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Protein

Oxysterols receptor LXR-alpha

Gene

NR1H3

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

Functioni

Nuclear receptor. Interaction with RXR shifts RXR from its role as a silent DNA-binding partner to an active ligand-binding subunit in mediating retinoid responses through target genes defined by LXRES. LXRES are DR4-type response elements characterized by direct repeats of two similar hexanuclotide half-sites spaced by four nucleotides. Plays an important role in the regulation of cholesterol homeostasis, regulating cholesterol uptake through MYLIP-dependent ubiquitination of LDLR, VLDLR and LRP8. Interplays functionally with RORA for the regulation of genes involved in liver metabolism (By similarity). Exhibits a ligand-dependent transcriptional activation activity (PubMed:25661920).By similarity1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi95 – 170Nuclear receptorPROSITE-ProRule annotationAdd BLAST76
Zinc fingeri98 – 118NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri134 – 158NR C4-typePROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

  • cholesterol binding Source: BHF-UCL
  • DNA binding Source: ProtInc
  • RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding Source: ProtInc
  • sequence-specific DNA binding Source: InterPro
  • steroid hormone receptor activity Source: InterPro
  • sterol response element binding Source: UniProtKB
  • transcription coactivator activity Source: ProtInc
  • transcription regulatory region DNA binding Source: BHF-UCL
  • zinc ion binding Source: InterPro

GO - Biological processi

  • apoptotic cell clearance Source: UniProtKB
  • cellular response to lipopolysaccharide Source: BHF-UCL
  • cholesterol homeostasis Source: BHF-UCL
  • lipid homeostasis Source: BHF-UCL
  • negative regulation of cholesterol storage Source: BHF-UCL
  • negative regulation of inflammatory response Source: BHF-UCL
  • negative regulation of interferon-gamma-mediated signaling pathway Source: BHF-UCL
  • negative regulation of lipid transport Source: BHF-UCL
  • negative regulation of macrophage activation Source: BHF-UCL
  • negative regulation of macrophage derived foam cell differentiation Source: BHF-UCL
  • negative regulation of pancreatic juice secretion Source: BHF-UCL
  • negative regulation of pinocytosis Source: BHF-UCL
  • negative regulation of secretion of lysosomal enzymes Source: BHF-UCL
  • negative regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  • positive regulation of cellular protein metabolic process Source: BHF-UCL
  • positive regulation of cholesterol efflux Source: BHF-UCL
  • positive regulation of cholesterol homeostasis Source: BHF-UCL
  • positive regulation of cholesterol transport Source: BHF-UCL
  • positive regulation of fatty acid biosynthetic process Source: BHF-UCL
  • positive regulation of lipoprotein lipase activity Source: BHF-UCL
  • positive regulation of receptor biosynthetic process Source: BHF-UCL
  • positive regulation of toll-like receptor 4 signaling pathway Source: BHF-UCL
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • positive regulation of triglyceride biosynthetic process Source: BHF-UCL
  • regulation of cholesterol homeostasis Source: UniProtKB
  • regulation of circadian rhythm Source: BHF-UCL
  • response to progesterone Source: BHF-UCL
  • sterol homeostasis Source: BHF-UCL
  • transcription initiation from RNA polymerase II promoter Source: Reactome
  • triglyceride homeostasis Source: BHF-UCL
Complete GO annotation...

Keywords - Molecular functioni

Activator, Receptor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000025434-MONOMER.
ReactomeiR-HSA-383280. Nuclear Receptor transcription pathway.
R-HSA-8866427. VLDLR internalisation and degradation.
SignaLinkiQ13133.
SIGNORiQ13133.

Chemistry databases

SwissLipidsiSLP:000000836.

Names & Taxonomyi

Protein namesi
Recommended name:
Oxysterols receptor LXR-alpha
Alternative name(s):
Liver X receptor alpha
Nuclear receptor subfamily 1 group H member 3
Gene namesi
Name:NR1H3
Synonyms:LXRA
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:7966. NR1H3.

Subcellular locationi

GO - Cellular componenti

  • nuclear chromatin Source: BHF-UCL
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • receptor complex Source: BHF-UCL
  • RNA polymerase II transcription factor complex Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi10062.
OpenTargetsiENSG00000025434.
PharmGKBiPA31751.

Chemistry databases

ChEMBLiCHEMBL2808.
GuidetoPHARMACOLOGYi602.

Polymorphism and mutation databases

BioMutaiNR1H3.
DMDMi23503089.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000535351 – 447Oxysterols receptor LXR-alphaAdd BLAST447

Proteomic databases

MaxQBiQ13133.
PaxDbiQ13133.
PeptideAtlasiQ13133.
PRIDEiQ13133.

