TMCO5A

gene
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Also known as MGC35118

Summary

TMCO5A (transmembrane and coiled-coil domains 5A, HGNC:28558) is a protein-coding gene on chromosome 15q14, encoding Transmembrane and coiled-coil domain-containing protein 5A (Q8N6Q1).

Predicted to be located in membrane.

Source: NCBI Gene 145942 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 51 total
  • MANE Select transcript: NM_152453

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28558
Approved symbolTMCO5A
Nametransmembrane and coiled-coil domains 5A
Location15q14
Locus typegene with protein product
StatusApproved
AliasesMGC35118
Ensembl geneENSG00000166069
Ensembl biotypeprotein_coding
Entrez145942

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000319669, ENST00000558148, ENST00000558158, ENST00000558625, ENST00000559502, ENST00000559813, ENST00000560653, ENST00000560841, ENST00000851987

RefSeq mRNA: 5 — MANE Select: NM_152453 NM_001330255, NM_001370735, NM_001370736, NM_001370737, NM_152453

CCDS: CCDS10046, CCDS81862

Canonical transcript exons

ENST00000319669 — 12 exons

ExonStartEnd
ENSE000012599613793525737935348
ENSE000012600763795103637951422
ENSE000025607233793464037934694
ENSE000034646103794219137942255
ENSE000034729523793631437936463
ENSE000035026113794334137943398
ENSE000035688923793815837938229
ENSE000035899733793734637937396
ENSE000036262073794765637947696
ENSE000036476873794114937941205
ENSE000036509013793684737936970
ENSE000036571713794167137941730

Expression profiles

Bgee: expression breadth broad, 66 present calls, max score 96.77.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0851 / max 78.0377, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1458490.08513

Top tissues by expression

205 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453396.77gold quality
right testisUBERON:000453496.57gold quality
spermCL:000001995.41gold quality
testisUBERON:000047393.82gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.79gold quality
adult organismUBERON:000702383.49gold quality
buccal mucosa cellCL:000233658.58silver quality
lower lobe of lungUBERON:000894958.52silver quality
olfactory segment of nasal mucosaUBERON:000538657.44gold quality
right uterine tubeUBERON:000130254.16gold quality
tendon of biceps brachiiUBERON:000818853.46gold quality
gall bladderUBERON:000211052.93gold quality
oviduct epitheliumUBERON:000480450.80silver quality
upper leg skinUBERON:000426250.08gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099150.04silver quality
skin of hipUBERON:000155449.82silver quality
nasal cavity mucosaUBERON:000182648.74gold quality
body of stomachUBERON:000116145.92gold quality
cauda epididymisUBERON:000436045.73silver quality
stomachUBERON:000094544.08gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality
mucosa of paranasal sinusUBERON:000503042.91gold quality
secondary oocyteCL:000065542.57gold quality
fallopian tubeUBERON:000388942.45gold quality
sural nerveUBERON:001548842.01gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450241.93gold quality
vastus lateralisUBERON:000137941.41gold quality
quadriceps femorisUBERON:000137741.37gold quality
superficial temporal arteryUBERON:000161441.33gold quality
biceps brachiiUBERON:000150741.13gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-134144yes32.25
E-ANND-3yes5.22

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

18 targeting TMCO5A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-4690-5P99.6566.24813
HSA-MIR-542-3P99.3467.581270
HSA-MIR-10399-5P99.1769.872610
HSA-MIR-6504-3P99.1769.312891
HSA-MIR-425499.1165.151315
HSA-MIR-471098.6165.961048
HSA-MIR-4691-5P98.4166.771343
HSA-MIR-6792-3P98.4166.861359
HSA-MIR-5088-3P98.2966.631310
HSA-MIR-369096.4465.18737
HSA-MIR-4757-3P88.8663.5551

Literature-anchored findings (GeneRIF, showing 1)

  • Longer survival was associated with hypomethylation at specific CpG sites (e.g. GREB1, TGIF and TOB1) and hypermethylation in other genes (e.g. TMCO5, PTPRN and GUCY2C). (PMID:21577013)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusTmco5ENSMUSG00000027355
rattus_norvegicusTmco5aENSRNOG00000005100

Paralogs (2): SMCO2 (ENSG00000165935), CCDC188 (ENSG00000234409)

Protein

Protein identifiers

Transmembrane and coiled-coil domain-containing protein 5AQ8N6Q1 (reviewed: Q8N6Q1)

All UniProt accessions (7): A0A024R9I9, Q8N6Q1, H0YL40, H0YLD3, H0YLN2, H0YLW5, H0YMD4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Endoplasmic reticulum membrane. Nucleus membrane.

