KRR1

gene
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Also known as RIP-1

Summary

KRR1 (KRR1 small subunit processome component, HGNC:5176) is a protein-coding gene on chromosome 12q21.2, encoding KRR1 small subunit processome component homolog (Q13601). Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. It is a common-essential gene (DepMap: required in 97.2% of cancer cell lines).

Enables RNA binding activity. Involved in ribosomal small subunit biogenesis. Located in chromosome; intercellular bridge; and nuclear lumen. Part of small-subunit processome.

Source: NCBI Gene 11103 — RefSeq curated summary.

At a glance

  • GWAS associations: 12
  • Clinical variants (ClinVar): 47 total
  • Cancer dependency (DepMap): dependent in 97.2% of screened cell lines (common-essential)
  • MANE Select transcript: NM_007043

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:5176
Approved symbolKRR1
NameKRR1 small subunit processome component
Location12q21.2
Locus typegene with protein product
StatusApproved
AliasesRIP-1
Ensembl geneENSG00000111615
Ensembl biotypeprotein_coding
OMIM612817
Entrez11103

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 3 retained_intron

ENST00000229214, ENST00000438169, ENST00000550023, ENST00000550898, ENST00000551070, ENST00000907976, ENST00000907977, ENST00000935725, ENST00000935726, ENST00000935727

RefSeq mRNA: 1 — MANE Select: NM_007043 NM_007043

CCDS: CCDS9012

Canonical transcript exons

ENST00000229214 — 10 exons

ExonStartEnd
ENSE000009373207550648475506609
ENSE000009373217550631675506399
ENSE000009373227550519875505254
ENSE000012391747550390475504074
ENSE000013625657549086375499951
ENSE000023768837551151375511609
ENSE000034888367550678275506916
ENSE000035959387550172375501816
ENSE000036155777550827475508446
ENSE000036530057550192375502000

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 98.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.5581 / max 1085.8300, expressed in 1802 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
13216443.55811802

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370198.11gold quality
oocyteCL:000002397.73gold quality
tendonUBERON:000004395.93gold quality
secondary oocyteCL:000065595.78gold quality
adrenal tissueUBERON:001830394.49gold quality
caput epididymisUBERON:000435894.45gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099194.44gold quality
cauda epididymisUBERON:000436094.08gold quality
mucosa of paranasal sinusUBERON:000503093.67gold quality
corpus epididymisUBERON:000435993.24gold quality
tonsilUBERON:000237292.40gold quality
islet of LangerhansUBERON:000000692.38gold quality
mammary ductUBERON:000176592.36gold quality
hair follicleUBERON:000207392.29gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450292.20gold quality
colonic epitheliumUBERON:000039792.15gold quality
stromal cell of endometriumCL:000225592.09gold quality
epithelium of mammary glandUBERON:000324492.06gold quality
olfactory segment of nasal mucosaUBERON:000538692.03gold quality
Brodmann (1909) area 23UBERON:001355491.93gold quality
biceps brachiiUBERON:000150791.85gold quality
esophagus mucosaUBERON:000246991.74gold quality
medial globus pallidusUBERON:000247791.52gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451191.48gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047391.38gold quality
cranial nerve IIUBERON:000094191.30gold quality
endometriumUBERON:000129591.20gold quality
minor salivary glandUBERON:000183091.15gold quality
synovial jointUBERON:000221791.13gold quality
bone marrowUBERON:000237191.03gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-9543yes6.62
E-ENAD-17no382.14
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

100 targeting KRR1, 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-340-5P100.0072.504437
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-12118100.0065.881270
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-477599.9875.006394
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-548AN99.9770.912817
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-552-5P99.9368.561583
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-311999.9271.342390
HSA-MIR-806399.9169.763146
HSA-MIR-219A-5P99.9173.36735

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 97.2% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

  • The antibody response to KRR1 was higher in sera of patients with invasive ductal carcinoma than in sera of patients with other histological types of breast tumors. (PMID:27847402)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriokrr1ENSDARG00000011246
mus_musculusKrr1ENSMUSG00000063334
rattus_norvegicusKrr1ENSRNOG00000004035
drosophila_melanogasterdbeFBGN0020305
caenorhabditis_elegansWBGENE00015461

Protein

Protein identifiers

KRR1 small subunit processome component homologQ13601 (reviewed: Q13601)

Alternative names: HIV-1 Rev-binding protein 2, KRR-R motif-containing protein 1, Rev-interacting protein 1

All UniProt accessions (1): Q13601

UniProt curated annotations — full annotation on UniProt →

Function. Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome.

