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Protein

Vascular cell adhesion protein 1

Gene

VCAM1

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

Functioni

Important in cell-cell recognition. Appears to function in leukocyte-endothelial cell adhesion. Interacts with integrin alpha-4/beta-1 (ITGA4/ITGB1) on leukocytes, and mediates both adhesion and signal transduction. The VCAM1/ITGA4/ITGB1 interaction may play a pathophysiologic role both in immune responses and in leukocyte emigration to sites of inflammation.

GO - Molecular functioni

  • cell adhesion molecule binding Source: BHF-UCL
  • integrin binding Source: UniProtKB
  • primary amine oxidase activity Source: UniProtKB

GO - Biological processi

  • acute inflammatory response Source: Ensembl
  • aging Source: Ensembl
  • amine metabolic process Source: UniProtKB
  • B cell differentiation Source: BHF-UCL
  • calcium-mediated signaling using intracellular calcium source Source: UniProtKB
  • cell adhesion Source: BHF-UCL
  • cell chemotaxis Source: Ensembl
  • cell-matrix adhesion Source: UniProtKB
  • cellular response to tumor necrosis factor Source: Ensembl
  • cellular response to vascular endothelial growth factor stimulus Source: Ensembl
  • chronic inflammatory response Source: Ensembl
  • extracellular matrix organization Source: Reactome
  • heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules Source: BHF-UCL
  • interferon-gamma-mediated signaling pathway Source: Reactome
  • leukocyte cell-cell adhesion Source: BHF-UCL
  • leukocyte tethering or rolling Source: UniProtKB
  • membrane to membrane docking Source: BHF-UCL
  • positive regulation of T cell proliferation Source: BHF-UCL
  • regulation of immune response Source: Reactome
  • response to ethanol Source: Ensembl
  • response to hypoxia Source: Ensembl
  • response to ionizing radiation Source: Ensembl
  • response to lipopolysaccharide Source: Ensembl
  • response to nicotine Source: Ensembl
  • response to nutrient Source: Ensembl
  • response to zinc ion Source: Ensembl
  • viral process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Cell adhesion, Host-virus interaction

Enzyme and pathway databases

BioCyciZFISH:ENSG00000162692-MONOMER.
ReactomeiR-HSA-198933. Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.
R-HSA-216083. Integrin cell surface interactions.
R-HSA-877300. Interferon gamma signaling.

Names & Taxonomyi

Protein namesi
Recommended name:
Vascular cell adhesion protein 1
Short name:
V-CAM 1
Short name:
VCAM-1
Alternative name(s):
INCAM-100
CD_antigen: CD106
Gene namesi
Name:VCAM1
Synonyms:L1CAM
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:12663. VCAM1.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini25 – 698ExtracellularSequence analysisAdd BLAST674
Transmembranei699 – 720HelicalSequence analysisAdd BLAST22
Topological domaini721 – 739CytoplasmicSequence analysisAdd BLAST19

GO - Cellular componenti

  • alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex Source: BHF-UCL
  • apical part of cell Source: BHF-UCL
  • cell surface Source: UniProtKB
  • early endosome Source: UniProtKB
  • endoplasmic reticulum Source: UniProtKB
  • external side of plasma membrane Source: BHF-UCL
  • extracellular exosome Source: UniProtKB
  • extracellular space Source: BHF-UCL
  • filopodium Source: BHF-UCL
  • Golgi apparatus Source: UniProtKB
  • integral component of membrane Source: UniProtKB-KW
  • microvillus Source: BHF-UCL
  • plasma membrane Source: Reactome
  • podosome Source: BHF-UCL
  • sarcolemma Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi7412.
OpenTargetsiENSG00000162692.
PharmGKBiPA37286.

Chemistry databases

ChEMBLiCHEMBL3735.
DrugBankiDB01136. Carvedilol.
DB00898. Ethanol.