Similarity. Belongs to the TMCO5 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N6Q1-11yes
Q8N6Q1-22

RefSeq proteins (5): NP_001317184, NP_001357664, NP_001357665, NP_001357666, NP_689666* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026617SMCO2/5Family

Pfam: PF14992

UniProt features (7 total): splice variant 2, sequence conflict 2, chain 1, transmembrane region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N6Q1-F185.190.61

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): chr15q14, SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP, GOCC_NUCLEAR_ENVELOPE, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_NUCLEAR_MEMBRANE, GOCC_ORGANELLE_SUBCOMPARTMENT, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOCC_ORGANELLE_ENVELOPE, GSE13522_CTRL_VS_T_CRUZI_BRAZIL_STRAIN_INF_SKIN_DN, SKP2_TARGET_GENES, MIR5088_3P, GSE15659_NAIVE_VS_PTPRC_NEG_CD4_TCELL_DN, GSE15659_NAIVE_CD4_TCELL_VS_RESTING_TREG_DN, GSE15659_NAIVE_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_DN

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): endoplasmic reticulum membrane (GO:0005789), nuclear membrane (GO:0031965), nucleus (GO:0005634), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
organelle membrane2
intracellular membrane-bounded organelle2
binding1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
nucleus1
nuclear envelope1
cytoplasm1
endomembrane system1
cellular anatomical structure1

Protein interactions and networks

STRING

560 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TMCO5AFAM209AQ5JX71705
TMCO5ATMEM225Q6GV28644
TMCO5AREDIC1Q86WS4628
TMCO5AC9orf43Q8TAL5608
TMCO5ASPATA16Q9BXB7590
TMCO5ATMCO2Q7Z6W1589
TMCO5ASPATA31G1Q5VYM1584
TMCO5AC20orf173Q96LM9578
TMCO5ACIMIP4O43247576
TMCO5AMAGEB16A2A368567
TMCO5ADHRS12A0PJE2543
TMCO5ANUDT17P0C025540
TMCO5ACABS1Q96KC9536
TMCO5AZFAND4Q86XD8531
TMCO5AGARIN1BQ96KD3509

IntAct

23 interactions, top by confidence:

ABTypeScore
TMCO5AC1orf216psi-mi:“MI:0915”(physical association)0.560
TMCO5ATSPAN18psi-mi:“MI:0915”(physical association)0.560
BET1TMCO5Apsi-mi:“MI:0915”(physical association)0.560
VAMP5TMCO5Apsi-mi:“MI:0915”(physical association)0.560
GOSR2TMCO5Apsi-mi:“MI:0915”(physical association)0.560
TMCO5ATMEM60psi-mi:“MI:0915”(physical association)0.560
TMCO5Apsi-mi:“MI:0915”(physical association)0.560
TMCO5AWDR12psi-mi:“MI:0915”(physical association)0.400
C1orf216TMCO5Apsi-mi:“MI:0915”(physical association)0.000
TSPAN18TMCO5Apsi-mi:“MI:0915”(physical association)0.000
GOSR2TMCO5Apsi-mi:“MI:0915”(physical association)0.000
TMEM60TMCO5Apsi-mi:“MI:0915”(physical association)0.000
BET1TMCO5Apsi-mi:“MI:0915”(physical association)0.000
VAMP5TMCO5Apsi-mi:“MI:0915”(physical association)0.000
TMCO5Apsi-mi:“MI:0915”(physical association)0.000

BioGRID (9): TMCO5A (Synthetic Lethality), TMCO5A (Two-hybrid), TMCO5A (Two-hybrid), TMCO5A (Two-hybrid), TMCO5A (Two-hybrid), TMCO5A (Two-hybrid), VAMP5 (Two-hybrid), PRH1 (Two-hybrid), WDR12 (Proximity Label-MS)

