ISL2

gene
On this page

Also known as FLJ10160

Summary

ISL2 (ISL LIM homeobox 2, HGNC:18524) is a protein-coding gene on chromosome 15q24.3, encoding Insulin gene enhancer protein ISL-2 (Q96A47). Transcriptional factor that defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in axonogenesis; neuron fate specification; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of neuron differentiation and neuron differentiation. Predicted to be located in chromatin. Predicted to be active in nucleus.

Source: NCBI Gene 64843 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 43 total
  • MANE Select transcript: NM_145805

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18524
Approved symbolISL2
NameISL LIM homeobox 2
Location15q24.3
Locus typegene with protein product
StatusApproved
AliasesFLJ10160
Ensembl geneENSG00000159556
Ensembl biotypeprotein_coding
OMIM609481
Entrez64843

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 1 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000290759, ENST00000558437, ENST00000558656

RefSeq mRNA: 1 — MANE Select: NM_145805 NM_145805

CCDS: CCDS10290

Canonical transcript exons

ENST00000290759 — 6 exons

ExonStartEnd
ENSE000011108557633777876337967
ENSE000012079357634171976342475
ENSE000012993407633677376336941
ENSE000034974267634113476341301
ENSE000035403837633825276338514
ENSE000036185597634027676340559

Expression profiles

Bgee: expression breadth broad, 100 present calls, max score 86.23.

FANTOM5 (CAGE): breadth broad, TPM avg 3.3937 / max 146.6949, expressed in 617 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1478422.1222431
1478410.9013396
1478400.209987
1478390.160342

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.23gold quality
esophagogastric junction muscularis propriaUBERON:003584169.77gold quality
lower esophagus muscularis layerUBERON:003583369.44gold quality
lower esophagusUBERON:001347369.37gold quality
granulocyteCL:000009469.34gold quality
mucosa of stomachUBERON:000119968.16gold quality
mucosa of transverse colonUBERON:000499167.87gold quality
vaginaUBERON:000099667.25gold quality
muscle layer of sigmoid colonUBERON:003580567.04gold quality
pituitary glandUBERON:000000765.52gold quality
urethraUBERON:000005764.96silver quality
penisUBERON:000098964.25gold quality
bloodUBERON:000017863.88gold quality
body of stomachUBERON:000116163.18gold quality
adenohypophysisUBERON:000219663.05gold quality
transverse colonUBERON:000115762.63gold quality
bone marrow cellCL:000209262.47silver quality
stomachUBERON:000094561.67gold quality
leukocyteCL:000073861.22gold quality
esophagusUBERON:000104360.80gold quality
colonUBERON:000115560.60gold quality
monocyteCL:000057660.45gold quality
prostate glandUBERON:000236760.24gold quality
small intestine Peyer’s patchUBERON:000345459.81gold quality
epithelium of nasopharynxUBERON:000195159.80gold quality
large intestineUBERON:000005959.73gold quality
intestineUBERON:000016059.43gold quality
small intestineUBERON:000210858.94gold quality
minor salivary glandUBERON:000183057.59gold quality
trigeminal ganglionUBERON:000167557.16silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.23
E-GEOD-99795no12.75

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

TargetRegulation
EPHB1Repression
INSActivation

JASPAR motifs

MotifNameFamily
MA0914.1ISL2HD-LIM
MA0914.2ISL2HD-LIM

JASPAR matrix evidence (PMIDs): PMID:7999775

Upstream regulators (CollecTRI, top): ATOH7

miRNA regulators (miRDB)

34 targeting ISL2, 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-6758-5P100.0066.211470
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-5692A100.0074.406850
HSA-MIR-806899.9873.852376
HSA-MIR-95-5P99.8972.173973
HSA-MIR-449299.8768.253611
HSA-MIR-3156-3P99.7666.72939
HSA-MIR-10394-5P99.6566.831852
HSA-MIR-613299.6065.831554
HSA-MIR-6836-5P99.6065.621538
HSA-MIR-17-3P99.5566.771311
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-444199.4966.563216
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-4763-3P99.1067.832649
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-427099.0266.261987
HSA-MIR-432698.9767.63962
HSA-MIR-29B-1-5P98.8668.351364
HSA-MIR-4477A98.8369.752952
HSA-MIR-887-5P98.8265.901347
HSA-MIR-797798.6566.182590
HSA-MIR-6754-5P98.6065.541627
HSA-MIR-6780A-3P98.4267.491518
HSA-MIR-6810-5P98.2966.21975
HSA-MIR-429998.2866.96850
HSA-MIR-6732-3P98.1767.52802
HSA-MIR-375-3P97.9165.12483

