ARL6IP4

gene
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Also known as SR-25SRp25SFRS20SRrp37

Summary

ARL6IP4 (ARF like GTPase 6 interacting protein 4, HGNC:18076) is a protein-coding gene on chromosome 12q24.31, encoding ADP-ribosylation factor-like protein 6-interacting protein 4 (Q66PJ3). Involved in modulating alternative pre-mRNA splicing with either 5’ distal site activation or preferential use of 3’ proximal site.

Enables identical protein binding activity. Predicted to be involved in RNA splicing. Predicted to be located in nucleus.

Source: NCBI Gene 51329 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 96 total
  • MANE Select transcript: NM_018694

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18076
Approved symbolARL6IP4
NameARF like GTPase 6 interacting protein 4
Location12q24.31
Locus typegene with protein product
StatusApproved
AliasesSR-25, SRp25, SFRS20, SRrp37
Ensembl geneENSG00000182196
Ensembl biotypeprotein_coding
OMIM607668
Entrez51329

Gene structure

Transcript identifiers

Ensembl transcripts: 84 — 75 protein_coding, 6 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000315580, ENST00000357866, ENST00000392433, ENST00000392435, ENST00000412505, ENST00000413381, ENST00000426960, ENST00000439686, ENST00000442210, ENST00000453766, ENST00000454885, ENST00000456762, ENST00000536073, ENST00000536502, ENST00000539576, ENST00000539770, ENST00000540382, ENST00000540708, ENST00000542099, ENST00000543566, ENST00000853809, ENST00000853810, ENST00000853811, ENST00000853812, ENST00000853813, ENST00000853814, ENST00000853815, ENST00000853816, ENST00000853817, ENST00000853818, ENST00000853819, ENST00000853820, ENST00000853821, ENST00000853822, ENST00000853823, ENST00000853824, ENST00000853825, ENST00000853826, ENST00000853827, ENST00000853828, ENST00000853829, ENST00000853830, ENST00000853831, ENST00000853832, ENST00000853833, ENST00000853834, ENST00000853835, ENST00000853836, ENST00000853837, ENST00000853838, ENST00000853839, ENST00000853840, ENST00000853841, ENST00000853842, ENST00000853843, ENST00000853844, ENST00000853845, ENST00000853846, ENST00000853847, ENST00000853848, ENST00000853849, ENST00000853850, ENST00000853851, ENST00000853852, ENST00000853853, ENST00000853854, ENST00000853855, ENST00000925030, ENST00000925031, ENST00000925032, ENST00000925033, ENST00000925034, ENST00000925035, ENST00000925036, ENST00000925037, ENST00000925038, ENST00000925039, ENST00000925040, ENST00000962562, ENST00000962563, ENST00000962564, ENST00000962565, ENST00000962566, ENST00000962567

RefSeq mRNA: 32 — MANE Select: NM_018694 NM_001002251, NM_001278378, NM_001278379, NM_001278380, NM_001400281, NM_001400282, NM_001400283, NM_001400284, NM_001400285, NM_001400300, NM_001400301, NM_001400302, NM_001400303, NM_001400304, NM_001400305, NM_001400306, NM_001400307, NM_001400308, NM_001400309, NM_001400310, NM_001400311, NM_001400312, NM_001400313, NM_001400314, NM_001400315, NM_001400316, NM_001400317, NM_001400318, NM_001400319, NM_001400320, NM_016638, NM_018694

CCDS: CCDS31923, CCDS45004, CCDS53843, CCDS61273, CCDS91764, CCDS91765

Canonical transcript exons

ENST00000315580 — 6 exons

ExonStartEnd
ENSE00001254056122981571122981879
ENSE00001641411122982620122982909
ENSE00003638724122981957122982074
ENSE00003672941122981129122981299
ENSE00003785915122982469122982538
ENSE00003917601122980681122980745

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 128.2455 / max 671.0581, expressed in 1827 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
128554119.11811827
1285502.62251094
1285562.26191319
1285511.3562734
1285550.8008448
1285530.7799490
1285520.5816358
1285570.4740154
1285580.250585

