IPO13

gene
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Also known as IMP13KIAA0724RANBP13

Summary

IPO13 (importin 13, HGNC:16853) is a protein-coding gene on chromosome 1p34.1, encoding Importin-13 (O94829). Functions in nuclear protein import as nuclear transport receptor. It is a common-essential gene (DepMap: required in 95.6% of cancer cell lines).

This gene encodes a member of the importin-beta family of nuclear transport proteins. The encoded protein mediates the import of specific cargo proteins from the cytoplasm to the nucleus and is dependent on the Ras-related nuclear protein-GTPase system. The encoded protein is also involved in nuclear export of the eukaryotic translation initiation factor 1A.

Source: NCBI Gene 9670 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 119 total
  • Cancer dependency (DepMap): dependent in 95.6% of screened cell lines (common-essential)
  • MANE Select transcript: NM_014652

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16853
Approved symbolIPO13
Nameimportin 13
Location1p34.1
Locus typegene with protein product
StatusApproved
AliasesIMP13, KIAA0724, RANBP13
Ensembl geneENSG00000117408
Ensembl biotypeprotein_coding
OMIM610411
Entrez9670

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 20 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000372339, ENST00000372343, ENST00000480902, ENST00000486876, ENST00000489061, ENST00000489773, ENST00000492152, ENST00000862660, ENST00000862661, ENST00000862662, ENST00000862663, ENST00000862664, ENST00000862665, ENST00000862666, ENST00000862667, ENST00000862668, ENST00000862669, ENST00000862670, ENST00000862671, ENST00000862672, ENST00000924210, ENST00000924211, ENST00000924212, ENST00000950460, ENST00000950461

RefSeq mRNA: 1 — MANE Select: NM_014652 NM_014652

CCDS: CCDS503

Canonical transcript exons

ENST00000372343 — 20 exons

ExonStartEnd
ENSE000007701394394941743950153
ENSE000007704144395797743958158
ENSE000007704944395824243958268
ENSE000007705624395846143958595
ENSE000007705634395874643958889
ENSE000007705644396024943960329
ENSE000007705764396116643961262
ENSE000007705774396426943964321
ENSE000007705804396657543966641
ENSE000007705824396672443966782
ENSE000007705934396693043967019
ENSE000007705964396731543967496
ENSE000014575794396758643968022
ENSE000014575884394695043947684
ENSE000032381454396087643961013
ENSE000034764904395719543957315
ENSE000035662724395740243957549
ENSE000036187764395681043956976
ENSE000036349484395632043956460
ENSE000036699184395656043956701

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 97.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.0202 / max 450.2358, expressed in 1817 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
256823.74961817
25671.1862502
25690.084430

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
C1 segment of cervical spinal cordUBERON:000646997.62gold quality
gastrocnemiusUBERON:000138897.11gold quality
apex of heartUBERON:000209897.07gold quality
spinal cordUBERON:000224096.93gold quality
hindlimb stylopod muscleUBERON:000425296.87gold quality
muscle of legUBERON:000138396.05gold quality
putamenUBERON:000187495.86gold quality
corpus callosumUBERON:000233695.81gold quality
inferior vagus X ganglionUBERON:000536395.75gold quality
right hemisphere of cerebellumUBERON:001489095.75gold quality
right frontal lobeUBERON:000281095.61gold quality
lateral globus pallidusUBERON:000247695.57gold quality
cerebellar hemisphereUBERON:000224595.37gold quality
cerebellar cortexUBERON:000212995.28gold quality
olfactory bulbUBERON:000226495.24silver quality
muscle organUBERON:000163095.19gold quality
caudate nucleusUBERON:000187395.17gold quality
amygdalaUBERON:000187695.08gold quality
nucleus accumbensUBERON:000188295.01gold quality
subthalamic nucleusUBERON:000190694.83gold quality
gluteal muscleUBERON:000200094.78gold quality
substantia nigra pars reticulataUBERON:000196694.51gold quality
left testisUBERON:000453394.47gold quality
substantia nigraUBERON:000203894.41gold quality
lower esophagus mucosaUBERON:003583494.36gold quality
right testisUBERON:000453494.35gold quality
midbrainUBERON:000189194.32gold quality
dorsal plus ventral thalamusUBERON:000189794.21gold quality
cerebellumUBERON:000203794.00gold quality
Brodmann (1909) area 9UBERON:001354093.98gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.60

