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Protein

Serine/arginine repetitive matrix protein 1

Gene

SRRM1

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

Functioni

Part of pre- and post-splicing multiprotein mRNP complexes. Involved in numerous pre-mRNA processing events. Promotes constitutive and exonic splicing enhancer (ESE)-dependent splicing activation by bridging together sequence-specific (SR family proteins, SFRS4, SFRS5 and TRA2B/SFRS10) and basal snRNP (SNRP70 and SNRPA1) factors of the spliceosome. Stimulates mRNA 3'-end cleavage independently of the formation of an exon junction complex. Binds both pre-mRNA and spliced mRNA 20-25 nt upstream of exon-exon junctions. Binds RNA and DNA with low sequence specificity and has similar preference for either double- or single-stranded nucleic acid substrates.6 Publications

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA 3'-end processing Source: Reactome
  • mRNA export from nucleus Source: Reactome
  • mRNA splicing, via spliceosome Source: UniProtKB
  • RNA export from nucleus Source: Reactome
  • RNA splicing Source: ProtInc
  • RNA splicing, via transesterification reactions Source: UniProtKB
  • termination of RNA polymerase II transcription Source: Reactome
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.

Protein family/group databases

TCDBi3.A.18.1.1. the nuclear mrna exporter (mrna-e) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine/arginine repetitive matrix protein 1
Alternative name(s):
SR-related nuclear matrix protein of 160 kDa
Short name:
SRm160
Ser/Arg-related nuclear matrix protein
Gene namesi
Name:SRRM1
Synonyms:SRM160
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:16638. SRRM1.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • cytosol Source: Reactome
  • nuclear matrix Source: UniProtKB-SubCell
  • nuclear speck Source: UniProtKB-SubCell
  • nucleoplasm Source: HPA
  • nucleus Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi20K → A: Strongly reduces DNA and RNA-binding. 1 Publication1
Mutagenesisi22K → A: Strongly reduces DNA and RNA-binding. 1 Publication1
Mutagenesisi23K → A: Strongly reduces DNA and RNA-binding. 1 Publication1

Organism-specific databases

DisGeNETi10250.
OpenTargetsiENSG00000133226.
PharmGKBiPA38177.

Polymorphism and mutation databases

BioMutaiSRRM1.
DMDMi83305833.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000763261 – 904Serine/arginine repetitive matrix protein 1Add BLAST904

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1 Publication1
Modified residuei7CitrullineBy similarity1
Modified residuei140N6-acetyllysineCombined sources1
Modified residuei220PhosphothreonineCombined sources1
Modified residuei227PhosphoserineCombined sources1
Cross-linki231Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)Combined sources
Modified residuei234PhosphoserineCombined sources1
Modified residuei240PhosphoserineCombined sources1
Modified residuei241PhosphothreonineCombined sources1
Cross-linki249Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei260PhosphoserineCombined sources1
Modified residuei389PhosphoserineCombined sources1 Publication1
Modified residuei391PhosphoserineCombined sources1
Modified residuei393PhosphoserineCombined sources1 Publication1
Modified residuei402PhosphoserineCombined sources1
Modified residuei406PhosphothreonineCombined sources1
Modified residuei414PhosphoserineCombined sources1
Modified residuei416PhosphothreonineCombined sources1
Modified residuei420PhosphoserineCombined sources1
Modified residuei429PhosphoserineCombined sources1
Modified residuei431PhosphoserineCombined sources1
Modified residuei436PhosphoserineCombined sources1
Modified residuei450PhosphoserineCombined sources1
Modified residuei452PhosphoserineCombined sources1
Modified residuei463PhosphoserineCombined sources1
Modified residuei465PhosphoserineCombined sources1
Modified residuei478PhosphoserineCombined sources1
Modified residuei524PhosphoserineCombined sources1
Modified residuei526PhosphoserineCombined sources1
Modified residuei528PhosphoserineCombined sources1
Modified residuei530PhosphoserineCombined sources1
Modified residuei532PhosphoserineCombined sources1
Modified residuei549PhosphoserineCombined sources1
Modified residuei551PhosphoserineCombined sources1
Modified residuei555PhosphothreonineCombined sources1
Modified residuei560PhosphoserineCombined sources1
Modified residuei562PhosphoserineCombined sources1
Modified residuei572PhosphothreonineCombined sources1
Modified residuei574PhosphothreonineCombined sources1
Modified residuei581PhosphothreonineCombined sources1
Modified residuei583PhosphoserineCombined sources1
Modified residuei596PhosphotyrosineCombined sources1
Modified residuei597PhosphoserineCombined sources1
Modified residuei605PhosphoserineCombined sources1
Modified residuei607PhosphoserineCombined sources1
Modified residuei614PhosphothreonineCombined sources1
Modified residuei616PhosphoserineCombined sources1
Modified residuei626PhosphoserineCombined sources1
Modified residuei628PhosphoserineCombined sources1
Modified residuei636PhosphoserineCombined sources1
Modified residuei638PhosphoserineCombined sources1
Modified residuei694PhosphoserineCombined sources1
Modified residuei695PhosphoserineBy similarity1
Modified residuei696PhosphoserineCombined sources1
Modified residuei705PhosphoserineCombined sources1
Modified residuei707PhosphoserineCombined sources1
Modified residuei713PhosphoserineCombined sources1
Modified residuei715PhosphoserineCombined sources1
Modified residuei718PhosphothreonineCombined sources1
Modified residuei738PhosphoserineCombined sources1
Modified residuei740PhosphoserineCombined sources1
Modified residuei748PhosphoserineCombined sources1
Modified residuei752PhosphoserineCombined sources1
Modified residuei754PhosphoserineCombined sources1
Modified residuei756PhosphoserineCombined sources1
Modified residuei769PhosphoserineCombined sources1
Modified residuei773PhosphoserineCombined sources1
Modified residuei775PhosphoserineCombined sources1
Modified residuei777PhosphoserineCombined sources1
Modified residuei778PhosphothreonineBy similarity1
Modified residuei781PhosphoserineCombined sources1
Modified residuei791PhosphoserineCombined sources1
Modified residuei793PhosphothreonineCombined sources1
Modified residuei795PhosphoserineCombined sources1
Modified residuei797PhosphoserineCombined sources1
Modified residuei802PhosphoserineCombined sources1
Modified residuei872PhosphothreonineCombined sources1
Modified residuei874PhosphoserineCombined sources1
Modified residuei901PhosphoserineCombined sources1

