Reviewed, UniProtKB/Swiss-Prot O14786 (NRP1_HUMAN)

Names and origin

Protein names

Recommended name:
    Neuropilin-1
Alternative name(s):
    Vascular endothelial cell growth factor 165 receptor
    CD_antigen=CD304

Gene names

Name:	NRP1
Synonyms:	NRP, VEGF165R

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	923 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	The membrane-bound isoform 1 is a receptor involved in the development of the cardiovascular system, in angiogenesis, in the formation of certain neuronal circuits and in organogenesis outside the nervous system. It mediates the chemorepulsant activity of semaphorins. It binds to semaphorin 3A, The PLGF-2 isoform of PGF, The VEGF-165 isoform of VEGF and VEGF-B. Coexpression with KDR results in increased VEGF-165 binding to KDR as well as increased chemotaxis. It may regulate VEGF-induced angiogenesis. The soluble isoform 2 binds VEGF-165 and appears to inhibit its binding to cells. It may also induce apoptosis by sequestering VEGF-165. May bind as well various members of the semaphorin family. Its expression has an averse effect on blood vessel number and integrity.
Subunit structure	Heterodimer with NRP2 Probable. Binds PLXNB1.
Subcellular location	Cell membrane; Single-pass type I membrane protein. Isoform 2: Secreted.
Tissue specificity	The expression of isoforms 1 and 2 does not seem to overlap. Isoform 1 is expressed by the blood vessels of different tissues. In the developing embryo it is found predominantly in the nervous system. In adult tissues, it is highly expressed in heart and placenta; moderately in lung, liver, skeletal muscle, kidney and pancreas; and low in adult brain. Isoform 2 is found in liver hepatocytes, kidney distal and proximal tubules.
Sequence similarities	Belongs to the neuropilin family. Contains 2 CUB domains. Contains 2 F5/8 type C domains. Contains 1 MAM domain.

Ontologies

Keywords
Biological process	Angiogenesis Differentiation Neurogenesis
Cellular component	Cell membrane Membrane Secreted
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Repeat Signal Transmembrane
Molecular function	Developmental protein Receptor
PTM	Disulfide bond Glycoprotein Heparan sulfate Phosphoprotein Proteoglycan
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	angiogenesis Inferred from electronic annotation. Source: UniProtKB-KW axon guidance Ref.1 Traceable author statement. Source: ProtInc cell adhesion Inferred from electronic annotation. Source: InterPro cell-cell signaling Ref.1 Traceable author statement. Source: ProtInc positive regulation of cell proliferation Ref.2 Traceable author statement. Source: ProtInc signal transduction Ref.1 Traceable author statement. Source: ProtInc
Cellular component	extracellular region Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	protein binding Inferred from physical interaction. Source: IntAct vascular endothelial growth factor receptor activity Ref.1 Traceable author statement. Source: ProtInc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
KDR	P35968	1	EBI-1187100,EBI-1005487
VEGFA	P15692	1	EBI-1187100,EBI-1026643

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O14786-1)

Also known as: Membrane-bound;

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: O14786-2)

Also known as: Soluble; SNRP1;

The sequence of this isoform differs from the canonical sequence as follows:
     642-644: EFP → GIK
     645-923: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 21

21

Ref.2 Ref.3

Chain

22 – 923

902

Neuropilin-1

PRO_0000021859

Regions

Topological domain

22 – 856

835

Extracellular Potential

Transmembrane

857 – 879

23

Potential

Topological domain

880 – 923

44

Cytoplasmic Potential

Domain

27 – 141

115

CUB 1

Domain

147 – 265

119

CUB 2

Domain

275 – 424

150

F5/8 type C 1

Domain

431 – 583

153

F5/8 type C 2

Domain

645 – 811

167

MAM

Amino acid modifications

Modified residue

920

1

Phosphotyrosine Ref.11

Glycosylation

150

1

N-linked (GlcNAc...) Ref.9

Glycosylation

261

1

N-linked (GlcNAc...)

Glycosylation

300

1

N-linked (GlcNAc...) Potential

Glycosylation

522

1

N-linked (GlcNAc...)

Glycosylation

612

1

O-linked (Xyl...) (chondroitin sulfate); alternate Ref.10

Glycosylation

612

1

O-linked (Xyl...) (heparan sulfate); alternate Ref.10

Glycosylation

842

1

N-linked (GlcNAc...) Potential

Disulfide bond

27 ↔ 54

Probable

Disulfide bond

82 ↔ 104

Probable

Disulfide bond

147 ↔ 173

Probable

Disulfide bond

206 ↔ 228

Probable

Disulfide bond

275 ↔ 424

By similarity

Disulfide bond

431 ↔ 583

By similarity

Natural variations

Alternative sequence

642 – 644

3

EFP → GIK in isoform 2.