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CRX, CTCF, PAX3, PAX6

miRNA regulators (miRDB)

26 targeting IPO13, 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-4425100.0067.591049
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-9-5P100.0072.282361
HSA-MIR-477599.9875.006394
HSA-MIR-4645-3P99.7669.33993
HSA-MIR-6513-5P99.4367.811071
HSA-MIR-465199.0667.572002
HSA-MIR-4695-5P99.0664.871151
HSA-MIR-6814-5P99.0366.681273
HSA-MIR-315498.9466.551455
HSA-MIR-60898.9367.832013
HSA-MIR-4709-3P98.8868.041594
HSA-MIR-950098.6266.541845
HSA-MIR-299-5P98.5671.141140
HSA-MIR-6795-5P98.5268.511277
HSA-MIR-5089-5P98.4566.061388
HSA-MIR-6815-5P96.0565.55662
HSA-MIR-6865-5P96.0565.58675
HSA-MIR-6726-5P95.9763.72841
HSA-MIR-92095.9763.95811
HSA-MIR-430095.8564.561003
HSA-MIR-5591-5P95.8564.761002
HSA-MIR-6802-5P94.9465.95366
HSA-MIR-135A-3P94.1966.09495

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 95.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 16)

  • Imp13 functions in myopodin import and the regulation of this event is critical for normal and abnormal cellular differentiation. (PMID:17828378)
  • Importin 13 mediates nuclear import of histone fold-containing chromatin accessibility complex heterodimers (PMID:19218565)
  • IPO13 is uniquely expressed by human limbal basal epithelial cells, and plays an important role in maintaining the phenotype, high proliferative potential, and less differentiation of corneal epithelial progenitor cells. (PMID:19593795)
  • IPO13 variation may improve nuclear bioavailability of endogenous glucocorticoids (PMID:19619331)
  • Data show that expression of IPO13, c-kit, telomerase, caspase3, and CD146 are decreased in endometrial polyps; however, the expression of bcl-2 was increased in polyps compared to the normal endometrial tissue. (PMID:21804459)
  • These results demonstrate an increased expression of IPO13 in endometriosis and endometrial carcinoma. (PMID:22648251)
  • Imp13 is able to bind and export eIF1A in vivo and that its function is essential. (PMID:23435562)
  • IPO13 may contribute to the pathogenesis of pterygium via modulation of K17 and c-Jun. (PMID:23559854)
  • IPO13 influenced intracellular distribution of CTCF. (PMID:23620300)
  • The anti- glucocorticoid receptor effect of respiratory syncytial virus was mediated by viral nonstructural protein 1, which likely functioned by competing with IPO13 for glucocorticoid receptor binding. (PMID:28968829)
  • this study significantly expands the repertoire of importin 13 cargoes and sets the basis for a more detailed characterization of this extremely versatile transport receptor. (PMID:29666159)
  • This study reports the identification of mutation (c.331C>T, p.R111C) in the IPO13 gene in a consanguineous family with ocular coloboma, microphthalmia, and cataract by a combination of whole-exome sequencing and homozygosity mapping. (PMID:29700284)
  • This is the first report that IPO13 can be phosphorylated at Ser193 and that this modification regulates IPO13 subcellular localization and nucleocytoplasmic transport function, with important implications for IPO13’s role in development and other processes. (PMID:30045875)
  • Importin 13 promotes NSCLC progression by mediating RFPL3 nuclear translocation and hTERT expression upregulation. (PMID:33082305)
  • Nuclear transporter Importin-13 plays a key role in the oxidative stress transcriptional response. (PMID:34625540)
  • The Nuclear Transporter Importin 13 Can Regulate Stress-Induced Cell Death through the Clusterin/KU70 Axis. (PMID:36672214)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioipo13bENSDARG00000060618
mus_musculusIpo13ENSMUSG00000033365
rattus_norvegicusIpo13ENSRNOG00000019758
drosophila_melanogastercdmFBGN0261532
caenorhabditis_elegansWBGENE00011807