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pituitary glandUBERON:000000799.06gold quality
adenohypophysisUBERON:000219699.02gold quality
amygdalaUBERON:000187698.99gold quality
temporal lobeUBERON:000187198.98gold quality
fundus of stomachUBERON:000116098.90gold quality
popliteal arteryUBERON:000225098.90gold quality
tibial arteryUBERON:000761098.90gold quality
muscle layer of sigmoid colonUBERON:003580598.90gold quality
esophagogastric junction muscularis propriaUBERON:003584198.90gold quality
right frontal lobeUBERON:000281098.88gold quality
lower esophagus muscularis layerUBERON:003583398.88gold quality
prostate glandUBERON:000236798.87gold quality
anterior cingulate cortexUBERON:000983598.87gold quality
lower esophagusUBERON:001347398.87gold quality
apex of heartUBERON:000209898.86gold quality
body of stomachUBERON:000116198.84gold quality
spleenUBERON:000210698.84gold quality
right hemisphere of cerebellumUBERON:001489098.84gold quality
left coronary arteryUBERON:000162698.82gold quality
left ovaryUBERON:000211998.82gold quality
left adrenal gland cortexUBERON:003582598.82gold quality
right coronary arteryUBERON:000162598.81gold quality
hypothalamusUBERON:000189898.80gold quality
dorsolateral prefrontal cortexUBERON:000983498.80gold quality
endocervixUBERON:000045898.79gold quality
body of pancreasUBERON:000115098.79gold quality
ascending aortaUBERON:000149698.79gold quality
thoracic aortaUBERON:000151598.79gold quality
frontal cortexUBERON:000187098.79gold quality
substantia nigraUBERON:000203898.79gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes12.98
E-HCAD-13yes7.36
E-MTAB-6142no314.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting ARL6IP4, 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-130B-5P99.8368.501888
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-425199.4069.193363
HSA-MIR-210-5P98.5764.37832
HSA-MIR-4640-5P97.4266.331543

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioarl6ip4ENSDARG00000105036
mus_musculusArl6ip4ENSMUSG00000029404
rattus_norvegicusArl6ip4ENSRNOG00000001080
drosophila_melanogasterCG18428FBGN0039149

Protein

Protein identifiers

ADP-ribosylation factor-like protein 6-interacting protein 4Q66PJ3 (reviewed: Q66PJ3)

Alternative names: HSP-975, HSVI-binding protein, SR-15, SRp25, Splicing factor SRrp37

All UniProt accessions (9): Q66PJ3, A0A0A0MTG7, A0A0C4DG62, A0A0C4DH18, A0A8C8KBE9, F5GYV5, F8WCT1, F8WEP2, H7BZV4

UniProt curated annotations — full annotation on UniProt →

Function. Involved in modulating alternative pre-mRNA splicing with either 5’ distal site activation or preferential use of 3’ proximal site. In case of infection by Herpes simplex virus (HSVI), may act as a splicing inhibitor of HSVI pre-mRNA.

Subunit / interactions. Interacts with ARL6. Interacts with ZCCHC17. Interacts with SRSF2.

Subcellular location. Nucleus. Nucleolus. Nucleus speckle.

Tissue specificity. Isoforms 3 and 7 were identified in brain, pancreas, prostate, and testis, but little or no message could be detected in other tissues.

Induction. In case of Herpes simplex virus (HSVI)-binding to cells.

Similarity. Belongs to the ARL6IP4 family.

