SRP9

gene
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Summary

SRP9 (signal recognition particle 9, HGNC:11304) is a protein-coding gene on chromosome 1q42.12, encoding Signal recognition particle 9 kDa protein (P49458). Component of the signal recognition particle (SRP) complex, a ribonucleoprotein complex that mediates the cotranslational targeting of secretory and membrane proteins to the endoplasmic reticulum (ER). It is a common-essential gene (DepMap: required in 95.4% of cancer cell lines).

Predicted to enable RNA binding activity and signal recognition particle binding activity. Predicted to be involved in SRP-dependent cotranslational protein targeting to membrane. Predicted to be located in cytosol. Predicted to be part of signal recognition particle, endoplasmic reticulum targeting.

Source: NCBI Gene 6726 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 10 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 95.4% of screened cell lines (common-essential)
  • MANE Select transcript: NM_003133

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11304
Approved symbolSRP9
Namesignal recognition particle 9
Location1q42.12
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000143742
Ensembl biotypeprotein_coding
OMIM600707
Entrez6726

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000304786, ENST00000366838, ENST00000366839, ENST00000619790, ENST00000626563, ENST00000650651, ENST00000651465, ENST00000651653, ENST00000651761, ENST00000861557, ENST00000924808, ENST00000924809, ENST00000924810

RefSeq mRNA: 2 — MANE Select: NM_003133 NM_001130440, NM_003133

CCDS: CCDS1546, CCDS44323

Canonical transcript exons

ENST00000304786 — 3 exons

ExonStartEnd
ENSE00000961765225783300225783368
ENSE00001442734225777826225778012
ENSE00003686398225789240225790464

Expression profiles

Bgee: expression breadth ubiquitous, 149 present calls, max score 99.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 70.9534 / max 2592.6961, expressed in 1816 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
882970.95341816

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
embryoUBERON:000092299.53gold quality
ganglionic eminenceUBERON:000402399.53gold quality
ventricular zoneUBERON:000305399.52gold quality
endometriumUBERON:000129599.41gold quality
cortical plateUBERON:000534399.40gold quality
adrenal tissueUBERON:001830399.33gold quality
islet of LangerhansUBERON:000000699.32gold quality
corpus callosumUBERON:000233699.24gold quality
hypothalamusUBERON:000189899.14gold quality
calcaneal tendonUBERON:000370199.13gold quality
rectumUBERON:000105299.11gold quality
substantia nigraUBERON:000203899.09gold quality
amygdalaUBERON:000187699.08gold quality
spinal cordUBERON:000224099.08gold quality
C1 segment of cervical spinal cordUBERON:000646999.08gold quality
temporal lobeUBERON:000187199.07gold quality
olfactory segment of nasal mucosaUBERON:000538699.06gold quality
smooth muscle tissueUBERON:000113599.05gold quality
gall bladderUBERON:000211099.05gold quality
Brodmann (1909) area 9UBERON:001354099.04gold quality
lymph nodeUBERON:000002999.03gold quality
right adrenal gland cortexUBERON:003582799.02gold quality
right adrenal glandUBERON:000123399.01gold quality
dorsolateral prefrontal cortexUBERON:000983499.01gold quality
nucleus accumbensUBERON:000188298.99gold quality
caudate nucleusUBERON:000187398.98gold quality
left adrenal glandUBERON:000123498.95gold quality
putamenUBERON:000187498.93gold quality
telencephalonUBERON:000189398.91gold quality
adrenal glandUBERON:000236998.91gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-4yes41.59
E-GEOD-84465yes23.31
E-MTAB-10042yes10.84
E-MTAB-6819no4013.41
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

87 targeting SRP9, 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-3925-3P100.0069.951237
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-570-3P99.9672.414910
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-365899.9673.874379
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 95.4% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 5)

  • PSB7, PRDX1, and SRP9 up-regulation as candidate biomarkers of colon cancer is discovered (PMID:18549262)
  • mutational study on SRP9/14 that identified and characterized regions and single residues essential for elongation arrest activity (PMID:20348448)
  • Dats show that Alu RNA promotes functional binding of Signal Recognition Particle proteins SRP9/14 to 40S ribosomal subunits. (PMID:25697503)
  • Investigation of SRP9 protein expression in breast cancer. (PMID:34727289)
  • Significance of signal recognition particle 9 nuclear translocation: Implications for pancreatic cancer prognosis and functionality. (PMID:38847231)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriosrp9ENSDARG00000042851
mus_musculusSrp9ENSMUSG00000026511
rattus_norvegicusSrp9ENSRNOG00000003211
drosophila_melanogasterSrp9FBGN0035827
caenorhabditis_elegansWBGENE00013984