Literature-anchored findings (GeneRIF, showing 3)

  • The broad expression of Isl-2 gene in tissues during embryogenesis and adult development suggests that it may be involved in both differentiation and maintenance of these tissues and might play an important role. (PMID:17091338)
  • Experiments in Isl2/EphA3 knock-in mice test the interactions between effects of molecular labels and correlated activity during the development of neural connectivity. (PMID:21190559)
  • ISL2 is a putative tumor suppressor whose epigenetic silencing reprograms the metabolism of pancreatic cancer. (PMID:35508175)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioisl2aENSDARG00000003971
danio_rerioisl2bENSDARG00000053499
mus_musculusIsl2ENSMUSG00000032318
rattus_norvegicusIsl2ENSRNOG00000015336
drosophila_melanogastertupFBGN0003896
caenorhabditis_eleganslim-7WBGENE00002989

Paralogs (1): ISL1 (ENSG00000016082)

Protein

Protein identifiers

Insulin gene enhancer protein ISL-2Q96A47 (reviewed: Q96A47)

All UniProt accessions (2): Q96A47, H0YN25

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional factor that defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways.

Subunit / interactions. Interacts with LHX4.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_665804* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR001781Znf_LIMDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR047169ISL1/2-likeFamily
IPR047244ISL1/2-like_LIM1Domain

Pfam: PF00046, PF00412

UniProt features (12 total): modified residue 3, region of interest 3, domain 2, compositionally biased region 2, chain 1, DNA-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96A47-F169.660.25

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 (3): 157, 279, 154

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 99 (showing top): GOBP_SPINAL_CORD_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_NEURON_DIFFERENTIATION, BENPORATH_ES_WITH_H3K27ME3, GOBP_RETINAL_GANGLION_CELL_AXON_GUIDANCE, GOBP_NEUROGENESIS, GOBP_CELL_DIFFERENTIATION_IN_SPINAL_CORD, GOBP_SPINAL_CORD_MOTOR_NEURON_DIFFERENTIATION, PATIL_LIVER_CANCER, GOBP_VENTRAL_SPINAL_CORD_DEVELOPMENT, GOBP_SPINAL_CORD_MOTOR_NEURON_CELL_FATE_SPECIFICATION, GOBP_REGULATION_OF_NEURON_DIFFERENTIATION, GOBP_PERIPHERAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION, GOBP_NEURON_FATE_SPECIFICATION, GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION, ZHAN_MULTIPLE_MYELOMA_HP_UP

GO Biological Process (13): axonogenesis (GO:0007409), spinal cord motor neuron cell fate specification (GO:0021520), visceral motor neuron differentiation (GO:0021524), retinal ganglion cell axon guidance (GO:0031290), negative regulation of neuron differentiation (GO:0045665), positive regulation of transcription by RNA polymerase II (GO:0045944), neuron fate specification (GO:0048665), neuron development (GO:0048666), peripheral nervous system neuron development (GO:0048935), regulation of DNA-templated transcription (GO:0006355), cell differentiation (GO:0030154), neuron differentiation (GO:0030182), neuron fate commitment (GO:0048663)

GO Molecular Function (7): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), cis-regulatory region sequence-specific DNA binding (GO:0000987), DNA binding (GO:0003677), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
neuron differentiation3
spinal cord motor neuron differentiation2
regulation of transcription by RNA polymerase II2
cell morphogenesis involved in neuron differentiation1
neuron projection morphogenesis1
axon development1
neuron fate specification1
axon guidance1
negative regulation of cell differentiation1
regulation of neuron differentiation1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
cell fate specification1
neuron fate commitment1
cell development1
neuron development1
peripheral nervous system neuron differentiation1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cellular developmental process1
cell differentiation1
generation of neurons1
cell fate commitment1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
transcription cis-regulatory region binding1
nucleic acid binding1
cation binding1
double-stranded DNA binding1
sequence-specific DNA binding1
binding1
DNA binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1182 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ISL2MNX1P50219808
ISL2NEUROG2Q9H2A3794
ISL2GDPD5Q8WTR4762
ISL2ZIC2O95409742
ISL2EPHB1P54762733
ISL2OLIG2Q13516708
ISL2LHX3Q9UBR4704
ISL2LHX4Q969G2683
ISL2LDB1Q86U70640
ISL2EVX1P49640626
ISL2GDPD2Q9HCC8597
ISL2VSX2P58304546
ISL2POU4F1Q01851543
ISL2POU4F2Q12837537
ISL2NKX6-2Q9C056518