Isoforms (10)

UniProt IDNamesCanonical?
Q66PJ3-88yes
Q66PJ3-11
Q66PJ3-22
Q66PJ3-33
Q66PJ3-44
Q66PJ3-55
Q66PJ3-66
Q66PJ3-77, SRrp37-2
Q66PJ3-99
Q66PJ3-1010

RefSeq proteins (32): NP_001002251, NP_001265307, NP_001265308, NP_001265309, NP_001387210, NP_001387211, NP_001387212, NP_001387213, NP_001387214, NP_001387229, NP_001387230, NP_001387231, NP_001387232, NP_001387233, NP_001387234, NP_001387235, NP_001387236, NP_001387237, NP_001387238, NP_001387239, NP_001387240, NP_001387241, NP_001387242, NP_001387243, NP_001387244, NP_001387245, NP_001387246, NP_001387247, NP_001387248, NP_001387249, NP_057722, NP_061164* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019532Nucl_RNA-splicing_assoc_SR-25Family

Pfam: PF10500

UniProt features (20 total): splice variant 8, compositionally biased region 4, modified residue 3, chain 1, region of interest 1, sequence variant 1, sequence conflict 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q66PJ3-F158.860.00

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 (4): 55, 148, 182, 199

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 96 (showing top): MULLIGHAN_NPM1_SIGNATURE_3_UP, TGCGCANK_UNKNOWN, GROSS_HYPOXIA_VIA_ELK3_UP, TCF11_01, GOBP_RNA_SPLICING, TCCAGAT_MIR5165P, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY, GOCC_RIBONUCLEOPROTEIN_GRANULE, GOCC_NUCLEOLUS, chr12q24, CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN, MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP, MARTENS_TRETINOIN_RESPONSE_DN, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS

GO Biological Process (2): mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (3): RNA binding (GO:0003723), protein binding (GO:0005515), identical protein binding (GO:0042802)

GO Cellular Component (3): nucleus (GO:0005634), nucleolus (GO:0005730), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
mRNA metabolic process1
nucleic acid binding1
binding1
protein binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular membraneless organelle1
nuclear ribonucleoprotein granule1

Protein interactions and networks

STRING

910 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ARL6IP4ZFYVE1Q9HBF4512
ARL6IP4TMEM11P17152474
ARL6IP4SUB1P53999452
ARL6IP4OGFOD2Q6N063449
ARL6IP4PNISRQ8TF01426
ARL6IP4THRAP3Q9Y2W1418
ARL6IP4PPIAP05092415
ARL6IP4ATAD2BQ9ULI0412
ARL6IP4ELP3Q9H9T3407
ARL6IP4RRP36Q96EU6400
ARL6IP4SNX19Q92543391
ARL6IP4MPHOSPH9Q99550384
ARL6IP4ENSAO43768383
ARL6IP4ABCB9Q9NP78370
ARL6IP4DGKIO75912367

IntAct

66 interactions, top by confidence:

ABTypeScore
PIK3CAPIK3R2psi-mi:“MI:0914”(association)0.900
CFTRESYT2psi-mi:“MI:0914”(association)0.710
SRPK2ARL6IP4psi-mi:“MI:0217”(phosphorylation reaction)0.690
CFTRHAX1psi-mi:“MI:0914”(association)0.610
ARL6IP4SRPK1psi-mi:“MI:0217”(phosphorylation reaction)0.590
ARL6IP4taxpsi-mi:“MI:0915”(physical association)0.490
taxARL6IP4psi-mi:“MI:0915”(physical association)0.490
CFTRCNOT1psi-mi:“MI:0914”(association)0.480
CPSF6DDX39Apsi-mi:“MI:0914”(association)0.480
ARL6IP4HNRNPMpsi-mi:“MI:0915”(physical association)0.400
ARL6IP4KRT18psi-mi:“MI:0915”(physical association)0.400
ARL6IP4ARL6IP4psi-mi:“MI:0915”(physical association)0.370
TMEM132AWWP2psi-mi:“MI:0914”(association)0.350
Ppp6cPLEKHG3psi-mi:“MI:0914”(association)0.350
DVL2NBASpsi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
KIE-1GTPBP10psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350
AP3B1psi-mi:“MI:0914”(association)0.350
GAB1JUPpsi-mi:“MI:0914”(association)0.350
DIPK2AC11orf98psi-mi:“MI:0914”(association)0.350
BMI1MEIS3P1psi-mi:“MI:0914”(association)0.350
RYBPFAM186Apsi-mi:“MI:0914”(association)0.350
SRPK2SNRPGP15psi-mi:“MI:0914”(association)0.350
CEP170FAM171A2psi-mi:“MI:0914”(association)0.350
POC5PDHXpsi-mi:“MI:0914”(association)0.350
SHANK3IGKV3D-15psi-mi:“MI:0914”(association)0.350
SNRPADDX39Apsi-mi:“MI:0914”(association)0.350