Post-translational modificationi

Citrullinated by PADI4.By similarity

Keywords - PTMi

Acetylation, Citrullination, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ8IYB3.
MaxQBiQ8IYB3.
PaxDbiQ8IYB3.
PeptideAtlasiQ8IYB3.
PRIDEiQ8IYB3.

PTM databases

iPTMnetiQ8IYB3.
PhosphoSitePlusiQ8IYB3.
SwissPalmiQ8IYB3.

Miscellaneous databases

PMAP-CutDBQ8IYB3.

Expressioni

Gene expression databases

BgeeiENSG00000133226.
CleanExiHS_SRRM1.
ExpressionAtlasiQ8IYB3. baseline and differential.
GenevisibleiQ8IYB3. HS.

Organism-specific databases

HPAiHPA049941.
HPA058612.

Interactioni

Subunit structurei

Identified in the spliceosome C complex. Found in a pre-mRNA splicing complex with SFRS4, SFRS5, SNRP70, SNRPA1, SRRM1 and SRRM2. Found in a pre-mRNA exonic splicing enhancer (ESE) complex with SNRP70, SNRPA1, SRRM1 and TRA2B/SFRS10. Found in a mRNA splicing-dependent exon junction complex (EJC) with DEK, PRPF8, NCBP1, RBM8A, RNPS1, SRRM1 and ALYREF/THOC4. Interacts with BAT1, CPSF1, RBM8A, RNPS1, and ALYREF/THOC4. Seems to be a compound of RNA export complexes that are released from speckles in a ATP-dependent manner.8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CLK2P497603EBI-1055880,EBI-750020

Protein-protein interaction databases

BioGridi115544. 158 interactors.
IntActiQ8IYB3. 22 interactors.
MINTiMINT-1683977.
STRINGi9606.ENSP00000326261.

Structurei

Secondary structure

1904
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi33 – 36Combined sources4
Turni40 – 42Combined sources3
Helixi46 – 48Combined sources3
Helixi49 – 60Combined sources12
Helixi66 – 74Combined sources9
Beta strandi77 – 79Combined sources3
Helixi82 – 89Combined sources8
Turni90 – 92Combined sources3
Helixi96 – 112Combined sources17
Beta strandi115 – 118Combined sources4
Helixi121 – 124Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1MP1NMR-A27-134[»]
ProteinModelPortaliQ8IYB3.
SMRiQ8IYB3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8IYB3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini27 – 126PWIPROSITE-ProRule annotationAdd BLAST100

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 156Necessary for mRNA 3'-end cleavage and cytoplasmic accumulationAdd BLAST156
Regioni1 – 151Necessary for DNA and RNA-bindingAdd BLAST151
Regioni300 – 688Necessary for speckles and matrix localizationAdd BLAST389