PTM databases

iPTMnetiQ13133.
PhosphoSitePlusiQ13133.

Expressioni

Tissue specificityi

Visceral organs specific expression. Strong expression was found in liver, kidney and intestine followed by spleen and to a lesser extent the adrenals.

Inductioni

By 9-cis retinoic acid (9CRA).

Gene expression databases

BgeeiENSG00000025434.
CleanExiHS_NR1H3.
ExpressionAtlasiQ13133. baseline and differential.
GenevisibleiQ13133. HS.

Organism-specific databases

HPAiCAB037109.
HPA036443.

Interactioni

Subunit structurei

Heterodimer of LXRA and RXR. Interacts with CCAR2 (via N-terminus) in a ligand-independent manner. Interacts with SIRT1 and this interaction is inhibited by CCAR2.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
EDF1O608694EBI-781356,EBI-781301
KDM1AO603412EBI-781356,EBI-710124
MDFIQ997503EBI-781356,EBI-724076
NCOA1Q1578815EBI-781356,EBI-455189
NCOR1O753762EBI-781356,EBI-347233
RXRBP287024EBI-11952806,EBI-748576
RXRBQ5STP93EBI-781356,EBI-10197393
RXRGP484436EBI-781356,EBI-712405
SUV39H1O434632EBI-781356,EBI-349968

Protein-protein interaction databases

BioGridi115373. 39 interactors.
IntActiQ13133. 25 interactors.
MINTiMINT-3027136.
STRINGi9606.ENSP00000387946.

Chemistry databases

BindingDBiQ13133.

Structurei

Secondary structure

1447
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi208 – 220Combined sources13
Helixi229 – 233Combined sources5
Helixi247 – 272Combined sources26
Helixi278 – 280Combined sources3
Helixi283 – 304Combined sources22
Turni308 – 311Combined sources4
Beta strandi312 – 315Combined sources4
Turni316 – 318Combined sources3
Beta strandi319 – 321Combined sources3
Helixi323 – 328Combined sources6
Helixi333 – 349Combined sources17
Helixi353 – 364Combined sources12
Beta strandi369 – 371Combined sources3
Helixi375 – 396Combined sources22
Helixi403 – 430Combined sources28
Helixi437 – 443Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UHLX-ray2.90B207-447[»]
3IPQX-ray2.00A182-447[»]
3IPSX-ray2.26A/B182-447[»]
3IPUX-ray2.40A/B182-447[»]
5AVIX-ray2.70A/C182-447[»]
5AVLX-ray2.80A182-447[»]
5HJSX-ray1.72A/B182-447[»]
ProteinModelPortaliQ13133.
SMRiQ13133.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ13133.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 96Transactivation AF-1; required for ligand-independent transactivation function1 PublicationAdd BLAST96
Regioni205 – 447Transactivation AF-2; required for ligand-dependent transactivation function; mediates interaction with CCAR21 PublicationAdd BLAST243
Regioni215 – 434Ligand-bindingSequence analysisAdd BLAST220

Sequence similaritiesi

Contains 1 nuclear receptor DNA-binding domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri98 – 118NR C4-typePROSITE-ProRule annotationAdd BLAST21
Zinc fingeri134 – 158NR C4-typePROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00850000132242.
HOGENOMiHOG000220845.
HOVERGENiHBG108655.
InParanoidiQ13133.
KOiK08536.
PhylomeDBiQ13133.
TreeFamiTF352167.

Family and domain databases

Gene3Di1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProiIPR023257. Liver_X_rcpt.
IPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR02034. LIVERXRECPTR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q13133-1) [UniParc]FASTAAdd to basket

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
MSLWLGAPVP DIPPDSAVEL WKPGAQDASS QAQGGSSCIL REEARMPHSA
60 70 80 90 100
GGTAGVGLEA AEPTALLTRA EPPSEPTEIR PQKRKKGPAP KMLGNELCSV
110 120 130 140 150
CGDKASGFHY NVLSCEGCKG FFRRSVIKGA HYICHSGGHC PMDTYMRRKC
160 170 180 190 200
QECRLRKCRQ AGMREECVLS EEQIRLKKLK RQEEEQAHAT SLPPRASSPP
210 220 230 240 250
QILPQLSPEQ LGMIEKLVAA QQQCNRRSFS DRLRVTPWPM APDPHSREAR
260 270 280 290 300
QQRFAHFTEL AIVSVQEIVD FAKQLPGFLQ LSREDQIALL KTSAIEVMLL
310 320 330 340 350
ETSRRYNPGS ESITFLKDFS YNREDFAKAG LQVEFINPIF EFSRAMNELQ
360 370 380 390 400
LNDAEFALLI AISIFSADRP NVQDQLQVER LQHTYVEALH AYVSIHHPHD
410 420 430 440
RLMFPRMLMK LVSLRTLSSV HSEQVFALRL QDKKLPPLLS EIWDVHE
Length:447
Mass (Da):50,396
Last modified:September 19, 2002 - v2
Checksum:i0D27B237440F8C9C
GO
Isoform 2 (identifier: Q13133-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     237-296: Missing.