Subunit / interactions. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3. (Microbial infection) Directly interacts with HIV-1 protein VPR. Also identified in a complex with NR3C1 and HIV-1 protein VPR.

Subcellular location. Nucleus. Nucleolus Nucleus. Cytoplasm.

Similarity. Belongs to the KRR1 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q13601-11yes
Q13601-22

RefSeq proteins (1): NP_008974* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004087KH_domDomain
IPR024166rRNA_assembly_KRR1Family
IPR036612KH_dom_type_1_sfHomologous_superfamily
IPR041174KRR1-like_KH1Domain
IPR048548KRR1-like_KH2Domain
IPR048549KRR1-like_KH2_eukDomain
IPR048550KRR1-like_KH1_eukDomain

Pfam: PF17903, PF21800

UniProt features (26 total): sequence conflict 9, modified residue 3, cross-link 3, region of interest 3, compositionally biased region 3, initiator methionine 1, chain 1, splice variant 1, sequence variant 1, domain 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
7MQ8ELECTRON MICROSCOPY3.6
7MQ9ELECTRON MICROSCOPY3.87

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q13601-F181.240.48

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 (6): 3, 5, 24, 340, 369, 2

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-6790901rRNA modification in the nucleus and cytosol
R-HSA-6791226Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72312rRNA processing
R-HSA-8868773rRNA processing in the nucleus and cytosol
R-HSA-8953854Metabolism of RNA

MSigDB gene sets: 174 (showing top): GOBP_RIBOSOME_BIOGENESIS, MORF_FLT1, YAGI_AML_WITH_INV_16_TRANSLOCATION, MORF_MSH3, GOBP_MATURATION_OF_SSU_RRNA, MORF_BRCA1, MORF_ESR1, MORF_RAD51L3, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, chr12q21, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, NOUZOVA_TRETINOIN_AND_H4_ACETYLATION, MORF_ATF2, MORF_BCL2L11

GO Biological Process (3): rRNA processing (GO:0006364), ribosomal small subunit biogenesis (GO:0042274), ribosome biogenesis (GO:0042254)

GO Molecular Function (3): RNA binding (GO:0003723), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (9): nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleolus (GO:0005730), cytoplasm (GO:0005737), membrane (GO:0016020), small-subunit processome (GO:0032040), intercellular bridge (GO:0045171), nucleus (GO:0005634), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
rRNA processing in the nucleus and cytosol2
Metabolism of RNA1
rRNA processing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
ribosome biogenesis2
ribonucleoprotein complex biogenesis2
binding2
nuclear lumen2
intracellular membraneless organelle2
RNA processing1
rRNA metabolic process1
nucleic acid binding1
intracellular anatomical structure1
nucleolus1
preribosome1
t-UTP complex1
nuclear protein-containing complex1
intracellular membrane-bounded organelle1
protein-containing complex1

Protein interactions and networks

STRING

2873 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KRR1KRI1Q8N9T8784
KRR1HNRNPKP61978753
KRR1PDCD11Q14690737
KRR1BYSLQ13895710
KRR1BMS1Q14692696
KRR1RRP7AQ9Y3A4692
KRR1UTP20O75691678
KRR1NOL6Q9H6R4678
KRR1DDX52Q9Y2R4665
KRR1WDR46O15213664
KRR1SUOXP51687649
KRR1DENND1AQ8TEH3642
KRR1FCF1Q9Y324627
KRR1HEATR1Q9H583625
KRR1PNO1Q9NRX1617

IntAct

218 interactions, top by confidence:

ABTypeScore
NOP10DKC1psi-mi:“MI:0914”(association)0.890
LARP7CCNT1psi-mi:“MI:0914”(association)0.850
RPS14KRR1psi-mi:“MI:0915”(physical association)0.740
H2AXPPM1Gpsi-mi:“MI:0914”(association)0.730
USP44CETN2psi-mi:“MI:0914”(association)0.690
H1-1RRP8psi-mi:“MI:0914”(association)0.640
SNRPA1HTATSF1psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
RPS14MAGEB2psi-mi:“MI:0914”(association)0.560
H1-6ZNF724psi-mi:“MI:0914”(association)0.530
H1-4IGF2BP3psi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
MAK16NVLpsi-mi:“MI:0914”(association)0.530
RPL7ZBTB24psi-mi:“MI:0914”(association)0.530
RPSADKC1psi-mi:“MI:0914”(association)0.530
ZCRB1DKC1psi-mi:“MI:0914”(association)0.530
NNOP56psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
NSA2TYW5psi-mi:“MI:0914”(association)0.530
RPS3ZNF316psi-mi:“MI:0914”(association)0.530
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
CCDC59GAPDHSpsi-mi:“MI:0914”(association)0.530

BioGRID (475): KRR1 (Affinity Capture-RNA), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Affinity Capture-MS), KRR1 (Two-hybrid), AATF (Co-fractionation)

ESM2 similar proteins: A5IQE7, A6QEP6, A6TZ71, A7WZ38, A8YZU0, A9GI17, B3LU25, B3MM49, B3N899, B4G9L6, B4JDU5, B4KF66, B4LTY6, B4N0P7, B4P2Y8, B4U4H7, B5VEQ2, B9DKS1, C0MH28, C8Z430, E7LRT8, E7QBZ1, O07633, O74777, P0C1E7, P17531, P18333, P25586, P56835, Q13601, Q2FJ50, Q2G0I5, Q2YS71, Q3B7L9, Q49VE6, Q4L3R9, Q54UU6, Q5FJL5, Q5HI83, Q5HRF2

Diamond homologs: B3LU25, B3MM49, B3N899, B4G9L6, B4JDU5, B4KF66, B4LTY6, B4N0P7, B4P2Y8, B5VEQ2, C8Z430, E7LRT8, E7QBZ1, O74777, P25586, Q13601, Q3B7L9, Q54UU6, Q8BGA5, Q9VPU8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 187 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
Eukaryotic Translation Initiation1333.4×8e-16
Cap-dependent Translation Initiation1333.4×8e-16
SARS-CoV-1 modulates host translation machinery1333.4×8e-16
Eukaryotic Translation Elongation1330.2×4e-15
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S1329.5×5e-15
Formation of Senescence-Associated Heterochromatin Foci (SAHF)528.0×7e-06
Nonsense-Mediated Decay (NMD)1427.2×1e-15
Influenza Viral RNA Transcription and Replication1425.1×4e-15

GO biological processes:

GO termPartnersFoldFDR
negative regulation of DNA recombination746.0×1e-08
chromosome condensation734.5×9e-08
maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)527.4×6e-05
regulation of mRNA splicing, via spliceosome525.9×7e-05
cytoplasmic translation2324.9×3e-23
ribosomal small subunit biogenesis1520.0×2e-13
ribosomal large subunit biogenesis718.1×9e-06
translation2313.8×3e-17

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance24
Likely benign8
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1948 predictions. Top by Δscore:

VariantEffectΔscore
12:75495571:TTACA:Tacceptor_loss1.0000
12:75495572:TACA:Tacceptor_loss1.0000
12:75495572:TACAG:Tacceptor_gain1.0000
12:75495573:ACAG:Aacceptor_loss1.0000
12:75495573:ACAGA:Aacceptor_gain1.0000
12:75495574:CAG:Cacceptor_gain1.0000
12:75495574:CAGA:Cacceptor_loss1.0000
12:75495575:A:AGacceptor_gain1.0000
12:75495575:A:Cacceptor_loss1.0000
12:75495575:AGA:Aacceptor_gain1.0000
12:75495575:AGAG:Aacceptor_gain1.0000
12:75495575:AGAGG:Aacceptor_gain1.0000
12:75495576:G:GAacceptor_gain1.0000
12:75495576:GA:Gacceptor_gain1.0000
12:75495576:GAG:Gacceptor_gain1.0000
12:75495576:GAGG:Gacceptor_gain1.0000
12:75495576:GAGGG:Gacceptor_gain1.0000
12:75495659:TGTGG:Tdonor_loss1.0000
12:75495660:GTG:Gdonor_gain1.0000
12:75495660:GTGGT:Gdonor_loss1.0000
12:75495661:TGGTG:Tdonor_loss1.0000
12:75495663:G:GGdonor_gain1.0000
12:75495664:T:Gdonor_loss1.0000
12:75495665:G:GTdonor_loss1.0000
12:75495666:AGTAA:Adonor_loss1.0000
12:75498684:A:AGacceptor_gain1.0000
12:75498685:A:Gacceptor_gain1.0000
12:75498692:A:AGacceptor_gain1.0000
12:75498693:G:GGacceptor_gain1.0000
12:75498721:G:GGdonor_gain1.0000