Polymorphism and mutation databases

BioMutaiVCAM1.
DMDMi137560.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 241 PublicationAdd BLAST24
ChainiPRO_000001499725 – 739Vascular cell adhesion protein 1Add BLAST715

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi47 ↔ 951 Publication
Disulfide bondi52 ↔ 991 Publication
Disulfide bondi137 ↔ 1951 Publication
Disulfide bondi246 ↔ 291PROSITE-ProRule annotation
Glycosylationi273N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi335 ↔ 383PROSITE-ProRule annotation
Glycosylationi365N-linked (GlcNAc...)Sequence analysis1
Glycosylationi417N-linked (GlcNAc...)Sequence analysis1
Glycosylationi463N-linked (GlcNAc...)Sequence analysis1
Glycosylationi531N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi534 ↔ 579PROSITE-ProRule annotation
Glycosylationi561N-linked (GlcNAc...)1 Publication1

Post-translational modificationi

Sialoglycoprotein.

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiP19320.
PaxDbiP19320.
PeptideAtlasiP19320.
PRIDEiP19320.

PTM databases

iPTMnetiP19320.
PhosphoSitePlusiP19320.

Miscellaneous databases

PMAP-CutDBP19320.

Expressioni

Tissue specificityi

Expressed on inflammed vascular endothelium, as well as on macrophage-like and dendritic cell types in both normal and inflammed tissue.

Inductioni

By cytokines (e.g. IL-1, TNF-alpha).

Gene expression databases

BgeeiENSG00000162692.
CleanExiHS_L1CAM.
HS_VCAM1.
ExpressionAtlasiP19320. baseline and differential.
GenevisibleiP19320. HS.

Organism-specific databases

HPAiCAB005426.
HPA034796.

Interactioni

Subunit structurei

Binds to ECMV-D capsid proteins and acts as a receptor for this virus.By similarity

GO - Molecular functioni

  • cell adhesion molecule binding Source: BHF-UCL
  • integrin binding Source: UniProtKB

Protein-protein interaction databases

BioGridi113255. 450 interactors.
IntActiP19320. 628 interactors.
STRINGi9606.ENSP00000294728.

Chemistry databases

BindingDBiP19320.

Structurei

Secondary structure

1739
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi26 – 38Combined sources13
Beta strandi43 – 51Combined sources9
Beta strandi56 – 61Combined sources6
Beta strandi68 – 74Combined sources7
Beta strandi77 – 84Combined sources8
Helixi87 – 89Combined sources3
Beta strandi91 – 99Combined sources9
Beta strandi102 – 114Combined sources13
Beta strandi120 – 125Combined sources6
Beta strandi133 – 144Combined sources12
Helixi145 – 147Combined sources3
Beta strandi148 – 154Combined sources7
Beta strandi157 – 163Combined sources7
Beta strandi169 – 171Combined sources3
Beta strandi174 – 182Combined sources9
Helixi186 – 188Combined sources3
Beta strandi192 – 199Combined sources8
Beta strandi209 – 216Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IJ9X-ray3.00A25-220[»]
1VCAX-ray1.80A/B25-226[»]
1VSCX-ray1.90A/B25-219[»]
ProteinModelPortaliP19320.
SMRiP19320.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP19320.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini25 – 105Ig-like C2-type 1Add BLAST81
Domaini109 – 212Ig-like C2-type 2Add BLAST104
Domaini223 – 309Ig-like C2-type 3Add BLAST87
Domaini312 – 399Ig-like C2-type 4Add BLAST88
Domaini408 – 506Ig-like C2-type 5Add BLAST99
Domaini511 – 595Ig-like C2-type 6Add BLAST85
Domaini600 – 684Ig-like C2-type 7Add BLAST85

Domaini

Either the first or the fourth Ig-like C2-type domain is required for VLA4-dependent cell adhesion.