BioGRID (162): ARL6IP4 (Two-hybrid), ARL6IP4 (Two-hybrid), ARL6IP4 (Two-hybrid), ARL6IP4 (Two-hybrid), THAP1 (Two-hybrid), JMJD6 (Affinity Capture-MS), CSNK2A2 (Affinity Capture-MS), ZRANB2 (Affinity Capture-MS), EIF3J (Affinity Capture-MS), SRPK1 (Affinity Capture-MS), CCDC9 (Affinity Capture-MS), C17orf85 (Affinity Capture-MS), ZC3H14 (Affinity Capture-MS), USP7 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1S3XQD6, A0A1S4AX27, A1A5I1, A2AR02, A6QLS2, B0BN49, O35986, O55035, O95218, P30189, P30414, P30415, Q19QU3, Q27450, Q28EE8, Q2HJC9, Q3B7G7, Q3KPW4, Q4P4G8, Q4V8I5, Q4V9W2, Q502P0, Q505I5, Q5BKY9, Q5F4A9, Q5R580, Q5R8J6, Q5RJP9, Q5VTL8, Q5XHJ5, Q5ZLM8, Q5ZLX5, Q66PJ3, Q6AXY7, Q6C1V6, Q6NQD9, Q6P7Y3, Q6ZUT1, Q7L4I2, Q80SY5

Diamond homologs: Q3KPW4, Q4V8I5, Q502P0, Q5F4A9, Q66PJ3, Q9JM93

SIGNOR signaling

1 interactions.

AEffectBMechanism
SGK3“down-regulates activity”ARL6IP4phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 84 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
Constitutive Signaling by EGFRvIII564.9×8e-07
Signaling by ERBB2 ECD mutants561.1×9e-07
Tie2 Signaling554.6×1e-06
Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants551.9×1e-06
Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants547.2×2e-06
Signaling by FGFR3 in disease545.1×2e-06
Signaling by ERBB2 KD Mutants538.5×5e-06
Downstream signal transduction534.6×8e-06

GO biological processes:

GO termPartnersFoldFDR
mRNA splicing, via spliceosome1013.3×2e-06
RNA splicing810.2×3e-04
mRNA processing78.0×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance84
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1183 predictions. Top by Δscore:

VariantEffectΔscore
12:122981864:G:GTdonor_gain1.0000
12:122981870:G:GTdonor_gain1.0000
12:122981955:A:AGacceptor_gain1.0000
12:122981956:G:GGacceptor_gain1.0000
12:122982113:G:GTdonor_gain1.0000
12:122980383:GTC:Gdonor_gain0.9900
12:122981227:A:Tdonor_gain0.9900
12:122981241:G:GTdonor_gain0.9900
12:122981875:CCCAG:Cdonor_loss0.9900
12:122981876:CCAGG:Cdonor_loss0.9900
12:122981877:CAG:Cdonor_loss0.9900
12:122981878:AGGT:Adonor_loss0.9900
12:122981879:GGT:Gdonor_loss0.9900
12:122981881:T:Gdonor_loss0.9900
12:122981956:GTC:Gacceptor_gain0.9900
12:122981956:GTCC:Gacceptor_gain0.9900
12:122981956:GTCCT:Gacceptor_gain0.9900
12:122982070:ACCAG:Adonor_loss0.9900
12:122982071:CCAG:Cdonor_loss0.9900
12:122982072:CAG:Cdonor_loss0.9900
12:122982073:AGGT:Adonor_loss0.9900
12:122982074:GG:Gdonor_loss0.9900
12:122982075:G:GCdonor_loss0.9900
12:122981226:G:GTdonor_gain0.9800
12:122981242:A:Tdonor_gain0.9800
12:122981856:C:Gdonor_gain0.9800
12:122982047:T:TAdonor_loss0.9800
12:122982048:G:GAdonor_loss0.9800
12:122982465:CCAG:Cacceptor_loss0.9800
12:122982466:CA:Cacceptor_loss0.9800