VSP_004339

Alternative sequence

645 – 923

279

Missing in isoform 2.

VSP_004340

Natural variant

179

1

V → A: dbSNP rs7079053. Ref.2 Ref.3 Ref.1 Ref.4 Ref.6

VAR_046536

Natural variant

561

1

F → L: dbSNP rs2228637.

VAR_046537

Natural variant

733

1

V → I: dbSNP rs2228638.

VAR_056957

Experimental info

Sequence conflict

26

1

K → E in AAC51759. Ref.1

Sequence conflict

749

1

D → H in AAC12921. Ref.2

Sequence conflict

855

1

D → E in AAC51759. Ref.1

Secondary structure

1

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923

Helix Strand Turn

Details...

Beta strand

149 – 151

3

Beta strand

153 – 159

7

Turn

161 – 164

4

Beta strand

172 – 178

7

Helix

180 – 182

3

Beta strand

185 – 193

9

Beta strand

208 – 217

10

Turn

218 – 220

3

Beta strand

223 – 227

5

Beta strand

235 – 238

4

Beta strand

240 – 248

9

Beta strand

257 – 264

8

Turn

281 – 283

3

Beta strand

284 – 286

3

Helix

288 – 290

3

Beta strand

291 – 294

4

Helix

299 – 301

3

Helix

303 – 306

4

Beta strand

326 – 342

17

Turn

347 – 349

3

Beta strand

352 – 367

16

Beta strand

369 – 371

3

Beta strand

385 – 389

5

Beta strand

391 – 414

24

Beta strand

417 – 424

8

Turn

437 – 439

3

Helix

444 – 446

3

Beta strand

447 – 449

3

Turn

450 – 453

4

Helix

459 – 462

4

Beta strand

485 – 502

18

Beta strand

515 – 525

11

Beta strand

534 – 537

4

Beta strand

544 – 547

4

Beta strand

550 – 566

17

Beta strand

570 – 572

3

Beta strand

576 – 584

9

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (Membrane-bound) [UniParc]. Last modified September 23, 2008. Version 3. Checksum: 1EAC2FA6C8FD6A0B	FASTA	923	103,134
	10 20 30 40 50 60 MERGLPLLCA VLALVLAPAG AFRNDKCGDT IKIESPGYLT SPGYPHSYHP SEKCEWLIQA 70 80 90 100 110 120 PDPYQRIMIN FNPHFDLEDR DCKYDYVEVF DGENENGHFR GKFCGKIAPP PVVSSGPFLF 130 140 150 160 170 180 IKFVSDYETH GAGFSIRYEI FKRGPECSQN YTTPSGVIKS PGFPEKYPNS LECTYIVFVP 190 200 210 220 230 240 KMSEIILEFE SFDLEPDSNP PGGMFCRYDR LEIWDGFPDV GPHIGRYCGQ KTPGRIRSSS 250 260 270 280 290 300 GILSMVFYTD SAIAKEGFSA NYSVLQSSVS EDFKCMEALG MESGEIHSDQ ITASSQYSTN 310 320 330 340 350 360 WSAERSRLNY PENGWTPGED SYREWIQVDL GLLRFVTAVG TQGAISKETK KKYYVKTYKI 370 380 390 400 410 420 DVSSNGEDWI TIKEGNKPVL FQGNTNPTDV VVAVFPKPLI TRFVRIKPAT WETGISMRFE 430 440 450 460 470 480 VYGCKITDYP CSGMLGMVSG LISDSQITSS NQGDRNWMPE NIRLVTSRSG WALPPAPHSY 490 500 510 520 530 540 INEWLQIDLG EEKIVRGIII QGGKHRENKV FMRKFKIGYS NNGSDWKMIM DDSKRKAKSF 550 560 570 580 590 600 EGNNNYDTPE LRTFPALSTR FIRIYPERAT HGGLGLRMEL LGCEVEAPTA GPTTPNGNLV 610 620 630 640 650 660 DECDDDQANC HSGTGDDFQL TGGTTVLATE KPTVIDSTIQ SEFPTYGFNC EFGWGSHKTF 670 680 690 700 710 720 CHWEHDNHVQ LKWSVLTSKT GPIQDHTGDG NFIYSQADEN QKGKVARLVS PVVYSQNSAH 730 740 750 760 770 780 CMTFWYHMSG SHVGTLRVKL RYQKPEEYDQ LVWMAIGHQG DHWKEGRVLL HKSLKLYQVI 790 800 810 820 830 840 FEGEIGKGNL GGIAVDDISI NNHISQEDCA KPADLDKKNP EIKIDETGST PGYEGEGEGD 850 860 870 880 890 900 KNISRKPGNV LKTLDPILIT IIAMSALGVL LGAVCGVVLY CACWHNGMSE RNLSALENYN 910 920 FELVDGVKLK KDKLNTQSTY SEA
	Isoform 2 (Soluble) (SNRP1). Checksum: 1F055D9E6DD9BE70	FASTA	644	71,935
	10 20 30 40 50 60 MERGLPLLCA VLALVLAPAG AFRNDKCGDT IKIESPGYLT SPGYPHSYHP SEKCEWLIQA 70 80 90 100 110 120 PDPYQRIMIN FNPHFDLEDR DCKYDYVEVF DGENENGHFR GKFCGKIAPP PVVSSGPFLF 130 140 150 160 170 180 IKFVSDYETH GAGFSIRYEI FKRGPECSQN YTTPSGVIKS PGFPEKYPNS LECTYIVFVP 190 200 210 220 230 240 KMSEIILEFE SFDLEPDSNP PGGMFCRYDR LEIWDGFPDV GPHIGRYCGQ KTPGRIRSSS 250 260 270 280 290 300 GILSMVFYTD SAIAKEGFSA NYSVLQSSVS EDFKCMEALG MESGEIHSDQ ITASSQYSTN 310 320 330 340 350 360 WSAERSRLNY PENGWTPGED SYREWIQVDL GLLRFVTAVG TQGAISKETK KKYYVKTYKI 370 380 390 400 410 420 DVSSNGEDWI TIKEGNKPVL FQGNTNPTDV VVAVFPKPLI TRFVRIKPAT WETGISMRFE 430 440 450 460 470 480 VYGCKITDYP CSGMLGMVSG LISDSQITSS NQGDRNWMPE NIRLVTSRSG WALPPAPHSY 490 500 510 520 530 540 INEWLQIDLG EEKIVRGIII QGGKHRENKV FMRKFKIGYS NNGSDWKMIM DDSKRKAKSF 550 560 570 580 590 600 EGNNNYDTPE LRTFPALSTR FIRIYPERAT HGGLGLRMEL LGCEVEAPTA GPTTPNGNLV 610 620 630 640 DECDDDQANC HSGTGDDFQL TGGTTVLATE KPTVIDSTIQ SGIK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Neuropilin is a receptor for the axonal chemorepellent semaphorin III." He Z., Tessier-Lavigne M. Cell 90:739-751(1997) [PubMed: 9288753] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT ALA-179.