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IIKS. Eukaryota.
ENOG4111F4V. LUCA.
GeneTreeiENSGT00830000128299.
HOGENOMiHOG000004820.
HOVERGENiHBG053965.
InParanoidiP19320.
KOiK06527.
OMAiGVYECES.
OrthoDBiEOG091G0590.
PhylomeDBiP19320.
TreeFamiTF333571.

Family and domain databases

Gene3Di2.60.40.10. 7 hits.
InterProiIPR003987. ICAM_VCAM_N.
IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR008424. Ig_C2-set.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR013106. Ig_V-set.
IPR013151. Immunoglobulin.
IPR003989. VCAM-1.
[Graphical view]
PfamiPF05790. C2-set. 2 hits.
PF07679. I-set. 3 hits.
PF00047. ig. 1 hit.
[Graphical view]
PRINTSiPR01472. ICAMVCAM1.
PR01474. VCAM1.
SMARTiSM00409. IG. 5 hits.
SM00408. IGc2. 5 hits.
SM00406. IGv. 2 hits.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 7 hits.
PROSITEiPS50835. IG_LIKE. 5 hits.
[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. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: P19320-1) [UniParc]FASTAAdd to basket
Also known as: Long, VCAM-7D

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
MPGKMVVILG ASNILWIMFA ASQAFKIETT PESRYLAQIG DSVSLTCSTT
60 70 80 90 100
GCESPFFSWR TQIDSPLNGK VTNEGTTSTL TMNPVSFGNE HSYLCTATCE
110 120 130 140 150
SRKLEKGIQV EIYSFPKDPE IHLSGPLEAG KPITVKCSVA DVYPFDRLEI
160 170 180 190 200
DLLKGDHLMK SQEFLEDADR KSLETKSLEV TFTPVIEDIG KVLVCRAKLH
210 220 230 240 250
IDEMDSVPTV RQAVKELQVY ISPKNTVISV NPSTKLQEGG SVTMTCSSEG
260 270 280 290 300
LPAPEIFWSK KLDNGNLQHL SGNATLTLIA MRMEDSGIYV CEGVNLIGKN
310 320 330 340 350
RKEVELIVQE KPFTVEISPG PRIAAQIGDS VMLTCSVMGC ESPSFSWRTQ
360 370 380 390 400
IDSPLSGKVR SEGTNSTLTL SPVSFENEHS YLCTVTCGHK KLEKGIQVEL
410 420 430 440 450
YSFPRDPEIE MSGGLVNGSS VTVSCKVPSV YPLDRLEIEL LKGETILENI
460 470 480 490 500
EFLEDTDMKS LENKSLEMTF IPTIEDTGKA LVCQAKLHID DMEFEPKQRQ
510 520 530 540 550
STQTLYVNVA PRDTTVLVSP SSILEEGSSV NMTCLSQGFP APKILWSRQL
560 570 580 590 600
PNGELQPLSE NATLTLISTK MEDSGVYLCE GINQAGRSRK EVELIIQVTP
610 620 630 640 650
KDIKLTAFPS ESVKEGDTVI ISCTCGNVPE TWIILKKKAE TGDTVLKSID
660 670 680 690 700
GAYTIRKAQL KDAGVYECES KNKVGSQLRS LTLDVQGREN NKDYFSPELL
710 720 730
VLYFASSLII PAIGMIIYFA RKANMKGSYS LVEAQKSKV
Note: Major isoform.
Length:739
Mass (Da):81,276
Last modified:November 1, 1990 - v1
Checksum:i050E2EBD39AC2FF4
GO
Isoform 2 (identifier: P19320-2) [UniParc]FASTAAdd to basket
Also known as: Short, VCAM-6D

The sequence of this isoform differs from the canonical sequence as follows:
     310-402: EKPFTVEISP...EKGIQVELYS → A

Show »
Length:647
Mass (Da):71,255
Checksum:i7EA67DB70AC91EF8
GO
Isoform 3 (identifier: P19320-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     52-113: Missing.