Note: No experimental confirmation available.
Show »
Length:387
Mass (Da):43,555
Checksum:i9C96CF2BBE66403C
GO
Isoform 3 (identifier: Q13133-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-45: Missing.

Note: No experimental confirmation available.
Show »
Length:402
Mass (Da):45,692
Checksum:i78EAE53CFB2358E7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti196A → R in AAA85856 (PubMed:7744246).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05058052G → V.Corresponds to variant rs41481445dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0449601 – 45Missing in isoform 3. 1 PublicationAdd BLAST45
Alternative sequenceiVSP_003664237 – 296Missing in isoform 2. 1 PublicationAdd BLAST60

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U22662 mRNA. Translation: AAA85856.1.
AK290614 mRNA. Translation: BAF83303.1.
AC018410 Genomic DNA. No translation available.
CH471064 Genomic DNA. Translation: EAW67949.1.
CH471064 Genomic DNA. Translation: EAW67942.1.
CH471064 Genomic DNA. Translation: EAW67943.1.
CH471064 Genomic DNA. Translation: EAW67944.1.
CH471064 Genomic DNA. Translation: EAW67947.1.
CH471064 Genomic DNA. Translation: EAW67948.1.
BC008819 mRNA. Translation: AAH08819.1.
BC041172 mRNA. Translation: AAH41172.1.
CCDSiCCDS44584.1. [Q13133-2]
CCDS44585.1. [Q13133-3]
CCDS7929.1. [Q13133-1]
PIRiI38975.
RefSeqiNP_001123573.1. NM_001130101.2. [Q13133-2]
NP_001123574.1. NM_001130102.2. [Q13133-3]
NP_005684.2. NM_005693.3. [Q13133-1]
XP_005252762.1. XM_005252705.1. [Q13133-1]
XP_005252763.1. XM_005252706.1. [Q13133-1]
XP_005252764.1. XM_005252707.4. [Q13133-1]
XP_005252766.1. XM_005252709.1. [Q13133-3]
XP_005252767.1. XM_005252710.1. [Q13133-3]
XP_005252770.1. XM_005252713.3. [Q13133-2]
XP_006718175.1. XM_006718112.1. [Q13133-1]
XP_006718176.1. XM_006718113.1. [Q13133-1]
XP_006718178.1. XM_006718115.1. [Q13133-3]
XP_006718179.1. XM_006718116.1. [Q13133-3]
XP_011518107.1. XM_011519805.2. [Q13133-1]
XP_016872547.1. XM_017017058.1. [Q13133-3]
UniGeneiHs.438863.