Paralogs (1): TNPO3 (ENSG00000064419)

Protein

Protein identifiers

Importin-13O94829 (reviewed: O94829)

Alternative names: Karyopherin-13, Ran-binding protein 13

All UniProt accessions (2): O94829, Q5T4X2

UniProt curated annotations — full annotation on UniProt →

Function. Functions in nuclear protein import as nuclear transport receptor. Serves as receptor for nuclear localization signals (NLS) in cargo substrates. Is thought to mediate docking of the importin/substrate complex to the nuclear pore complex (NPC) through binding to nucleoporin and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to the importin, the importin/substrate complex dissociates and importin is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. Mediates the nuclear import of UBC9, the RBM8A/MAGOH complex, PAX6 and probably other members of the paired homeobox family. Also mediates nuclear export of eIF-1A, and the cytoplasmic release of eIF-1A is triggered by the loading of import substrates onto IPO13.

Subunit / interactions. Interacts with UBC9, RAN, RBM8A, eIF-1A and PAX6.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Expressed in fetal brain, heart, intestine and kidney.

Similarity. Belongs to the importin beta family.

RefSeq proteins (1): NP_055467* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001494Importin-beta_NDomain
IPR011989ARM-likeHomologous_superfamily
IPR013598Exportin-1/Importin-b-likeDomain
IPR016024ARM-type_foldHomologous_superfamily
IPR040520Importin_rep_3Repeat
IPR040709Importin_rep_1Repeat
IPR040944Importin_rep_2Repeat
IPR051345Importin_beta-like_NTRFamily
IPR057941TPR_TNPO3_IPO13_2ndRepeat
IPR057942TPR_TNPO3_IPO13_3rdRepeat
IPR058537TPR_TNPO3_IPO13_4thRepeat

Pfam: PF03810, PF08389, PF18773, PF18786, PF18806, PF24138, PF24139, PF24140

UniProt features (98 total): helix 60, repeat 20, turn 12, sequence conflict 3, chain 1, domain 1, strand 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
2X19X-RAY DIFFRACTION2.8
2XWUX-RAY DIFFRACTION2.8
3ZJYX-RAY DIFFRACTION3.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O94829-F190.600.80

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 109 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, RNGTGGGC_UNKNOWN, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GCANCTGNY_MYOD_Q6, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOMF_GTPASE_BINDING, USF_C, GOBP_NUCLEAR_TRANSPORT, BROWNE_HCMV_INFECTION_24HR_UP, MYCMAX_01, chr1p34, ZIC1_01, NRF2_Q4, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE

GO Biological Process (3): protein import into nucleus (GO:0006606), intracellular protein transport (GO:0006886), protein transport (GO:0015031)

GO Molecular Function (2): small GTPase binding (GO:0031267), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular protein localization2
intracellular protein transport1
protein localization to nucleus1
import into nucleus1
establishment of protein localization to organelle1
protein transport1
intracellular transport1
transport1
establishment of protein localization1
GTPase binding1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

916 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
IPO13BAIAP3O94812813
IPO13XPOTO43592783
IPO13XPO4Q9C0E2775
IPO13IPO11Q9UI26775
IPO13IPO9Q96P70759
IPO13IPO7O95373735
IPO13IPO4Q8TEX9734
IPO13ARXQ96QS3730
IPO13IPO5O00410722
IPO13UBE2IP50550714
IPO13IPO8O15397707
IPO13TNPO2O14787692
IPO13SHOX2O60902689
IPO13XPO7Q9UIA9674
IPO13TNPO1Q92973673