Note: No experimental confirmation available.
Show »
Length:677
Mass (Da):74,346
Checksum:iCA0C2F8A7E51EC83
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti182F → G (PubMed:1377228).Curated1
Sequence conflicti402S → T (PubMed:1707234).Curated1
Sequence conflicti728S → P in BAG59286 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04995118M → I.Corresponds to variant rs34228330dbSNPEnsembl.1
Natural variantiVAR_014309318S → F.1 PublicationCorresponds to variant rs3783611dbSNPEnsembl.1
Natural variantiVAR_014310384T → A.1 PublicationCorresponds to variant rs3783612dbSNPEnsembl.1
Natural variantiVAR_014311413G → A.1 PublicationCorresponds to variant rs3783613dbSNPEnsembl.1
Natural variantiVAR_049952421V → I.Corresponds to variant rs34100871dbSNPEnsembl.1
Natural variantiVAR_049953488H → R.Corresponds to variant rs34199378dbSNPEnsembl.1
Natural variantiVAR_014312716I → L.1 PublicationCorresponds to variant rs3783615dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_04463652 – 113Missing in isoform 3. 1 PublicationAdd BLAST62
Alternative sequenceiVSP_002580310 – 402EKPFT…VELYS → A in isoform 2. 1 PublicationAdd BLAST93

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M30257 mRNA. Translation: AAA51917.1.
X53051 mRNA. Translation: CAA37218.1.
M60335 mRNA. Translation: AAA61269.1.
M73255 Genomic DNA. Translation: AAA61270.1.
AF536818 Genomic DNA. Translation: AAM96190.1.
AK291732 mRNA. Translation: BAF84421.1.
AK296692 mRNA. Translation: BAG59286.1.
AC093428 Genomic DNA. No translation available.
CH471097 Genomic DNA. Translation: EAW72950.1.
BC017276 mRNA. Translation: AAH17276.3.
BC068490 mRNA. Translation: AAH68490.2.
BC085003 mRNA. Translation: AAH85003.1.
M92431 Genomic DNA. No translation available.
CCDSiCCDS55617.1. [P19320-3]
CCDS773.1. [P19320-1]
CCDS774.1. [P19320-2]
PIRiA41288.
B41288.
RefSeqiNP_001069.1. NM_001078.3. [P19320-1]
NP_001186763.1. NM_001199834.1. [P19320-3]
NP_542413.1. NM_080682.2. [P19320-2]
UniGeneiHs.109225.

Genome annotation databases

EnsembliENST00000294728; ENSP00000294728; ENSG00000162692. [P19320-1]
ENST00000347652; ENSP00000304611; ENSG00000162692. [P19320-2]
ENST00000370119; ENSP00000359137; ENSG00000162692. [P19320-3]
GeneIDi7412.
KEGGihsa:7412.
UCSCiuc001dti.5. human. [P19320-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Web resourcesi

Wikipedia

VCAM1 entry

SeattleSNPs
Functional Glycomics Gateway - Glycan Binding

VCAM-1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M30257 mRNA. Translation: AAA51917.1.
X53051 mRNA. Translation: CAA37218.1.
M60335 mRNA. Translation: AAA61269.1.
M73255 Genomic DNA. Translation: AAA61270.1.
AF536818 Genomic DNA. Translation: AAM96190.1.
AK291732 mRNA. Translation: BAF84421.1.
AK296692 mRNA. Translation: BAG59286.1.
AC093428 Genomic DNA. No translation available.
CH471097 Genomic DNA. Translation: EAW72950.1.
BC017276 mRNA. Translation: AAH17276.3.
BC068490 mRNA. Translation: AAH68490.2.
BC085003 mRNA. Translation: AAH85003.1.
M92431 Genomic DNA. No translation available.
CCDSiCCDS55617.1. [P19320-3]
CCDS773.1. [P19320-1]
CCDS774.1. [P19320-2]
PIRiA41288.
B41288.
RefSeqiNP_001069.1. NM_001078.3. [P19320-1]
NP_001186763.1. NM_001199834.1. [P19320-3]
NP_542413.1. NM_080682.2. [P19320-2]
UniGeneiHs.109225.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IJ9X-ray3.00A25-220[»]
1VCAX-ray1.80A/B25-226[»]
1VSCX-ray1.90A/B25-219[»]
ProteinModelPortaliP19320.
SMRiP19320.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113255. 450 interactors.
IntActiP19320. 628 interactors.
STRINGi9606.ENSP00000294728.