IntAct

55 interactions, top by confidence:

ABTypeScore
LHX4ISL2psi-mi:“MI:0915”(physical association)0.760
PYGO1BCL9psi-mi:“MI:0914”(association)0.700
SSBP3LHX1psi-mi:“MI:0914”(association)0.570
LDB1ISL2psi-mi:“MI:0915”(physical association)0.560
LMO3ZBTB43psi-mi:“MI:0914”(association)0.550
SSBP4LDB2psi-mi:“MI:0914”(association)0.550
SSBP2CLEC18Apsi-mi:“MI:0914”(association)0.530
LHX4THAP12psi-mi:“MI:0914”(association)0.530
ARIH1SPOPpsi-mi:“MI:0914”(association)0.530
SSBP4GM2Apsi-mi:“MI:0914”(association)0.530
SYNGAP1IGF2BP3psi-mi:“MI:0914”(association)0.530
SYNGAP1SEC16Apsi-mi:“MI:0914”(association)0.530
PICK1ILVBLpsi-mi:“MI:0914”(association)0.530
IFNA10ISL2psi-mi:“MI:0915”(physical association)0.370
IFNA21ISL2psi-mi:“MI:0915”(physical association)0.370
IFNA4ISL2psi-mi:“MI:0915”(physical association)0.370
IFNA7ISL2psi-mi:“MI:0915”(physical association)0.370
SSBP3LHX2psi-mi:“MI:0914”(association)0.350
COPS5FBLL1psi-mi:“MI:0914”(association)0.350
LMO2APBB1psi-mi:“MI:0914”(association)0.350
IDI2LMX1Bpsi-mi:“MI:0914”(association)0.350
SSBP3LHX1psi-mi:“MI:0914”(association)0.350
LHX1AIFM1psi-mi:“MI:0914”(association)0.350
LHX3HALpsi-mi:“MI:0914”(association)0.350
LHX4FLOT1psi-mi:“MI:0914”(association)0.350
DYRK1ATEX13Dpsi-mi:“MI:0914”(association)0.350

BioGRID (73): ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), LDB1 (Two-hybrid), LHX3 (Reconstituted Complex)

ESM2 similar proteins: A0JNI8, A2I8Z7, A2PZF9, G5EC36, G5EE86, G5EEA1, P20154, P29673, P29674, P34764, P34765, P36198, P36200, P37137, P48742, P50211, P50212, P50458, P50481, P52889, P53405, P53406, P53407, P53408, P53409, P53411, P53412, P61371, P61372, P61373, P61374, P61375, P61376, P63006, P63007, P63008, Q1LWV4, Q5IS44, Q5IS89, Q68EY3

Diamond homologs: A0JNI8, A2I8Z7, A2PZF9, G5EC36, G5EE86, O14639, O35652, O60663, O88609, O94929, O97581, P20154, P25791, P25800, P25801, P29673, P29674, P34764, P34765, P36198, P36200, P37137, P48742, P50211, P50212, P50458, P50480, P50481, P52889, P53405, P53406, P53407, P53408, P53409, P53410, P53411, P53412, P53413, P53667, P53668

SIGNOR signaling

1 interactions.

AEffectBMechanism
LHX3“up-regulates activity”ISL2binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 55 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
SARS-CoV-2 activates/modulates innate and adaptive immune responses512.8×2e-03

GO biological processes:

GO termPartnersFoldFDR
neuron differentiation917.7×4e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance40
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

898 predictions. Top by Δscore:

VariantEffectΔscore
15:76337777:GAGAA:Gacceptor_gain1.0000
15:76337968:GTGA:Gdonor_loss1.0000
15:76337969:T:Gdonor_loss1.0000
15:76340135:G:GTdonor_gain1.0000
15:76340555:AGACG:Adonor_gain1.0000
15:76340556:GACG:Gdonor_gain1.0000
15:76340556:GACGG:Gdonor_gain1.0000
15:76340559:GGTG:Gdonor_loss1.0000
15:76340560:G:Adonor_loss1.0000
15:76340560:G:GGdonor_gain1.0000
15:76340561:T:Gdonor_loss1.0000
15:76341132:A:AGacceptor_gain1.0000
15:76341133:G:GGacceptor_gain1.0000
15:76341133:GA:Gacceptor_gain1.0000
15:76341298:GCTG:Gdonor_gain1.0000
15:76341300:TGGTG:Tdonor_loss1.0000
15:76341301:GGT:Gdonor_loss1.0000
15:76341302:G:GGdonor_gain1.0000
15:76341302:GTGAG:Gdonor_loss1.0000
15:76341303:T:Adonor_loss1.0000
15:76336939:AGA:Adonor_gain0.9900
15:76336940:GA:Gdonor_gain0.9900
15:76336940:GAG:Gdonor_gain0.9900
15:76336942:G:GGdonor_gain0.9900
15:76337772:C:CAacceptor_gain0.9900
15:76337774:GCA:Gacceptor_loss0.9900
15:76337775:CA:Cacceptor_loss0.9900
15:76337776:A:ACacceptor_loss0.9900
15:76337776:A:AGacceptor_gain0.9900
15:76337777:G:GAacceptor_gain0.9900

AlphaMissense

2360 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:76337798:T:AC27S1.000
15:76337798:T:CC27R1.000
15:76337799:G:AC27Y1.000
15:76337799:G:CC27S1.000
15:76337800:C:GC27W1.000
15:76337807:T:AC30S1.000
15:76337807:T:CC30R1.000
15:76337808:G:AC30Y1.000
15:76337808:G:CC30S1.000
15:76337808:G:TC30F1.000
15:76337809:C:GC30W1.000
15:76337838:T:CL40P1.000
15:76337861:T:AW48R1.000
15:76337861:T:CW48R1.000
15:76337862:G:CW48S1.000
15:76337863:G:CW48C1.000
15:76337863:G:TW48C1.000
15:76337864:C:GH49D1.000
15:76337866:C:AH49Q1.000
15:76337866:C:GH49Q1.000
15:76337873:T:AC52S1.000
15:76337873:T:CC52R1.000
15:76337874:G:AC52Y1.000
15:76337874:G:CC52S1.000
15:76337874:G:TC52F1.000
15:76337875:C:GC52W1.000
15:76337877:T:AL53H1.000
15:76337877:T:CL53P1.000
15:76337882:T:AC55S1.000
15:76337882:T:CC55R1.000

dbSNP variants (sampled 300 via entrez): RS1000191675 (15:76338559 C>A), RS1001063008 (15:76340660 A>G), RS1001369842 (15:76340434 C>G), RS1001414775 (15:76339486 C>T), RS1002049240 (15:76336611 ACCCAACCCACC>A), RS1002372018 (15:76339871 T>C), RS1002802662 (15:76338610 G>C), RS1002878541 (15:76340141 G>A,C), RS1003250502 (15:76342232 G>T), RS1003470214 (15:76342017 A>T), RS1003724703 (15:76335852 G>C), RS1004100584 (15:76340774 C>A), RS1004722496 (15:76341000 A>C,G), RS1004864055 (15:76340962 C>G,T), RS1004938593 (15:76334819 A>G)

Disease associations

OMIM: gene MIM:609481 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST006479_152Diverticular disease1.000000e-07
GCST006479_153Diverticular disease7.000000e-06
GCST007876_30Estimated glomerular filtration rate3.000000e-25

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009959diverticular disease

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, increases methylation2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Silverincreases expression2
FR900359decreases phosphorylation1
dicrotophosincreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
beta-lapachoneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
tetrabromobisphenol Aincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
ochratoxin Adecreases expression1
potassium chromate(VI)affects cotreatment, increases expression1
S-(1,2-dichlorovinyl)cysteineincreases expression1
mercuric bromideaffects cotreatment, increases expression1
epigallocatechin gallateaffects cotreatment, increases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
abrineincreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amideincreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, increases expression1
PCI 5002affects cotreatment, increases expression1
Sunitinibincreases expression1
Arsenic Trioxideincreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicincreases abundance, increases expression, affects cotreatment1
Hexachlorocyclohexaneincreases expression1
Cisplatinincreases expression1
Cyclophosphamidedecreases expression1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

CellosaurusNameCategorySex
CVCL_A3I6SEES3-1V human ISL2, clone1Embryonic stem cellMale
CVCL_A3I7SEES3-1V human ISL2, clone2Embryonic stem cellMale
CVCL_A3I8SEES3-1V human ISL2, clone3Embryonic stem cellMale

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.