Genome annotation databases

EnsembliENST00000395397; ENSP00000378793; ENSG00000025434. [Q13133-3]
ENST00000405853; ENSP00000384745; ENSG00000025434. [Q13133-2]
ENST00000407404; ENSP00000385801; ENSG00000025434. [Q13133-2]
ENST00000441012; ENSP00000387946; ENSG00000025434. [Q13133-1]
ENST00000467728; ENSP00000420656; ENSG00000025434. [Q13133-1]
GeneIDi10062.
KEGGihsa:10062.
UCSCiuc001nek.4. human. [Q13133-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U22662 mRNA. Translation: AAA85856.1.
AK290614 mRNA. Translation: BAF83303.1.
AC018410 Genomic DNA. No translation available.
CH471064 Genomic DNA. Translation: EAW67949.1.
CH471064 Genomic DNA. Translation: EAW67942.1.
CH471064 Genomic DNA. Translation: EAW67943.1.
CH471064 Genomic DNA. Translation: EAW67944.1.
CH471064 Genomic DNA. Translation: EAW67947.1.
CH471064 Genomic DNA. Translation: EAW67948.1.
BC008819 mRNA. Translation: AAH08819.1.
BC041172 mRNA. Translation: AAH41172.1.
CCDSiCCDS44584.1. [Q13133-2]
CCDS44585.1. [Q13133-3]
CCDS7929.1. [Q13133-1]
PIRiI38975.
RefSeqiNP_001123573.1. NM_001130101.2. [Q13133-2]
NP_001123574.1. NM_001130102.2. [Q13133-3]
NP_005684.2. NM_005693.3. [Q13133-1]
XP_005252762.1. XM_005252705.1. [Q13133-1]
XP_005252763.1. XM_005252706.1. [Q13133-1]
XP_005252764.1. XM_005252707.4. [Q13133-1]
XP_005252766.1. XM_005252709.1. [Q13133-3]
XP_005252767.1. XM_005252710.1. [Q13133-3]
XP_005252770.1. XM_005252713.3. [Q13133-2]
XP_006718175.1. XM_006718112.1. [Q13133-1]
XP_006718176.1. XM_006718113.1. [Q13133-1]
XP_006718178.1. XM_006718115.1. [Q13133-3]
XP_006718179.1. XM_006718116.1. [Q13133-3]
XP_011518107.1. XM_011519805.2. [Q13133-1]
XP_016872547.1. XM_017017058.1. [Q13133-3]
UniGeneiHs.438863.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UHLX-ray2.90B207-447[»]
3IPQX-ray2.00A182-447[»]
3IPSX-ray2.26A/B182-447[»]
3IPUX-ray2.40A/B182-447[»]
5AVIX-ray2.70A/C182-447[»]
5AVLX-ray2.80A182-447[»]
5HJSX-ray1.72A/B182-447[»]
ProteinModelPortaliQ13133.
SMRiQ13133.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115373. 39 interactors.
IntActiQ13133. 25 interactors.
MINTiMINT-3027136.
STRINGi9606.ENSP00000387946.

Chemistry databases

BindingDBiQ13133.
ChEMBLiCHEMBL2808.
GuidetoPHARMACOLOGYi602.
SwissLipidsiSLP:000000836.

PTM databases

iPTMnetiQ13133.
PhosphoSitePlusiQ13133.

Polymorphism and mutation databases

BioMutaiNR1H3.
DMDMi23503089.

Proteomic databases

MaxQBiQ13133.
PaxDbiQ13133.
PeptideAtlasiQ13133.
PRIDEiQ13133.

Protocols and materials databases

DNASUi10062.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000395397; ENSP00000378793; ENSG00000025434. [Q13133-3]
ENST00000405853; ENSP00000384745; ENSG00000025434. [Q13133-2]
ENST00000407404; ENSP00000385801; ENSG00000025434. [Q13133-2]
ENST00000441012; ENSP00000387946; ENSG00000025434. [Q13133-1]
ENST00000467728; ENSP00000420656; ENSG00000025434. [Q13133-1]
GeneIDi10062.
KEGGihsa:10062.
UCSCiuc001nek.4. human. [Q13133-1]

Organism-specific databases

CTDi10062.
DisGeNETi10062.
GeneCardsiNR1H3.
HGNCiHGNC:7966. NR1H3.
HPAiCAB037109.
HPA036443.
MIMi602423. gene.
neXtProtiNX_Q13133.
OpenTargetsiENSG00000025434.
PharmGKBiPA31751.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3575. Eukaryota.
ENOG410XRZC. LUCA.
GeneTreeiENSGT00850000132242.
HOGENOMiHOG000220845.
HOVERGENiHBG108655.
InParanoidiQ13133.
KOiK08536.
PhylomeDBiQ13133.
TreeFamiTF352167.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000025434-MONOMER.
ReactomeiR-HSA-383280. Nuclear Receptor transcription pathway.
R-HSA-8866427. VLDLR internalisation and degradation.
SignaLinkiQ13133.
SIGNORiQ13133.

Miscellaneous databases

EvolutionaryTraceiQ13133.
GeneWikiiLiver_X_receptor_alpha.
GenomeRNAii10062.
PROiQ13133.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000025434.
CleanExiHS_NR1H3.
ExpressionAtlasiQ13133. baseline and differential.
GenevisibleiQ13133. HS.

Family and domain databases

Gene3Di1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProiIPR023257. Liver_X_rcpt.
IPR000536. Nucl_hrmn_rcpt_lig-bd.
IPR001723. Nuclear_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamiPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSiPR02034. LIVERXRECPTR.
PR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTiSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMiSSF48508. SSF48508. 1 hit.
PROSITEiPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNR1H3_HUMAN
AccessioniPrimary (citable) accession number: Q13133
Secondary accession number(s): A8K3J9
, D3DQR1, Q8IW13, Q96H87
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: September 19, 2002
Last modified: November 30, 2016
This is version 177 of the entry and version 2 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, Reference proteome

Documents

  1. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.