Protein

Protein identifiers

Signal recognition particle 9 kDa proteinP49458 (reviewed: P49458)

All UniProt accessions (4): P49458, E9PE20, Q659G3, Q6P2S0

UniProt curated annotations — full annotation on UniProt →

Function. Component of the signal recognition particle (SRP) complex, a ribonucleoprotein complex that mediates the cotranslational targeting of secretory and membrane proteins to the endoplasmic reticulum (ER). SRP9 together with SRP14 and the Alu portion of the SRP RNA, constitutes the elongation arrest domain of SRP. The complex of SRP9 and SRP14 is required for SRP RNA binding.

Subunit / interactions. Heterodimer with SRP14; binds RNA as heterodimer. Component of a signal recognition particle complex that consists of a 7SL RNA molecule of 300 nucleotides and six protein subunits: SRP72, SRP68, SRP54, SRP19, SRP14 and SRP9.

Subcellular location. Cytoplasm.

Similarity. Belongs to the SRP9 family.

Isoforms (2)

UniProt IDNamesCanonical?
P49458-11yes
P49458-22

RefSeq proteins (2): NP_001123912, NP_003124* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008832SRP9Family
IPR009018Signal_recog_particle_SRP9/14Homologous_superfamily
IPR039432SRP9_domDomain
IPR039914SRP9-likeFamily

Pfam: PF05486

UniProt features (15 total): strand 5, helix 3, turn 2, initiator methionine 1, chain 1, sequence conflict 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
5AOXX-RAY DIFFRACTION2.04
1E8OX-RAY DIFFRACTION3.2
7NFXELECTRON MICROSCOPY3.2
4UYKX-RAY DIFFRACTION3.22
4UYJX-RAY DIFFRACTION3.35
1E8SX-RAY DIFFRACTION4
1RY1ELECTRON MICROSCOPY12

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P49458-F190.410.85

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 52

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-1799339SRP-dependent cotranslational protein targeting to membrane
R-HSA-392499Metabolism of proteins
R-HSA-72766Translation

MSigDB gene sets: 228 (showing top): MORF_MTA1, MORF_MBD4, MODULE_151, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, MODULE_150, MORF_HDAC1, GOBP_PROTEIN_TARGETING, MORF_RAD21, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, GOBP_REGULATION_OF_TRANSLATIONAL_ELONGATION, MORF_HDAC2, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, MODULE_149, MORF_PSMC2

GO Biological Process (2): SRP-dependent cotranslational protein targeting to membrane (GO:0006614), negative regulation of translational elongation (GO:0045900)

GO Molecular Function (4): RNA binding (GO:0003723), signal recognition particle binding (GO:0005047), 7S RNA binding (GO:0008312), protein binding (GO:0005515)

GO Cellular Component (6): signal recognition particle receptor complex (GO:0005785), signal recognition particle, endoplasmic reticulum targeting (GO:0005786), cytosol (GO:0005829), cytoplasm (GO:0005737), signal recognition particle (GO:0048500), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Translation1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm2
cellular anatomical structure2
translation1
cotranslational protein targeting to membrane1
protein targeting to ER1
translational elongation1
regulation of translational elongation1
negative regulation of translation1
nucleic acid binding1
ribonucleoprotein complex binding1
RNA binding1
binding1
rough endoplasmic reticulum membrane1
membrane protein complex1
endoplasmic reticulum protein-containing complex1
signal recognition particle1
intracellular anatomical structure1
ribonucleoprotein complex1
protein-containing complex1

Protein interactions and networks

STRING

2232 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SRP9SRP14P37108999
SRP9SRP72O76094999
SRP9SRP19P09132999
SRP9SRP68Q9UHB9999
SRP9SRP54P13624997
SRP9SRPRAP08240681
SRP9SRPRBQ9Y5M8644
SRP9COG3Q96JB2601
SRP9PABPC1P11940580
SRP9SPCS1Q9Y6A9570
SRP9SZRD1Q7Z422531
SRP9SEC61GP38384523
SRP9HNRNPKP61978506
SRP9SEC61A1P38378504
SRP9SHMT1P34896496

IntAct

183 interactions, top by confidence:

ABTypeScore
SRP9SRP14psi-mi:“MI:0915”(physical association)0.890
SRP14SRP9psi-mi:“MI:0915”(physical association)0.890
SRP9SRP72psi-mi:“MI:0914”(association)0.730
PTK2TGFB1I1psi-mi:“MI:0914”(association)0.680
ACTN2SRP9psi-mi:“MI:0915”(physical association)0.560
RYBPSRP9psi-mi:“MI:0915”(physical association)0.560
SRP9DPP9psi-mi:“MI:0915”(physical association)0.560
CDHR3SRP9psi-mi:“MI:0915”(physical association)0.560
CC2D2AOFD1psi-mi:“MI:2364”(proximity)0.420
SGCDSRP9psi-mi:“MI:0915”(physical association)0.400
TK2psi-mi:“MI:0915”(physical association)0.400
OTUB1psi-mi:“MI:0914”(association)0.350
psi-mi:“MI:0914”(association)0.350
Edc4C4BPApsi-mi:“MI:0914”(association)0.350
EXOSC1MPHOSPH6psi-mi:“MI:0914”(association)0.350
DUX4CBX3psi-mi:“MI:0914”(association)0.350
E7COPEpsi-mi:“MI:0914”(association)0.350

BioGRID (525): SRP9 (Affinity Capture-MS), SRP9 (Affinity Capture-MS), SRP9 (Proximity Label-MS), SRP9 (Proximity Label-MS), SRP9 (Proximity Label-MS), SRP9 (Proximity Label-MS), SRP9 (Proximity Label-MS), SRP9 (Proximity Label-MS), SRP9 (Proximity Label-MS), SRP9 (Affinity Capture-MS), SRP9 (Affinity Capture-MS), SRP9 (Affinity Capture-MS), SRP9 (Affinity Capture-MS), SRP9 (Two-hybrid), SRP54 (Affinity Capture-MS)

ESM2 similar proteins: A0A140F3K6, A0A6M3VZT9, A0RVX7, A1KRS4, A4IR79, A4VSE9, A4VYN7, A8ALC5, A9A5J1, A9VI08, B1MXP9, B7IYP1, B8DCF0, C5D4Z2, I6WJ72, O26903, O27943, O29789, O30321, O32124, P0DW82, P18005, P41063, P49458, P51429, Q03R44, Q03YQ1, Q04ER0, Q0AZQ0, Q12NR2, Q16BB4, Q1WT33, Q2LQ83, Q2RHZ4, Q2W1Y0, Q3JYN3, Q47269, Q57778, Q5KWU6, Q65GS6

Diamond homologs: O04438, P21262, P34642, P49458, P49962, Q4R6I6, Q55GL2, Q9SMU7, Q9VSC1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 139 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Loss of Nlp from mitotic centrosomes610.2×6e-03
Loss of proteins required for interphase microtubule organization from the centrosome610.2×6e-03
AURKA Activation by TPX269.8×6e-03
Anchoring of the basal body to the plasma membrane89.7×1e-03
Recruitment of mitotic centrosome proteins and complexes68.8×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance2
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

579 predictions. Top by Δscore:

VariantEffectΔscore
1:225778008:TGAAG:Tdonor_loss1.0000
1:225778013:GT:Gdonor_loss1.0000
1:225778014:T:Gdonor_loss1.0000
1:225783364:TAGTT:Tdonor_gain1.0000
1:225783366:GTT:Gdonor_gain1.0000
1:225783367:TT:Tdonor_gain1.0000
1:225783369:G:GGdonor_gain1.0000
1:225783365:AGTT:Adonor_gain0.9900
1:225783366:GTTG:Gdonor_gain0.9900
1:225783367:TTGT:Tdonor_gain0.9900
1:225783367:TTGTA:Tdonor_loss0.9900
1:225783368:TGTA:Tdonor_loss0.9900
1:225783369:G:Adonor_loss0.9900
1:225783370:T:TGdonor_loss0.9900
1:225783371:AA:Adonor_loss0.9900
1:225783372:A:AAdonor_loss0.9900
1:225783373:G:Adonor_loss0.9900
1:225789238:A:AGacceptor_gain0.9900
1:225789239:G:GGacceptor_gain0.9900
1:225789239:GT:Gacceptor_gain0.9900
1:225778105:G:GTdonor_gain0.9800
1:225778142:T:Gdonor_gain0.9800
1:225783299:GGCAC:Gacceptor_gain0.9800
1:225778866:TT:Tdonor_gain0.9700
1:225783298:A:AGacceptor_gain0.9700
1:225783299:G:GGacceptor_gain0.9700
1:225783293:GTTTC:Gacceptor_loss0.9600
1:225783294:TTTCA:Tacceptor_loss0.9600
1:225783295:TTCA:Tacceptor_loss0.9600
1:225783297:CA:Cacceptor_loss0.9600