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi163 – 726Arg-richAdd BLAST564
Compositional biasi210 – 417Pro-richAdd BLAST208
Compositional biasi278 – 756Ser-richAdd BLAST479
Compositional biasi550 – 799Pro-richAdd BLAST250
Compositional biasi809 – 835Lys-richAdd BLAST27
Compositional biasi836 – 865Ala-richAdd BLAST30

Sequence similaritiesi

Belongs to the splicing factor SR family.Curated
Contains 1 PWI domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2146. Eukaryota.
ENOG4111IMU. LUCA.
GeneTreeiENSGT00730000111080.
HOGENOMiHOG000231139.
HOVERGENiHBG054044.
InParanoidiQ8IYB3.
KOiK13171.
PhylomeDBiQ8IYB3.
TreeFamiTF318972.

Family and domain databases

Gene3Di1.20.1390.10. 1 hit.
InterProiIPR002483. PWI_dom.
[Graphical view]
PfamiPF01480. PWI. 1 hit.
[Graphical view]
SMARTiSM00311. PWI. 1 hit.
[Graphical view]
SUPFAMiSSF101233. SSF101233. 1 hit.
PROSITEiPS51025. PWI. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8IYB3-1) [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
MDAGFFRGTS AEQDNRFSNK QKKLLKQLKF AECLEKKVDM SKVNLEVIKP
60 70 80 90 100
WITKRVTEIL GFEDDVVIEF IFNQLEVKNP DSKMMQINLT GFLNGKNARE
110 120 130 140 150
FMGELWPLLL SAQENIAGIP SAFLELKKEE IKQRQIEQEK LASMKKQDED
160 170 180 190 200
KDKRDKEEKE SSREKRERSR SPRRRKSRSP SPRRRSSPVR RERKRSHSRS
210 220 230 240 250
PRHRTKSRSP SPAPEKKEKT PELPEPSVKV KEPSVQEATS TSDILKVPKP
260 270 280 290 300
EPIPEPKEPS PEKNSKKEKE KEKTRPRSRS RSKSRSRTRS RSPSHTRPRR
310 320 330 340 350
RHRSRSRSYS PRRRPSPRRR PSPRRRTPPR RMPPPPRHRR SRSPVRRRRR
360 370 380 390 400
SSASLSGSSS SSSSSRSRSP PKKPPKRTSS PPRKTRRLSP SASPPRRRHR
410 420 430 440 450
PSPPATPPPK TRHSPTPQQS NRTRKSRVSV SPGRTSGKVT KHKGTEKRES
460 470 480 490 500
PSPAPKPRKV ELSESEEDKG GKMAAADSVQ QRRQYRRQNQ QSSSDSGSSS
510 520 530 540 550
SSEDERPKRS HVKNGEVGRR RRHSPSRSAS PSPRKRQKET SPRGRRRRSP
560 570 580 590 600
SPPPTRRRRS PSPAPPPRRR RTPTPPPRRR TPSPPPRRRS PSPRRYSPPI
610 620 630 640 650
QRRYSPSPPP KRRTASPPPP PKRRASPSPP PKRRVSHSPP PKQRSSPVTK
660 670 680 690 700
RRSPSLSSKH RKGSSPSRST REARSPQPNK RHSPSPRPRA PQTSSSPPPV
710 720 730 740 750
RRGASSSPQR RQSPSPSTRP IRRVSRTPEP KKIKKAASPS PQSVRRVSSS
760 770 780 790 800
RSVSGSPEPA AKKPPAPPSP VQSQSPSTNW SPAVPVKKAK SPTPSPSPPR
810 820 830 840 850
NSDQEGGGKK KKKKKDKKHK KDKKHKKHKK HKKEKAVAAA AAAAVTPAAI
860 870 880 890 900
AAATTTLAQE EPVAAPEPKK ETESEAEDNL DDLEKHLREK ALRSMRKAQV

SPQS
Length:904
Mass (Da):102,335
Last modified:December 6, 2005 - v2
Checksum:i27D4D2A48EDBFED3
GO
Isoform 2 (identifier: Q8IYB3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     305-308: RSRS → DKM
     407-407: Missing.

