EFR3A

UniProt ID: A0A9L0S4L8
Organism: Equus caballus
Review Status: COMPLETE
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Gene Description

EFR3A (protein EFR3 homolog A) is a large ARM/HEAT-repeat scaffold of the EFR3 family (PANTHER PTHR12444:SF1). In mammals EFR3A is the membrane anchor of the plasma-membrane phosphatidylinositol 4-kinase complex (PI4KA with TTC7 and HYCC): an N-terminal Cys-rich motif is palmitoylated and, together with a conserved basic patch on the N-terminal repeat rod, holds the protein at the inner leaflet of the plasma membrane, while its C-terminal region binds TTC7 and thereby recruits the kinase, supporting plasma-membrane PI4P synthesis. This record (A0A9L0S4L8, 796 aa) is an alternative product of the horse EFR3A gene (Ensembl ENSECAG00000014883) that starts from an alternative first exon. It lacks the sequence equivalent to human residues 2-26, including the Cys6-Cys9 palmitoylation motif, but keeps the basic patch and the rest of the scaffold (98% identical to human). The full-length horse product is A0A3Q2GU27 (821 aa). Without the palmitoylation motif, this form may not be anchored at the plasma membrane.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005886 plasma membrane
IEA
GO_REF:0000120 		UNDECIDED
Summary: Plasma membrane is the established location of EFR3A from the same PANTHER subfamily (SF1; human Q14156 by IDA/EXP, and the full-length horse product A0A3Q2GU27 by IBA). But this accession is an alternative-first-exon product that lacks the N-terminal Cys6-Cys9 palmitoylation motif, and mammalian EFR3A mutated at those four cysteines is cytosolic. The ARBA rule, which assigns "Lipid-anchor" localization, does not check whether the motif is present.
Reason: The localization is right for the gene but cannot be transferred to this product form without evidence. Re-analysis (RESULTS-rereview.md) shows that A0A9L0S4L8 comes from the same Ensembl gene as the full-length horse model A0A3Q2GU27. It uses a different first exon, so human residues 2-26 are unpaired and nothing aligns to the human Cys6-Cys9 motif. In human/rodent cells the C6S/C7S/C8S/C9S EFR3A mutant is cytosolic (PMID:23229899), and the palmitoylation-deficient EFR3B mutant cannot recruit TTC7B or PI4KA to the membrane. The N-terminal basic patch (mouse K50, R53, R61, R68, R70, mapped to horse K25, R28, R36, R43, R45 in this model) is retained. In mammals that patch is required but has not been shown to be sufficient, because palmitoylation is also required for membrane association (PMID:24360784). Whether the short form is expressed, and where it localizes, has not been tested. I neither accept nor remove the row. The term is correct for the canonical gene product. Removing it would claim mislocalization, which no experiment has shown. Accepting it would ignore direct mutational evidence that a non-palmitoylated EFR3A does not reach the membrane.
Supporting Evidence:
file:HORSE/EFR3A/EFR3A-bioinformatics/RESULTS-rereview.md
All horse EFR3A models derive from Ensembl gene(s): ENSECAG00000014883.4.
PMID:23229899
palmitoylation-deficient mutants (C6S/C7S/C8S/C9S for EFR3A and C5S/C7S/C8S for EFR3B) were localized in the cytosol
PMID:24360784
Unlike Efr3 of fungi, Efr3 of higher eukaryotes is N-terminally palmitoylated, and palmitoylation is required for plasma membrane association
PMID:24360784
Thus, the basic patch of mammalian Efr3 is required for correct localization to the plasma membrane.
file:human/EFR3A/EFR3A-uniprot.txt
PTM: Palmitoylated at its N-terminus, anchoring the protein to the

Core Functions

EFR3-family scaffold of the plasma-membrane PI4KA complex. The conserved ARM/HEAT repeat rod, with its N-terminal basic patch, and the C-terminal region that binds TTC7 are retained in this product. The N-terminal palmitoylation motif that anchors canonical EFR3A at the plasma membrane is missing. So complex assembly through the conserved scaffold is plausible, but recruiting the kinase to the membrane is not established for this form, and no GO term is asserted here.