[2]	"Neuropilin-1 is expressed by endothelial and tumor cells as an isoform-specific receptor for vascular endothelial growth factor." Soker S., Takashima S., Miao H.-Q., Neufeld G., Klagsbrun M. Cell 92:735-745(1998) [PubMed: 9529250] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 22-39, VARIANT ALA-179. Tissue: Mammary gland.
[3]	"Identification of a natural soluble neuropilin-1 that binds vascular endothelial growth factor: in vivo expression and antitumor activity." Gagnon M.L., Bielenberg D.R., Gechtman Z., Miao H.-Q., Takashima S., Soker S., Klagsbrun M. Proc. Natl. Acad. Sci. U.S.A. 97:2573-2578(2000) [PubMed: 10688880] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), PROTEIN SEQUENCE OF 22-31, VARIANT ALA-179. Tissue: Prostatic adenocarcinoma.
[4]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT ALA-179.
[5]	"The DNA sequence and comparative analysis of human chromosome 10." Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J. Nature 429:375-381(2004) [PubMed: 15164054] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT ALA-179. Tissue: Kidney.
[7]	"Plexins are a large family of receptors for transmembrane, secreted and GPI-anchored semaphorins in vertebrates." Tamagnone L., Artigiani S., Chen H., He Z., Ming G.-L., Song H.-L., Chedotal A., Winberg M.L., Goodman C.S., Poo M.-M., Tessier-Lavigne M., Comoglio P.M. Cell 99:71-80(1999) [PubMed: 10520995] [Abstract] Cited for: INTERACTION WITH PLXNB1.
[8]	"Neuropilin-2 and neuropilin-1 are receptors for the 165-amino acid form of vascular endothelial growth factor (VEGF) and of placenta growth factor-2, but only neuropilin-2 functions as a receptor for the 145-amino acid form of VEGF." Gluzman-Poltorak Z., Cohen T., Herzog Y., Neufeld G. J. Biol. Chem. 275:18040-18045(2000) [PubMed: 10748121] [Abstract] Cited for: CHARACTERIZATION.
[9]	"Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry." Liu T., Qian W.-J., Gritsenko M.A., Camp D.G. II, Monroe M.E., Moore R.J., Smith R.D. J. Proteome Res. 4:2070-2080(2005) [PubMed: 16335952] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-150, MASS SPECTROMETRY. Tissue: Plasma.
[10]	"Glycosaminoglycan modification of neuropilin-1 modulates VEGFR2 signaling." Shintani Y., Takashima S., Asano Y., Kato H., Liao Y., Yamazaki S., Tsukamoto O., Seguchi O., Yamamoto H., Fukushima T., Sugahara K., Kitakaze M., Hori M. EMBO J. 25:3045-3055(2006) [PubMed: 16763549] [Abstract] Cited for: GLYCOSYLATION AT SER-612.
[11]	"Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer." Rikova K., Guo A., Zeng Q., Possemato A., Yu J., Haack H., Nardone J., Lee K., Reeves C., Li Y., Hu Y., Tan Z., Stokes M., Sullivan L., Mitchell J., Wetzel R., Macneill J., Ren J.M. , Yuan J., Bakalarski C.E., Villen J., Kornhauser J.M., Smith B., Li D., Zhou X., Gygi S.P., Gu T.-L., Polakiewicz R.D., Rush J., Comb M.J. Cell 131:1190-1203(2007) [PubMed: 18083107] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-920, MASS SPECTROMETRY.
[12]	"Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry." Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H. J. Proteome Res. 8:651-661(2009) [PubMed: 19159218] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-150; ASN-261 AND ASN-522, MASS SPECTROMETRY. Tissue: Liver.
[13]	"Crystal structure of the human neuropilin-1 b1 domain." Lee C.C., Kreusch A., McMullan D., Ng K., Spraggon G. Structure 11:99-108(2003) [PubMed: 12517344] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 273-427.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AF018956 mRNA. Translation: AAC51759.1.
AF016050 mRNA. Translation: AAC12921.1.
AF145712 mRNA. Translation: AAF44344.1.
BT006995 mRNA. Translation: AAP35641.1.
AL353600, AL121748 Genomic DNA. Translation: CAI16997.1.
AL121748, AL353600 Genomic DNA. Translation: CAI40248.1.
BC007533 mRNA. Translation: AAH07533.1.