AlphaMissense

2664 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:122981998:C:TP355S0.999
12:122981999:C:AP355H0.998
12:122982005:C:TT357I0.998
12:122982018:G:CW361C0.998
12:122982018:G:TW361C0.998
12:122981997:G:CK354N0.997
12:122981997:G:TK354N0.997
12:122982002:T:CM356T0.997
12:122982009:G:CK358N0.997
12:122982009:G:TK358N0.997
12:122982016:T:AW361R0.997
12:122982016:T:CW361R0.997
12:122981973:G:CQ346H0.996
12:122981973:G:TQ346H0.996
12:122981993:T:CM353T0.996
12:122981994:G:AM353I0.996
12:122981994:G:CM353I0.996
12:122981994:G:TM353I0.996
12:122981998:C:AP355T0.996
12:122981999:C:GP355R0.996
12:122981989:G:CA352P0.995
12:122981995:A:GK354E0.995
12:122982478:G:CK383N0.995
12:122982478:G:TK383N0.995
12:122982499:G:CE390D0.995
12:122982499:G:TE390D0.995
12:122981981:G:CR349P0.994
12:122982498:A:TE390V0.993
12:122982647:T:CF413L0.993
12:122982649:C:AF413L0.993

dbSNP variants (sampled 300 via entrez): RS1000828804 (12:122983190 G>A), RS1001513226 (12:122980630 C>A,T), RS1002151142 (12:122979743 G>C), RS1002178266 (12:122978285 C>T), RS1002217306 (12:122980770 C>A,G,T), RS1002250193 (12:122979435 T>C), RS1002601013 (12:122981477 C>A,G,T), RS1004976175 (12:122980761 C>A,G,T), RS1005427244 (12:122982847 C>G), RS1005540244 (12:122983095 C>T), RS1005844496 (12:122982352 A>C,G), RS1005949809 (12:122979380 G>C), RS1006848035 (12:122983275 G>C), RS1007774412 (12:122981915 C>G,T), RS1008443750 (12:122980133 A>G)

Disease associations

OMIM: gene MIM:607668 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST002149_20Schizophrenia2.000000e-08
GCST002539_19Schizophrenia2.000000e-14
GCST004521_72Autism spectrum disorder or schizophrenia8.000000e-12
GCST006803_10Schizophrenia6.000000e-16
GCST007277_17Tourette syndrome2.000000e-06
GCST010703_43Brain morphology (MOSTest)1.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases abundance, increases expression4
Air Pollutantsaffects cotreatment, increases abundance, increases expression, affects expression2
Arsenicdecreases expression, increases abundance, increases expression2
Ozoneaffects cotreatment, increases expression, increases abundance, affects expression2
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, increases expression1
triphenyl phosphateaffects expression1
alpha-pineneincreases expression, increases abundance, affects cotreatment1
beta-lapachonedecreases expression1
cobaltous chloridedecreases expression1
methacrylaldehydeincreases expression, increases abundance, affects cotreatment1
licochalcone Bincreases expression1
Acetaminophendecreases expression1
Acroleinaffects cotreatment, increases expression, increases abundance1
Atrazineincreases expression1
Benzo(a)pyreneincreases methylation1
Caffeineaffects phosphorylation1
Dexamethasoneaffects cotreatment, increases expression1
Enzyme Inhibitorsincreases O-linked glycosylation, decreases activity1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Methotrexateaffects response to substance1
Phthalic Acidsdecreases methylation1
Ribonucleotidesaffects binding1
Seleniumincreases expression1
Smokedecreases expression1
Valproic Acidincreases methylation1
Vitamin Eincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B2S6Abcam HEK293T ARL6IP4 KOTransformed cell lineFemale

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.