IntAct

150 interactions, top by confidence:

ABTypeScore
PBX4IPO13psi-mi:“MI:0915”(physical association)0.830
IPO13PBX4psi-mi:“MI:0915”(physical association)0.830
IPO13EIF1AXpsi-mi:“MI:0915”(physical association)0.750
EIF1AXIPO13psi-mi:“MI:0915”(physical association)0.750
IPO13EIF1AXpsi-mi:“MI:0407”(direct interaction)0.750
IPO13RANpsi-mi:“MI:0407”(direct interaction)0.730
RANIPO13psi-mi:“MI:0407”(direct interaction)0.730
IPO13RANpsi-mi:“MI:0915”(physical association)0.730
IPO13UBE2Ipsi-mi:“MI:0407”(direct interaction)0.720
UBE2IIPO13psi-mi:“MI:0407”(direct interaction)0.720
IPO13UBE2Ipsi-mi:“MI:0915”(physical association)0.720
PITX1IPO13psi-mi:“MI:0915”(physical association)0.670

BioGRID (135): PBX4 (Two-hybrid), IPO13 (Affinity Capture-RNA), IPO13 (Affinity Capture-MS), IPO13 (Affinity Capture-MS), IPO13 (Affinity Capture-MS), IPO13 (Affinity Capture-MS), IPO13 (Affinity Capture-MS), IPO13 (Affinity Capture-MS), IPO13 (Two-hybrid), IPO13 (Two-hybrid), IPO13 (Affinity Capture-Western), IPO13 (Affinity Capture-MS), IPO13 (Affinity Capture-MS), IPO13 (Affinity Capture-MS), IPO13 (Affinity Capture-MS)

ESM2 similar proteins: A0A3L7I2I8, A0JMZ3, A5HK05, A7MB89, A7YWD2, O60733, O75031, O94829, O94955, P0C7A6, P42694, P49754, P97570, P97819, Q05AL1, Q1LVW0, Q29RM5, Q2KI54, Q2T9K6, Q3UFS0, Q3UJZ3, Q4V890, Q5KU39, Q5R6S3, Q5R974, Q5T9G4, Q5TYQ1, Q5VZK9, Q68FK4, Q6DFV5, Q6EDY6, Q6NYU2, Q6QI06, Q6R327, Q7T3P8, Q8C0T1, Q8CEF1, Q8IUR7, Q8NFZ0, Q91W86

Diamond homologs: A7YWD2, O94829, Q5R974, Q5ZIC8, Q8K0C1, Q9JM04

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 126 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
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell78.2×5e-03
G alpha (q) signalling events97.0×2e-03

GO biological processes:

GO termPartnersFoldFDR
phospholipase C-activating G protein-coupled receptor signaling pathway78.9×6e-03
positive regulation of cytosolic calcium ion concentration77.9×6e-03
positive regulation of ERK1 and ERK2 cascade86.5×6e-03
G protein-coupled receptor signaling pathway144.9×8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance94
Likely benign4
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3473 predictions. Top by Δscore:

VariantEffectΔscore
1:43956317:TAG:Tacceptor_loss1.0000
1:43956318:AG:Aacceptor_gain1.0000
1:43956319:G:GAacceptor_loss1.0000
1:43956319:GG:Gacceptor_gain1.0000
1:43956319:GGT:Gacceptor_gain1.0000
1:43956319:GGTAC:Gacceptor_gain1.0000
1:43956446:C:Tdonor_gain1.0000
1:43956457:CCCG:Cdonor_loss1.0000
1:43956459:CGGT:Cdonor_loss1.0000
1:43956460:GGTA:Gdonor_loss1.0000
1:43956461:G:Tdonor_loss1.0000
1:43956462:T:Cdonor_loss1.0000
1:43956469:TG:Tdonor_gain1.0000
1:43956470:GG:Gdonor_gain1.0000
1:43957193:A:AGacceptor_gain1.0000
1:43957193:AG:Aacceptor_gain1.0000
1:43957194:G:GGacceptor_gain1.0000
1:43957194:GG:Gacceptor_gain1.0000
1:43957976:GGA:Gacceptor_gain1.0000
1:43958108:TGC:Tdonor_gain1.0000
1:43958157:AGG:Adonor_loss1.0000
1:43958158:GG:Gdonor_loss1.0000
1:43958159:GT:Gdonor_loss1.0000
1:43958458:CA:Cacceptor_loss1.0000
1:43958459:A:AGacceptor_gain1.0000
1:43958459:A:Cacceptor_loss1.0000
1:43958460:G:GTacceptor_gain1.0000
1:43958460:GA:Gacceptor_gain1.0000
1:43958460:GAC:Gacceptor_gain1.0000
1:43958460:GACA:Gacceptor_gain1.0000

AlphaMissense

6291 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:43949430:T:CL33P1.000
1:43949478:T:AL49Q1.000
1:43949478:T:CL49P1.000
1:43949507:T:AW59R1.000
1:43949507:T:CW59R1.000
1:43949509:G:CW59C1.000
1:43949509:G:TW59C1.000
1:43949561:T:CF77L1.000
1:43949563:T:AF77L1.000
1:43949563:T:GF77L1.000
1:43949564:G:AG78R1.000
1:43949564:G:CG78R1.000
1:43949564:G:TG78W1.000
1:43949565:G:AG78E1.000
1:43949568:C:AA79D1.000
1:43949577:T:CL82P1.000
1:43949585:A:GK85E1.000
1:43949587:G:CK85N1.000
1:43949587:G:TK85N1.000
1:43949646:T:CL105P1.000
1:43949700:T:CL123P1.000
1:43950017:T:AW229R1.000
1:43950017:T:CW229R1.000
1:43956427:G:CR310P1.000
1:43956666:A:CS357R1.000
1:43956668:C:AS357R1.000
1:43956668:C:GS357R1.000
1:43956687:T:AW364R1.000
1:43956687:T:CW364R1.000
1:43956697:T:CL367P1.000

dbSNP variants (sampled 300 via entrez): RS1000323710 (1:43965150 G>T), RS1000807373 (1:43965185 T>G), RS1000859824 (1:43965517 C>A,T), RS1001196506 (1:43950393 A>G,T), RS1001350474 (1:43948696 G>T), RS1001426243 (1:43965663 C>G), RS1001540623 (1:43965300 A>G,T), RS1001800276 (1:43949101 G>A,C), RS1001870957 (1:43963606 C>G), RS1002554937 (1:43966992 T>A), RS1002662166 (1:43966054 G>A), RS1002758938 (1:43950443 T>A,G), RS1003142757 (1:43959775 T>C), RS1003383622 (1:43952668 GAT>G), RS1003541325 (1:43952337 T>C)

Disease associations

OMIM: gene MIM:610411 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST004521_235Autism spectrum disorder or schizophrenia4.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, increases expression, affects cotreatment, affects expression, increases abundance3
Aflatoxin B1increases expression, increases methylation2
aristolochic acid Iincreases expression1
bisphenol Faffects cotreatment, increases expression1
ginger extractaffects cotreatment, affects expression, increases abundance1
2,4,6-tribromophenoldecreases expression1
triphenyl phosphateaffects expression1
decabromobiphenyl etherdecreases expression1
tetrabromobisphenol Adecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
(+)-JQ1 compoundincreases expression1
Resveratrolincreases expression1
Sunitinibincreases expression1
Acetaminophenincreases expression1
Calcitrioldecreases expression1
Cisplatinincreases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinincreases expression, affects cotreatment1
Oils, Volatileincreases abundance, affects cotreatment, affects expression1
Smokedecreases expression1
Tretinoindecreases expression1
Zearalenoneincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Lactic Aciddecreases expression1

Clinical trials (associated diseases)

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

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