AlphaMissense

2526 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:75504009:A:CF242L1.000
12:75504009:A:TF242L1.000
12:75504011:A:GF242L1.000
12:75504018:C:AW239C1.000
12:75504018:C:GW239C1.000
12:75504020:A:GW239R1.000
12:75504020:A:TW239R1.000
12:75504052:A:GL228S1.000
12:75504067:A:GM223T1.000
12:75505198:T:AK220N1.000
12:75505198:T:GK220N1.000
12:75505214:G:TP215Q1.000
12:75505216:A:CH214Q1.000
12:75505216:A:TH214Q1.000
12:75505217:T:CH214R1.000
12:75505218:G:CH214D1.000
12:75506338:C:TG194E1.000
12:75506339:C:GG194R1.000
12:75506339:C:TG194R1.000
12:75506350:A:TV190D1.000
12:75506359:C:TG187E1.000
12:75506360:C:GG187R1.000
12:75506360:C:TG187R1.000
12:75506376:A:CC181W1.000
12:75506389:A:GL177P1.000
12:75506506:C:TG166D1.000
12:75506507:C:GG166R1.000
12:75506520:T:AR161S1.000
12:75506520:T:GR161S1.000
12:75506521:C:GR161T1.000

dbSNP variants (sampled 300 via entrez): RS1000708245 (12:75500374 C>CTCAATA), RS1000779003 (12:75506811 G>A), RS1000806805 (12:75497266 T>C), RS1000972255 (12:75510896 G>A), RS1000984369 (12:75503724 C>A,T), RS1001076824 (12:75491034 T>C), RS1001321188 (12:75492412 A>G), RS1001602953 (12:75505398 G>A), RS1001826806 (12:75498410 T>G), RS1001944167 (12:75512035 T>C), RS1001987913 (12:75512076 A>G,T), RS1002019025 (12:75511857 G>A), RS1002205769 (12:75500011 A>G), RS1002288375 (12:75494253 A>G), RS1002297888 (12:75495877 AAAC>A,AAACAAC)

Disease associations

OMIM: gene MIM:612817 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

StudyTraitp-value
GCST002041_7Blood trace element (Cu levels)3.000000e-06
GCST003144_6Polycystic ovary syndrome2.000000e-08
GCST003518_77Daytime sleep phenotypes8.000000e-06
GCST005984_58Glomerular filtration rate1.000000e-11
GCST005985_38Creatinine levels1.000000e-12
GCST005986_15Blood urea nitrogen levels6.000000e-09
GCST006061_120Atrial fibrillation4.000000e-10
GCST006061_121Atrial fibrillation8.000000e-09
GCST007089_12Polycystic ovary syndrome2.000000e-09
GCST007344_10Estimated glomerular filtration rate1.000000e-08
GCST009723_31Vertical cup-disc ratio (adjusted for vertical disc diameter)3.000000e-08
GCST010396_209Gut microbiota (bacterial taxa, hurdle binary method)4.000000e-06

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0005267serum copper measurement
EFO:0007828daytime rest measurement
EFO:0006939cup-to-disc ratio measurement
EFO:0007874gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
FR900359increases phosphorylation1
TAK-243decreases sumoylation1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
nickel sulfatedecreases expression1
nivalenolincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608increases reaction, affects binding1
ICG 001decreases expression1
jinfukangdecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Vorinostatincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicincreases methylation1
Benzo(a)pyreneaffects methylation1
Coaldecreases expression, increases abundance1
Dinitrochlorobenzeneaffects binding1
Estradiolaffects expression1
Golddecreases expression1
Ivermectindecreases expression1
Methotrexateaffects response to substance1
Mitoxantroneaffects response to substance1
Piroxicamincreases expression1
Ribonucleotidesaffects binding1
Seleniumdecreases expression1
Smokedecreases expression, increases abundance1
Thimerosalincreases expression1
Valproic Aciddecreases expression1

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): polycystic ovary syndrome