Chemistry databases

BindingDBiP19320.
ChEMBLiCHEMBL3735.
DrugBankiDB01136. Carvedilol.
DB00898. Ethanol.

PTM databases

iPTMnetiP19320.
PhosphoSitePlusiP19320.

Polymorphism and mutation databases

BioMutaiVCAM1.
DMDMi137560.

Proteomic databases

MaxQBiP19320.
PaxDbiP19320.
PeptideAtlasiP19320.
PRIDEiP19320.

Protocols and materials databases

DNASUi7412.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000294728; ENSP00000294728; ENSG00000162692. [P19320-1]
ENST00000347652; ENSP00000304611; ENSG00000162692. [P19320-2]
ENST00000370119; ENSP00000359137; ENSG00000162692. [P19320-3]
GeneIDi7412.
KEGGihsa:7412.
UCSCiuc001dti.5. human. [P19320-1]

Organism-specific databases

CTDi7412.
DisGeNETi7412.
GeneCardsiVCAM1.
HGNCiHGNC:12663. VCAM1.
HPAiCAB005426.
HPA034796.
MIMi192225. gene.
neXtProtiNX_P19320.
OpenTargetsiENSG00000162692.
PharmGKBiPA37286.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IIKS. Eukaryota.
ENOG4111F4V. LUCA.
GeneTreeiENSGT00830000128299.
HOGENOMiHOG000004820.
HOVERGENiHBG053965.
InParanoidiP19320.
KOiK06527.
OMAiGVYECES.
OrthoDBiEOG091G0590.
PhylomeDBiP19320.
TreeFamiTF333571.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000162692-MONOMER.
ReactomeiR-HSA-198933. Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.
R-HSA-216083. Integrin cell surface interactions.
R-HSA-877300. Interferon gamma signaling.

Miscellaneous databases

ChiTaRSiVCAM1. human.
EvolutionaryTraceiP19320.
GeneWikiiVCAM-1.
GenomeRNAii7412.
PMAP-CutDBP19320.
PROiP19320.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000162692.
CleanExiHS_L1CAM.
HS_VCAM1.
ExpressionAtlasiP19320. baseline and differential.
GenevisibleiP19320. HS.

Family and domain databases

Gene3Di2.60.40.10. 7 hits.
InterProiIPR003987. ICAM_VCAM_N.
IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR008424. Ig_C2-set.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR013106. Ig_V-set.
IPR013151. Immunoglobulin.
IPR003989. VCAM-1.
[Graphical view]
PfamiPF05790. C2-set. 2 hits.
PF07679. I-set. 3 hits.
PF00047. ig. 1 hit.
[Graphical view]
PRINTSiPR01472. ICAMVCAM1.
PR01474. VCAM1.
SMARTiSM00409. IG. 5 hits.
SM00408. IGc2. 5 hits.
SM00406. IGv. 2 hits.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 7 hits.
PROSITEiPS50835. IG_LIKE. 5 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiVCAM1_HUMAN
AccessioniPrimary (citable) accession number: P19320
Secondary accession number(s): A8K6R7
, B4DKS4, E9PDD1, Q6NUP8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: November 1, 1990
Last modified: November 2, 2016
This is version 210 of the entry and version 1 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

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

Documents

  1. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
  2. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. 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.