Supporting Evidence:
  • PMID:24360784
    Its C-terminal half interacts with both Stt4 and unstructured regions that form the C terminus of Efr3 (Efr3-C), thereby linking Efr3 and Stt4.
  • PMID:26571211
    FAM126A is an intrinsic component of the plasma membrane phosphatidylinositol 4-kinase complex that comprises PI4KIIIΞ± and its adaptors TTC7 and EFR3
  • file:HORSE/EFR3A/EFR3A-bioinformatics/RESULTS-rereview.md
    K50->K25 R53->R28 R61->R36 R68->R43 R70->R45

References

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Suggested Questions for Experts

Q: Does the horse EFR3A locus encode a product that begins with the metazoan-conserved N-terminal Cys-rich motif? The selected 796-residue model retains the initiator Met but deletes the region equivalent to human residues 2-26, so the palmitoylation motif (human Cys6-Cys9) is absent - and that motif is what anchors the protein to the plasma membrane.

Q: If a leaderless short form is genuinely expressed in horse, does it still assemble with PI4KA, TTC7 and HYCC? The downstream HEAT/ARM scaffold is 98% identical, so complex assembly and membrane anchoring may dissociate in this protein form.

Q: Human isoform Q14156-2 lacks residues 1-36, removing the same N-terminal Cys cluster absent from the selected horse model. Could the equine short form correspond to an alternative first exon rather than to the canonical product?

Suggested Experiments

Experiment: 5-prime RACE plus long-read sequencing of EFR3A transcripts from horse brain and another EFR3A-expressing tissue to establish the translation start and first-exon structure; rerun the paired alignment in EFR3A-bioinformatics on the corrected sequence.

Hypothesis: The equine EFR3A locus produces a transcript encoding the conserved N-terminal Cys-rich motif, and A0A9L0S4L8 reflects an incorrect translation start rather than a non-palmitoylated equine product.

Type: transcript 5-prime mapping / gene-model validation

Experiment: Express tagged versions of the selected 796-residue sequence and of a motif-restored equine form in a mammalian cell line; score plasma-membrane versus cytosolic distribution by confocal imaging and test palmitoylation directly by bioorthogonal metabolic labeling, using human EFR3A and its C6S/C7S/C8S/C9S mutant as the positive and negative controls established in PMID:23229899.

Hypothesis: The selected horse form fails to reach the plasma membrane because it lacks the palmitoylation motif, while a motif-bearing equine form localizes normally.

Type: palmitoylation labeling and localization assay

Experiment: Co-immunoprecipitate tagged horse EFR3A forms against TTC7A/TTC7B, PI4KA and HYCC1/HYCC2, and assay plasma-membrane PtdIns4P in human EFR3A-depleted cells complemented with each form, so that binding and functional recruitment are scored independently.

Hypothesis: Membrane anchoring and complex assembly are separable - the conserved scaffold binds TTC7 and PI4KA even in a form that cannot be palmitoylated.

Type: complex assembly and functional complementation

Knowledge Gaps

What is not known β€” curated, literature-grounded statements of the open unknowns (the inverse of core functions).

Gap: It is not known whether the alternative-first-exon EFR3A product is expressed in any horse tissue, or whether a leaderless EFR3A can reach the plasma membrane and recruit TTC7/PI4KA using only its basic patch.

BIOLOGY

What is known: What is established is that A0A9L0S4L8 is an annotated Ensembl transcript of the horse EFR3A gene. It differs from the full-length A0A3Q2GU27 only in its first exon. In human and rodent cells, EFR3A without its Cys6-Cys9 palmitoylation sites is cytosolic.

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML Β· EFR3A-protnlm-predictions-review.yaml Β· Review status: COMPLETE

Assessment of 1 ProtNLM GO predictions for the selected horse EFR3A protein, using mammalian experimental findings and an explicit comparison of the horse sequence.