ESM2 similar proteins: A0A0A6YYL3, A2A2Z9, A6NC57, A8MYB1, A9JSR5, A9UM82, A9ZSY0, D3ZNV2, F4K1B4, G5EBL8, H3BUK9, O14043, P34606, Q01649, Q08B20, Q0VBY1, Q19UN5, Q32L59, Q4UJ75, Q501X2, Q5CZ79, Q5M7B7, Q5SQ80, Q5TYW2, Q5VUR7, Q66HB6, Q6AY08, Q7FAD5, Q7TPV2, Q7Z7B0, Q80X59, Q811D2, Q86Y13, Q86YR6, Q8IVF6, Q8N6Q1, Q8NF67, Q8WXW3, Q95JR0, Q96AA8

Diamond homologs: A8MYB1, D3ZNV2, Q32L59, Q80X59, Q8N6Q1, Q9D9D5, O02751, Q588U8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

51 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance47
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1403 predictions. Top by Δscore:

VariantEffectΔscore
15:37936844:CAGGC:Cacceptor_loss1.0000
15:37936845:A:AGacceptor_gain1.0000
15:37936845:AG:Aacceptor_gain1.0000
15:37936845:AGGCT:Aacceptor_gain1.0000
15:37936846:G:GTacceptor_gain1.0000
15:37936846:GG:Gacceptor_gain1.0000
15:37936846:GGCTG:Gacceptor_gain1.0000
15:37936929:G:Tdonor_gain1.0000
15:37936953:G:GTdonor_gain1.0000
15:37936966:GACTT:Gdonor_gain1.0000
15:37936971:G:GGdonor_gain1.0000
15:37936979:G:GTdonor_gain1.0000
15:37936987:G:Tdonor_gain1.0000
15:37937340:TCACA:Tacceptor_loss1.0000
15:37937341:CACA:Cacceptor_loss1.0000
15:37937343:CA:Cacceptor_loss1.0000
15:37942254:GT:Gdonor_gain1.0000
15:37947697:G:GGdonor_gain1.0000
15:37935294:GAT:Gdonor_gain0.9900
15:37935296:T:TGdonor_gain0.9900
15:37936296:T:TAacceptor_gain0.9900
15:37936297:G:Aacceptor_gain0.9900
15:37936461:GAG:Gdonor_gain0.9900
15:37936465:T:Adonor_loss0.9900
15:37936846:GGC:Gacceptor_gain0.9900
15:37936846:GGCT:Gacceptor_gain0.9900
15:37936924:A:Tdonor_gain0.9900
15:37936930:A:Tdonor_gain0.9900
15:37936967:ACTT:Adonor_gain0.9900
15:37936968:CTT:Cdonor_gain0.9900

AlphaMissense

1926 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:37951224:T:CL286S0.886
15:37937386:T:CL102P0.842
15:37951085:A:CS240R0.838
15:37951087:C:AS240R0.838
15:37951087:C:GS240R0.838
15:37951159:G:CR264S0.829
15:37951159:G:TR264S0.829
15:37941702:T:CL159P0.826
15:37951109:T:CF248L0.825
15:37951111:C:AF248L0.825
15:37951111:C:GF248L0.825
15:37951117:T:AN250K0.810
15:37951117:T:GN250K0.810
15:37936411:G:CA30P0.793
15:37951171:G:CW268C0.792
15:37951171:G:TW268C0.792
15:37951140:T:GL258R0.791
15:37951176:T:CL270P0.783
15:37936969:T:CL88P0.779
15:37951176:T:AL270H0.778
15:37941198:T:CL146P0.774
15:37936353:A:CK10N0.773
15:37936353:A:TK10N0.773
15:37936382:T:CL20P0.762
15:37936352:A:TK10I0.759
15:37941714:A:CQ163P0.743
15:37941716:G:CA164P0.740
15:37941730:G:CK168N0.734
15:37941730:G:TK168N0.734
15:37951140:T:AL258Q0.733

