        110        120 
NGHVQSPRFP NSYPRNLLLT WWLRSQEKTR IQLSFDHQFG LEEAENDICR YDFVEVEEVS 

       130        140        150        160        170        180 
ESSTVVRGRW CGHKEIPPRI TSRTNQIKIT FKSDDYFVAK PGFKIYYSFV EDFQPEAASE 

       190        200        210        220        230        240 
TNWESVTSSF SGVSYHSPSI TDPTLTADAL DKTVAEFDTV EDLLKHFNPV SWQDDLENLY 

       250        260        270        280        290        300 
LDTPHYRGRS YHDRKSKVDL DRLNDDVKRY SCTPRNHSVN LREELKLTNA VFFPRCLLVQ 

       310        320        330        340        350        360 
RCGGNCGCGT VNWKSCTCSS GKTVKKYHEV LKFEPGHFKR RGKAKNMALV DIQLDHHERC 

       370 
DCICSSRPPR 

« Hide

Isoform 2 [UniParc].

Checksum: 4273B8715A7DBC97
Show »

FASTA36442,127
Isoform 3 (Short) [UniParc].

Checksum: 3AA92B3236B16809
Show »

FASTA26130,289

References

« Hide 'large scale' references
[1]"PDGF D, a novel protease-activated growth factor."
LaRochelle W.J., Jeffers M., McDonald W.F., Chillakuru R.A., Giese N.A., Lokker N.A., Sullivan C., Boldog F.L., Yang M., Vernet C., Burgess C.E., Fernandez E., Deegler L.L., Rittman B., Shimkets J., Shimkets R.A., Rothberg J.M., Lichenstein H.S.
Nat. Cell Biol. 3:517-521(2001) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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]"PDGF signaling in cells and mice."
Tallquist M., Kazlauskas A.
Cytokine Growth Factor Rev. 15:205-213(2004) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF335583 mRNA. Translation: AAK38839.1.
AK003359 mRNA. Translation: BAB22735.2.
AK141551 mRNA. Translation: BAE24732.1.
BC030896 mRNA. Translation: AAH30896.1.
RefSeqNP_082200.1. NM_027924.2.
XP_006509948.1. XM_006509885.1.
XP_006509949.1. XM_006509886.1.
UniGeneMm.390122.

3D structure databases

ProteinModelPortalQ925I7.
SMRQ925I7. Positions 9-206, 263-365.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING10090.ENSMUSP00000056240.

PTM databases

PhosphoSiteQ925I7.

Proteomic databases

PaxDbQ925I7.
PRIDEQ925I7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000058692; ENSMUSP00000056240; ENSMUSG00000032006. [Q925I7-2]
ENSMUST00000168039; ENSMUSP00000128388; ENSMUSG00000032006. [Q925I7-1]
GeneID71785.
KEGGmmu:71785.
UCSCuc009oby.1. mouse. [Q925I7-1]
uc009obz.1. mouse. [Q925I7-2]
uc012gnq.1. mouse. [Q925I7-3]

Organism-specific databases

CTD80310.
MGIMGI:1919035. Pdgfd.

Phylogenomic databases

eggNOGNOG148355.
GeneTreeENSGT00390000005171.
HOGENOMHOG000261610.
HOVERGENHBG057324.
InParanoidQ925I7.
KOK05450.
OMAHYRGRSY.
OrthoDBEOG7VB2FN.
PhylomeDBQ925I7.
TreeFamTF332130.

Gene expression databases

BgeeQ925I7.
CleanExMM_PDGFD.
GenevestigatorQ925I7.

Family and domain databases

Gene3D2.60.120.290. 1 hit.
InterProIPR000859. CUB_dom.
IPR000072. PDGF/VEGF_dom.
IPR027123. PDGFC/D.
[Graphical view]
PANTHERPTHR10127:SF13. PTHR10127:SF13. 1 hit.
PfamPF00431. CUB. 1 hit.
PF00341. PDGF. 1 hit.
[Graphical view]
SMARTSM00042. CUB. 1 hit.
SM00141. PDGF. 1 hit.
[Graphical view]
SUPFAMSSF49854. SSF49854. 1 hit.
PROSITEPS01180. CUB. 1 hit.
PS50278. PDGF_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio334516.
PROQ925I7.
SOURCESearch...

Entry information

Entry namePDGFD_MOUSE
AccessionPrimary (citable) accession number: Q925I7
Secondary accession number(s): Q3URF6, Q8K2L3, Q9D1L8
Entry history
Integrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: December 1, 2001
Last modified: April 16, 2014
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot