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Protein

Pigment epithelium-derived factor

Gene

SERPINF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Neurotrophic protein; induces extensive neuronal differentiation in retinoblastoma cells. Potent inhibitor of angiogenesis. As it does not undergo the S (stressed) to R (relaxed) conformational transition characteristic of active serpins, it exhibits no serine protease inhibitory activity.2 Publications

GO - Molecular functioni

  • serine-type endopeptidase inhibitor activity Source: ProtInc

GO - Biological processi

Enzyme and pathway databases

SIGNORiP36955

Protein family/group databases

MEROPSiI04.979

Names & Taxonomyi

Protein namesi
Recommended name:
Pigment epithelium-derived factor
Short name:
PEDF
Alternative name(s):
Cell proliferation-inducing gene 35 protein
EPC-1
Serpin F1
Gene namesi
Name:SERPINF1
Synonyms:PEDF
ORF Names:PIG35
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

EuPathDBiHostDB:ENSG00000132386.10
HGNCiHGNC:8824 SERPINF1
MIMi172860 gene
neXtProtiNX_P36955

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Involvement in diseasei

Osteogenesis imperfecta 6 (OI6)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI6 is a severe, autosomal recessive form compatible with OI type III in the Sillence classification.
See also OMIM:613982

Keywords - Diseasei

Dwarfism, Osteogenesis imperfecta

Organism-specific databases

DisGeNETi5176
MalaCardsiSERPINF1
MIMi613982 phenotype
OpenTargetsiENSG00000132386
Orphaneti216812 Osteogenesis imperfecta type 3
PharmGKBiPA35508

Polymorphism and mutation databases

BioMutaiSERPINF1
DMDMi313104314

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 19Add BLAST19
ChainiPRO_000003250820 – 418Pigment epithelium-derived factorAdd BLAST399

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei20Pyrrolidone carboxylic acid1 Publication1
Modified residuei24Phosphoserine; by CK21 Publication1
Modified residuei114Phosphoserine; by CK21 Publication1
Modified residuei227Phosphoserine; by PKA1 Publication1
Glycosylationi285N-linked (GlcNAc...) (complex) asparagine4 Publications1

Post-translational modificationi

The N-terminus is blocked. Extracellular phosphorylation enhances antiangiogenic activity.1 Publication
N- and O-glycosylated. O-glycosylated with a core 1 or possibly core 8 glycan.5 Publications

Keywords - PTMi

Glycoprotein, Phosphoprotein, Pyrrolidone carboxylic acid

Proteomic databases

EPDiP36955
MaxQBiP36955
PaxDbiP36955
PeptideAtlasiP36955
PRIDEiP36955
ProteomicsDBi55243

2D gel databases

REPRODUCTION-2DPAGEiIPI00006114

PTM databases

GlyConnecti645
iPTMnetiP36955
PhosphoSitePlusiP36955

Expressioni

Tissue specificityi

Retinal pigment epithelial cells and blood plasma.1 Publication

Developmental stagei

Expressed in quiescent cells.

Gene expression databases

BgeeiENSG00000132386 Expressed in 226 organ(s), highest expression level in pigmented layer of retina
CleanExiHS_SERPINF1
ExpressionAtlasiP36955 baseline and differential
GenevisibleiP36955 HS

Organism-specific databases

HPAiHPA005825

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
EPM2AIP1Q7L7758EBI-2932733,EBI-6255981

Protein-protein interaction databases

BioGridi111202, 18 interactors
IntActiP36955, 8 interactors
MINTiP36955
STRINGi9606.ENSP00000254722

Structurei

Secondary structure

1418
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP36955
SMRiP36955
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36955

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni371 – 383O-glycosylated at one siteAdd BLAST13

Domaini

The N-terminal (AA 44-121) exhibits neurite outgrowth-inducing activity. The C-terminal exposed loop (AA 382-418) is essential for serpin activity.

Sequence similaritiesi

Belongs to the serpin family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiKOG2392 Eukaryota
COG4826 LUCA
GeneTreeiENSGT00920000149046
HOGENOMiHOG000115489
HOVERGENiHBG106911
InParanoidiP36955
KOiK19614
OMAiLNCKIAQ
OrthoDBiEOG091G09UU
PhylomeDBiP36955
TreeFamiTF317350

Family and domain databases

CDDicd02052 PEDF, 1 hit
InterProiView protein in InterPro
IPR033832 PEDF
IPR023795 Serpin_CS
IPR023796 Serpin_dom
IPR000215 Serpin_fam
IPR036186 Serpin_sf
PANTHERiPTHR11461 PTHR11461, 1 hit
PfamiView protein in Pfam
PF00079 Serpin, 1 hit
SMARTiView protein in SMART
SM00093 SERPIN, 1 hit
SUPFAMiSSF56574 SSF56574, 1 hit
PROSITEiView protein in PROSITE
PS00284 SERPIN, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

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

This entry has 1 described isoform and 10 potential isoforms that are computationally mapped.Show allAlign All

P36955-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MQALVLLLCI GALLGHSSCQ NPASPPEEGS PDPDSTGALV EEEDPFFKVP
60 70 80 90 100
VNKLAAAVSN FGYDLYRVRS STSPTTNVLL SPLSVATALS ALSLGAEQRT
110 120 130 140 150
ESIIHRALYY DLISSPDIHG TYKELLDTVT APQKNLKSAS RIVFEKKLRI
160 170 180 190 200
KSSFVAPLEK SYGTRPRVLT GNPRLDLQEI NNWVQAQMKG KLARSTKEIP
210 220 230 240 250
DEISILLLGV AHFKGQWVTK FDSRKTSLED FYLDEERTVR VPMMSDPKAV
260 270 280 290 300
LRYGLDSDLS CKIAQLPLTG SMSIIFFLPL KVTQNLTLIE ESLTSEFIHD
310 320 330 340 350
IDRELKTVQA VLTVPKLKLS YEGEVTKSLQ EMKLQSLFDS PDFSKITGKP
360 370 380 390 400
IKLTQVEHRA GFEWNEDGAG TTPSPGLQPA HLTFPLDYHL NQPFIFVLRD
410
TDTGALLFIG KILDPRGP
Length:418
Mass (Da):46,312
Last modified:November 30, 2010 - v4
Checksum:i7630DD2B4026A0D3
GO

Computationally mapped potential isoform sequencesi

There are 10 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
I3L2R7I3L2R7_HUMAN
Pigment epithelium-derived factor
SERPINF1
132Annotation score:
I3L1U4I3L1U4_HUMAN
Pigment epithelium-derived factor
SERPINF1
114Annotation score:
I3L3Z3I3L3Z3_HUMAN
Pigment epithelium-derived factor
SERPINF1
111Annotation score:
I3L425I3L425_HUMAN
Pigment epithelium-derived factor
SERPINF1
87Annotation score:
I3L4Z0I3L4Z0_HUMAN
Pigment epithelium-derived factor
SERPINF1
128Annotation score:
I3L4N7I3L4N7_HUMAN
Pigment epithelium-derived factor
SERPINF1
138Annotation score:
I3L107I3L107_HUMAN
Pigment epithelium-derived factor
SERPINF1
99Annotation score:
I3L4F9I3L4F9_HUMAN
Pigment epithelium-derived factor
SERPINF1
90Annotation score:
A0A0J9YXW2A0A0J9YXW2_HUMAN
Pigment epithelium-derived factor
SERPINF1
43Annotation score:
A0A0J9YXF9A0A0J9YXF9_HUMAN
Pigment epithelium-derived factor
SERPINF1
28Annotation score:

Sequence cautioni

The sequence AAA84914 differs from that shown. Reason: Frameshift at position 356.Curated
The sequence AAA93524 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti97 – 98EQ → DE in AAA60058 (PubMed:8434014).Curated2
Sequence conflicti97 – 98EQ → DE in AAB38685 (Ref. 10) Curated2

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00912672T → M Polymorphism; confirmed at protein level. 10 PublicationsCorresponds to variant dbSNP:rs1136287EnsemblClinVar.1
Natural variantiVAR_025500132P → R1 PublicationCorresponds to variant dbSNP:rs1804145EnsemblClinVar.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M76979 mRNA Translation: AAA60058.1
U29953 Genomic DNA Translation: AAA84914.1 Frameshift.
AF400442 mRNA Translation: AAK92491.1
BT007222 mRNA Translation: AAP35886.1
AY513280 mRNA Translation: AAT08033.1
AB593011 mRNA Translation: BAJ83966.1
AB593012 mRNA Translation: BAJ83967.1
AB593013 mRNA Translation: BAJ83968.1
AC130343 Genomic DNA No translation available.
AC130689 Genomic DNA No translation available.
CH471108 Genomic DNA Translation: EAW90577.1
BC000522 mRNA Translation: AAH00522.1
BC013984 mRNA Translation: AAH13984.1
AH004879 Genomic DNA Translation: AAB38685.1
M90439 mRNA Translation: AAA93524.1 Different initiation.
CCDSiCCDS11012.1
PIRiA46046
A47281
RefSeqiNP_001316832.1, NM_001329903.1
NP_002606.3, NM_002615.6
UniGeneiHs.532768

Genome annotation databases

EnsembliENST00000254722; ENSP00000254722; ENSG00000132386
GeneIDi5176
KEGGihsa:5176
UCSCiuc002ftl.4 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M76979 mRNA Translation: AAA60058.1
U29953 Genomic DNA Translation: AAA84914.1 Frameshift.
AF400442 mRNA Translation: AAK92491.1
BT007222 mRNA Translation: AAP35886.1
AY513280 mRNA Translation: AAT08033.1
AB593011 mRNA Translation: BAJ83966.1
AB593012 mRNA Translation: BAJ83967.1
AB593013 mRNA Translation: BAJ83968.1
AC130343 Genomic DNA No translation available.
AC130689 Genomic DNA No translation available.
CH471108 Genomic DNA Translation: EAW90577.1
BC000522 mRNA Translation: AAH00522.1
BC013984 mRNA Translation: AAH13984.1
AH004879 Genomic DNA Translation: AAB38685.1
M90439 mRNA Translation: AAA93524.1 Different initiation.
CCDSiCCDS11012.1
PIRiA46046
A47281
RefSeqiNP_001316832.1, NM_001329903.1
NP_002606.3, NM_002615.6
UniGeneiHs.532768

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IMVX-ray2.85A21-418[»]
ProteinModelPortaliP36955
SMRiP36955
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111202, 18 interactors
IntActiP36955, 8 interactors
MINTiP36955
STRINGi9606.ENSP00000254722

Protein family/group databases

MEROPSiI04.979

PTM databases

GlyConnecti645
iPTMnetiP36955
PhosphoSitePlusiP36955

Polymorphism and mutation databases

BioMutaiSERPINF1
DMDMi313104314

2D gel databases

REPRODUCTION-2DPAGEiIPI00006114

Proteomic databases

EPDiP36955
MaxQBiP36955
PaxDbiP36955
PeptideAtlasiP36955
PRIDEiP36955
ProteomicsDBi55243

Protocols and materials databases

DNASUi5176
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000254722; ENSP00000254722; ENSG00000132386
GeneIDi5176
KEGGihsa:5176
UCSCiuc002ftl.4 human

Organism-specific databases

CTDi5176
DisGeNETi5176
EuPathDBiHostDB:ENSG00000132386.10
GeneCardsiSERPINF1
H-InvDBiHIX0013408
HGNCiHGNC:8824 SERPINF1
HPAiHPA005825
MalaCardsiSERPINF1
MIMi172860 gene
613982 phenotype
neXtProtiNX_P36955
OpenTargetsiENSG00000132386
Orphaneti216812 Osteogenesis imperfecta type 3
PharmGKBiPA35508
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2392 Eukaryota
COG4826 LUCA
GeneTreeiENSGT00920000149046
HOGENOMiHOG000115489
HOVERGENiHBG106911
InParanoidiP36955
KOiK19614
OMAiLNCKIAQ
OrthoDBiEOG091G09UU
PhylomeDBiP36955
TreeFamiTF317350

Enzyme and pathway databases

SIGNORiP36955

Miscellaneous databases

ChiTaRSiSERPINF1 human
EvolutionaryTraceiP36955
GeneWikiiPEDF
GenomeRNAii5176
PROiPR:P36955
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000132386 Expressed in 226 organ(s), highest expression level in pigmented layer of retina
CleanExiHS_SERPINF1
ExpressionAtlasiP36955 baseline and differential
GenevisibleiP36955 HS

Family and domain databases

CDDicd02052 PEDF, 1 hit
InterProiView protein in InterPro
IPR033832 PEDF
IPR023795 Serpin_CS
IPR023796 Serpin_dom
IPR000215 Serpin_fam
IPR036186 Serpin_sf
PANTHERiPTHR11461 PTHR11461, 1 hit
PfamiView protein in Pfam
PF00079 Serpin, 1 hit
SMARTiView protein in SMART
SM00093 SERPIN, 1 hit
SUPFAMiSSF56574 SSF56574, 1 hit
PROSITEiView protein in PROSITE
PS00284 SERPIN, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPEDF_HUMAN
AccessioniPrimary (citable) accession number: P36955
Secondary accession number(s): F1T092
, Q13236, Q2TU83, Q96CT1, Q96R01, Q9BWA4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: November 30, 2010
Last modified: October 10, 2018
This is version 190 of the entry and version 4 of the sequence. See 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  4. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
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