AlphaMissense

572 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:225777959:T:AW7R0.999
1:225777959:T:CW7R0.999
1:225777968:T:CF10L0.999
1:225777969:T:CF10S0.999
1:225777970:C:AF10L0.999
1:225777970:C:GF10L0.999
1:225777981:C:AA14D0.999
1:225777961:G:CW7C0.998
1:225777961:G:TW7C0.998
1:225777980:G:CA14P0.998
1:225789249:T:GY51D0.998
1:225783303:C:AR26S0.997
1:225783318:T:CY31H0.997
1:225783318:T:GY31D0.997
1:225789278:G:CK60N0.997
1:225789278:G:TK60N0.997
1:225789304:T:CL69P0.997
1:225783304:G:CR26P0.996
1:225783355:C:TT43I0.996
1:225789256:C:TT53I0.996
1:225777990:T:CL17P0.995
1:225783346:T:AV40D0.995
1:225777960:G:CW7S0.994
1:225777969:T:GF10C0.994
1:225783319:A:CY31S0.994
1:225789274:T:AV59E0.994
1:225789276:A:GK60E0.994
1:225777968:T:AF10I0.993
1:225777992:T:GY18D0.993
1:225789249:T:AY51N0.993

dbSNP variants (sampled 300 via entrez): RS1000465567 (1:225781790 A>G), RS1000484206 (1:225785176 T>G), RS1000793867 (1:225781498 C>A), RS1000955648 (1:225778153 C>A,G,T), RS1001085638 (1:225783585 T>C), RS1001200822 (1:225783189 G>A), RS1001266450 (1:225784000 GT>G,GTT,GTTT), RS1001528845 (1:225780788 C>A), RS1001560052 (1:225781102 T>C), RS1001866036 (1:225789622 CAT>C), RS1002426753 (1:225788358 A>G), RS1002536818 (1:225779544 C>T), RS1002567846 (1:225779923 C>T), RS1002771108 (1:225786070 T>G), RS1002779553 (1:225784543 C>T)

Disease associations

OMIM: gene MIM:600707 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST003447_2Neuroticism2.000000e-08
GCST004607_209Plateletcrit2.000000e-09
GCST006464_3Endometrial cancer8.000000e-07
GCST009312_20Antisaccade task score5.000000e-06
GCST90002388_54Lymphocyte count2.000000e-13
GCST90002392_255Mean corpuscular volume5.000000e-13
GCST90002400_542Plateletcrit5.000000e-14
GCST90002401_405Platelet distribution width2.000000e-13
GCST90002402_264Platelet count1.000000e-09
GCST90002404_449Red cell distribution width1.000000e-12

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0007660neuroticism measurement
EFO:0007985platelet crit
EFO:0007969cognitive inhibition measurement
EFO:0004587lymphocyte count
EFO:0007984platelet component distribution width
EFO:0004309platelet count
EFO:0009188Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725084 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 3 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.27Kd5323nMCHEMBL3752910
5.27ED505323nMCHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 10 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149487: Binding affinity to human SRP9 incubated for 45 mins by Kinobead based pull down assaykd5.3228uM

CTD chemical–gene interactions

54 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, decreases expression, increases expression4
sodium arsenitedecreases expression2
Air Pollutantsaffects expression, increases abundance, decreases expression2
Particulate Matterdecreases expression, increases abundance, affects cotreatment2
aristolochic acid Idecreases expression1
bisphenol Faffects cotreatment, decreases expression1
dicrotophosdecreases expression1
terbufosdecreases methylation1
beta-lapachonedecreases expression1
arseniteaffects binding, increases reaction1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
perfluorooctanoic aciddecreases expression1
manganese chlorideincreases abundance, increases expression1
4-hydroxy-2-nonenalaffects binding1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
chloropicrinincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrinedecreases expression1
jinfukangdecreases expression1
LDN 193189affects cotreatment, increases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Ethanolincreases abundance, affects cotreatment, decreases expression1
Arsenicdecreases expression1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation1
Cisplatindecreases expression1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652529BindingBinding affinity to human SRP9 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B3I6Abcam HEK293T SRP9 KOTransformed cell lineFemale

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): endometrial carcinoma