dbSNP variants (sampled 300 via entrez): RS1000030387 (15:38001072 A>T), RS1000053992 (15:37961568 C>T), RS1000081242 (15:37955745 C>G), RS1000119165 (15:37960184 CT>C), RS1000155534 (15:38036506 A>T), RS1000192168 (15:37994520 A>G), RS1000195090 (15:37948081 C>A), RS1000222217 (15:37964907 A>G), RS1000224077 (15:38029276 C>A), RS1000247387 (15:37987904 A>C,T), RS1000257978 (15:38023199 T>C), RS1000284542 (15:38007373 G>A), RS1000290646 (15:37950329 C>G,T), RS1000360936 (15:38030713 A>G), RS1000362092 (15:37936027 G>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): prostate cancer (MONDO:0008315)

Orphanet (1): Familial prostate cancer (Orphanet:1331)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

StudyTraitp-value
GCST002829_8Urate levels in overweight individuals2.000000e-07
GCST003875_15Gut microbiota (bacterial taxa)4.000000e-08
GCST005348_37Total body bone mineral density5.000000e-10
GCST005795_1Femoral neck bone mineral density2.000000e-08
GCST005796_25Lumbar spine bone mineral density3.000000e-07
GCST006041_11Major depressive disorder1.000000e-08
GCST009391_1977Metabolite levels6.000000e-06
GCST009548_4NASH resolution in nonalcoholic steatohepatitis6.000000e-06
GCST010989_70Body size at age 104.000000e-08

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0004531urate measurement
EFO:0007874gut microbiome measurement
EFO:0007883taxonomic microbiome measurement
EFO:0007785femoral neck bone mineral density
EFO:0007701spine bone mineral density
EFO:0008534tryptophan measurement
EFO:0009785remission
EFO:0009819comparative body size at age 10, self-reported

MeSH disease descriptors (1)

DescriptorNameTree numbers
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

ChemicalActions (top 5)PubMed papers
propionaldehydedecreases expression1
bisphenol Adecreases methylation1
2-palmitoylglycerolincreases expression1
Benzo(a)pyreneincreases methylation1
Caffeinedecreases phosphorylation1
Tobacco Smoke Pollutiondecreases expression1
Aflatoxin B1decreases methylation1
Antirheumatic Agentsincreases expression1

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00029224PHASE4COMPLETEDTreatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997PHASE4COMPLETEDOpen-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609PHASE4COMPLETEDThe Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623PHASE4SUSPENDEDThe Plenaxis® Experience Study
NCT00106392PHASE4COMPLETEDA Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029PHASE4UNKNOWNMR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485PHASE4COMPLETEDAngelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219PHASE4COMPLETEDZoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271PHASE4COMPLETEDEffect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146PHASE4COMPLETEDStudy to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554PHASE4COMPLETEDOpen-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098PHASE4COMPLETEDDocetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696PHASE4COMPLETEDCasodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139PHASE4COMPLETEDEffect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765PHASE4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690PHASE4COMPLETEDEvaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708PHASE4COMPLETEDLocal Anesthesia for Prostate Biopsy
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213PHASE4COMPLETEDCompare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330PHASE4TERMINATEDDissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966PHASE4COMPLETEDRadical Prostatectomy and Perioperative Fluid Therapy
NCT00805701PHASE4COMPLETEDStudy Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027PHASE4COMPLETEDEffect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269PHASE4UNKNOWNCan Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277PHASE4COMPLETEDStudy of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800PHASE4COMPLETEDDoes Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199PHASE4COMPLETEDGlobal Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226PHASE4COMPLETEDEvaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563PHASE4COMPLETEDRandomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905PHASE4COMPLETEDStudy to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672PHASE4COMPLETED3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143PHASE4TERMINATEDProspective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742PHASE4UNKNOWNComparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563PHASE4COMPLETEDHydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874PHASE4COMPLETEDEfficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472PHASE4TERMINATEDFirmagon (Degarelix) Intermittent Therapy
NCT01547416PHASE4COMPLETEDThe Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544PHASE4COMPLETEDThe Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749PHASE4UNKNOWNEvaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635PHASE4COMPLETEDStudy of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.