IPI

IPI00299594.
IPI00607733.

UniGene

Hs.131704
Hs.714624

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1KEX	X-ray	1.90	A	273-427	[»]
2QQI	X-ray	1.80	A	273-586	[»]
2QQM	X-ray	2.00	A	141-586	[»]
2QQN	X-ray	2.20	A	273-427	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:5743N.

IntAct

O14786. 2 interactions.

PTM databases

PhosphoSite

O14786.

Proteomic databases

PRIDE

O14786.

Genome annotation databases

Ensembl

ENSG00000099250. Homo sapiens. [Contig view]

Organism-specific databases

GeneCards

GC10M033506.

H-InvDB

HIX0008755.

HGNC

HGNC:8004. NRP1.

HPA

CAB004511.

MIM

602069. gene.

PharmGKB

PA31783.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

O14786.

HOVERGEN

O14786.

OMA

O14786. LECTYII.

Enzyme and pathway databases

Pathway_Interaction_DB

vegfr1_2_pathway. Signaling events mediated by VEGFR1 and VEGFR2.
vegfr1_pathway. VEGFR1 specific signals.

Reactome

REACT_12529. Signaling by VEGF.

Gene expression databases

ArrayExpress

O14786.

Bgee

O14786.

CleanEx

HS_NRP1.

GermOnline

ENSG00000099250. Homo sapiens.

Family and domain databases

InterPro

IPR000421. Coagulation_factor_5/8-type_C.
IPR000859. CUB.
IPR000998. MAM.
IPR014648. Neuropilin.
[Graphical view]

Gene3D

G3DSA:2.60.120.290. CUB. 2 hits.

Pfam

PF00431. CUB. 2 hits.
PF00754. F5_F8_type_C. 2 hits.
PF00629. MAM. 1 hit.
[Graphical view]

PIRSF

PIRSF036960. Neuropilin. 1 hit.

PRINTS

PR00020. MAMDOMAIN.

SMART

SM00042. CUB. 2 hits.
SM00231. FA58C. 2 hits.
SM00137. MAM. 1 hit.
[Graphical view]

PROSITE

PS01180. CUB. 2 hits.
PS01285. FA58C_1. 2 hits.
PS01286. FA58C_2. 2 hits.
PS50022. FA58C_3. 2 hits.
PS00740. MAM_1. 1 hit.
PS50060. MAM_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

DrugBank

DB00039. Palifermin.
DB04895. Pegaptanib.

SOURCE

Search...

Entry information

Entry name

NRP1_HUMAN

Accession

Primary (citable) accession number: O14786
Secondary accession number(s): O60461, Q5T7F3, Q96IH5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	September 23, 2008
Last modified:	June 16, 2009
This is version 99 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)