Show »
Length:902
Mass (Da):102,126
Checksum:i0211C6D93260EF32
GO

Sequence cautioni

The sequence AAC09321 differs from that shown. Reason: Frameshift at position 791.Curated
The sequence AAP97290 differs from that shown. Reason: Frameshift at position 791.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti269K → Q (PubMed:9531537).Curated1
Sequence conflicti269K → Q (Ref. 2) Curated1
Sequence conflicti275R → Q in AAH36187 (PubMed:15489334).Curated1
Sequence conflicti413H → D (PubMed:9531537).Curated1
Sequence conflicti413H → D (Ref. 2) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_024065170R → H.1 PublicationCorresponds to variant rs17857102dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_016522305 – 308RSRS → DKM in isoform 2. 2 Publications4
Alternative sequenceiVSP_016523407Missing in isoform 2. 2 Publications1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF048977 mRNA. Translation: AAC09321.1. Frameshift.
AF419855 mRNA. Translation: AAP97290.1. Frameshift.
AL445648, AL445686 Genomic DNA. Translation: CAH73090.1.
AL445686, AL445648 Genomic DNA. Translation: CAI14682.1.
BC036187 mRNA. Translation: AAH36187.1.
CCDSiCCDS255.1. [Q8IYB3-1]
RefSeqiNP_001290377.1. NM_001303448.1.
NP_001290378.1. NM_001303449.1.
NP_005830.2. NM_005839.3. [Q8IYB3-1]
UniGeneiHs.18192.

Genome annotation databases

EnsembliENST00000323848; ENSP00000326261; ENSG00000133226. [Q8IYB3-1]
GeneIDi10250.
KEGGihsa:10250.
UCSCiuc001bjm.4. human. [Q8IYB3-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF048977 mRNA. Translation: AAC09321.1. Frameshift.
AF419855 mRNA. Translation: AAP97290.1. Frameshift.
AL445648, AL445686 Genomic DNA. Translation: CAH73090.1.
AL445686, AL445648 Genomic DNA. Translation: CAI14682.1.
BC036187 mRNA. Translation: AAH36187.1.
CCDSiCCDS255.1. [Q8IYB3-1]
RefSeqiNP_001290377.1. NM_001303448.1.
NP_001290378.1. NM_001303449.1.
NP_005830.2. NM_005839.3. [Q8IYB3-1]
UniGeneiHs.18192.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1MP1NMR-A27-134[»]
ProteinModelPortaliQ8IYB3.
SMRiQ8IYB3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115544. 158 interactors.
IntActiQ8IYB3. 22 interactors.
MINTiMINT-1683977.
STRINGi9606.ENSP00000326261.

Protein family/group databases

TCDBi3.A.18.1.1. the nuclear mrna exporter (mrna-e) family.

PTM databases

iPTMnetiQ8IYB3.
PhosphoSitePlusiQ8IYB3.
SwissPalmiQ8IYB3.

Polymorphism and mutation databases

BioMutaiSRRM1.
DMDMi83305833.

Proteomic databases

EPDiQ8IYB3.
MaxQBiQ8IYB3.
PaxDbiQ8IYB3.
PeptideAtlasiQ8IYB3.
PRIDEiQ8IYB3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000323848; ENSP00000326261; ENSG00000133226. [Q8IYB3-1]
GeneIDi10250.
KEGGihsa:10250.
UCSCiuc001bjm.4. human. [Q8IYB3-1]

Organism-specific databases

CTDi10250.
DisGeNETi10250.
GeneCardsiSRRM1.
H-InvDBHIX0023530.
HIX0160039.
HGNCiHGNC:16638. SRRM1.
HPAiHPA049941.
HPA058612.
MIMi605975. gene.
neXtProtiNX_Q8IYB3.
OpenTargetsiENSG00000133226.
PharmGKBiPA38177.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2146. Eukaryota.
ENOG4111IMU. LUCA.
GeneTreeiENSGT00730000111080.
HOGENOMiHOG000231139.
HOVERGENiHBG054044.
InParanoidiQ8IYB3.
KOiK13171.
PhylomeDBiQ8IYB3.
TreeFamiTF318972.

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.

Miscellaneous databases

ChiTaRSiSRRM1. human.
EvolutionaryTraceiQ8IYB3.
GeneWikiiSRRM1.
GenomeRNAii10250.
PMAP-CutDBQ8IYB3.
PROiQ8IYB3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000133226.
CleanExiHS_SRRM1.
ExpressionAtlasiQ8IYB3. baseline and differential.
GenevisibleiQ8IYB3. HS.

Family and domain databases

Gene3Di1.20.1390.10. 1 hit.
InterProiIPR002483. PWI_dom.
[Graphical view]
PfamiPF01480. PWI. 1 hit.
[Graphical view]
SMARTiSM00311. PWI. 1 hit.
[Graphical view]
SUPFAMiSSF101233. SSF101233. 1 hit.
PROSITEiPS51025. PWI. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSRRM1_HUMAN
AccessioniPrimary (citable) accession number: Q8IYB3
Secondary accession number(s): O60585, Q5VVN4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: December 6, 2005
Last modified: November 30, 2016
This is version 146 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: 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.