Source documents: genes/human/EFR3A/EFR3A-uniprot.txt Β· genes/HORSE/EFR3A/EFR3A-bioinformatics/RESULTS.md Β· projects/PROTNLM_EVALUATION/mammal-benchmark/horse40-predictions.csv Β· genes/HORSE/EFR3A/EFR3A-bioinformatics/alignment.txt Β· genes/HORSE/EFR3A/EFR3A-bioinformatics/RESULTS-rereview.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0072659 protein localization to plasma membrane GO_BP
NPI β€” Nonparalog incorrect Review score: 0/2
Prediction method: ProtNLM2 Β· Version: UniProt API snapshot 2026-09-08
DOMAIN ARCHITECTURE MISMATCH
Review rationale: Recruitment of the PI4KA complex to the plasma membrane is the core process of EFR3A, and the horse EFR3A gene already carries GO:0072659 by IBA on its full-length product A0A3Q2GU27, so the term is not novel at the gene level. It is incorrect for this exact product, on the basis of positive experimental refutation rather than absence of evidence. EFR3A takes part in this process as the membrane anchor of the PI4KA complex: EFR3 proteins are the membrane localization signal of the complex, and in higher eukaryotes palmitoylation of the N-terminal Cys-rich motif is required for plasma membrane association (PMID:38746453; PMID:24360784). A0A9L0S4L8 is an alternative-first-exon product (N-terminus MIDKDGLVKADMEK..., no cysteine and no Gly2 myristoylation site) that aligns to human EFR3A at 98.24% identity downstream but lacks human residues 2-26, including the Cys6-Cys9 palmitoylation cluster. It retains the conserved basic patch, which is the only other targeting element identified, but in mammalian cells that patch is an additional, not a sufficient, signal: the C6S/C7S/C8S/C9S EFR3A mutant keeps the basic patch and the TTC7-binding scaffold yet is cytosolic, and the equivalent palmitoylation-deficient EFR3B mutant cannot recruit TTC7B and PI4KA to the plasma membrane (PMID:23229899). That mutant reproduces the defect of this accession, so the anchoring mechanism through which EFR3A contributes to the process is shown experimentally to fail without the missing motif. A contribution through incorporation into a complex anchored by another palmitoylated EFR3 copy has not been described. Training-set membership is unknown.
Supporting Evidence:
  • file:human/EFR3A/EFR3A-uniprot.txt: "CC -!- FUNCTION: Component of a complex required to localize CC phosphatidylinositol 4-kinase (PI4K) to the plasma membrane CC (PubMed:23229899, PubMed:25608530, PubMed:26571211). The complex acts CC as a regulator of phosphatidylinositol 4-phosphate (PtdIns(4)P) CC synthesis (Probable). In the complex, EFR3A probably acts as the CC membrane-anchoring component (PubMed:23229899). Also involved in CC responsiveness to G protein-coupled receptors; it is however unclear CC whether this role is direct or indirect (PubMed:25380825). CC {ECO:0000269|PubMed:23229899, ECO:0000269|PubMed:25380825, CC ECO:0000269|PubMed:25608530, ECO:0000305}."
  • file:HORSE/EFR3A/EFR3A-bioinformatics/RESULTS.md: "The horse sequence A0A9L0S4L8 (796 residues) aligns to human Q14156 (821 residues) with 98.24% identity across 796 paired residues. Paired coverage is 96.95% of the human sequence and 100.0% of the horse sequence."
  • file:HORSE/EFR3A/EFR3A-bioinformatics/alignment.txt: "target 0 MPTRVCCCCSALRPRYKRLVDNIFPEDPKDGLVKTDMEKLTFYAVSAPEKLDRIGSYLAE 0 |-------------------------..||||||.||||||||||||||||||||||||| query 0 M-------------------------IDKDGLVKADMEKLTFYAVSAPEKLDRIGSYLAE"
  • file:HORSE/EFR3A/EFR3A-bioinformatics/RESULTS-rereview.md: "MIDKDGLVKADMEKLTFYAVSAPEKLDRIG | 98.24% over 796 | 2-26 | ---- | K50->K25 R53->R28 R61->R36 R68->R43 R70->R45"
  • PMID:23229899: "Accordingly, a bioorthogonal metabolic labeling approach (Hang et al., 2011) revealed that FLAG-tagged EFR3A and EFR3B were palmitoylated at the N-terminal Cys-rich motif (Fig. 4 B). Importantly, palmitoylation-deficient mutants (C6S/C7S/C8S/C9S for EFR3A and C5S/C7S/C8S for EFR3B) were localized in the cytosol (Fig. 4 C), and the EFR3B palmitoylation-deficient mutant was unable to recruit tagged TTC7B and M1-PI4KIIIΞ± to the plasma membrane (Fig. S2)."
  • PMID:24360784: "Unlike Efr3 of fungi, Efr3 of higher eukaryotes is N-terminally palmitoylated, and palmitoylation is required for plasma membrane association"
  • PMID:24360784: "To investigate whether the basic patch, which is conserved in mammalian Efr3, provides an additional targeting activity"
  • PMID:38746453: "EFR3 proteins act as the membrane localization signal for the PI4KA complex"

Deep Research

Cyberian

(EFR3A-deep-research-cyberian.md)

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πŸ“š Additional Documentation

Notes

(EFR3A-notes.md)

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Bioinformatics Results

(RESULTS.md)

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πŸ“„ View Raw YAML

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