id: A0A9L0JLY3 gene_symbol: BICDL1 taxon: id: NCBITaxon:9793 label: Equus asinus status: COMPLETE description: Assessment of 4 ProtNLM2 GO predictions for donkey BICDL1 (A0A9L0JLY3), scored for this exact product. A0A9L0JLY3 is a non-canonical splice form of the donkey BICDL1 gene that keeps the N-terminal CC1 box and the C-terminal Rab6-binding region but lacks a 49-residue central coiled-coil segment (human Q6ZP65 residues 255-303) present in human, mouse and every other donkey product, and includes the alternative exon of human isoform 2 (95.99% identity to human Q6ZP65 over 524 paired residues). The canonical product of the same gene (A0A9L0K8K5) already carries all four predicted terms in GOA as Ensembl Compara transfers from mouse Bicdl1, so none of the predictions is novel at the gene level. Small GTPase binding depends on the retained C-terminal region and is assessed CNN. Dynactin binding and centrosome localization depend on the coiled coil that lies along dynactin in the BICDR1-dynein-dynactin cryo-EM structure; because the missing segment falls within that stretch and no experiment tests the shortened adaptor, both are assessed UNC. Neuron projection development is assessed NPI, because the mouse evidence behind it is an overexpression phenotype in which BICDR-1 inhibits neurite outgrowth indirectly by retaining Rab6 secretory vesicles near the centrosome; the positive process term misstates that relationship. A PubMed search (BICDL1, BICDR1, BICDR-1, CCDC64) found no further experimental work bearing on these terms beyond PMID:20360680 and the dynein-dynactin structural studies. ProtNLM2 emitted no non-GO function-text or subcellular-location output for this accession in the frozen snapshot. source_documents: - genes/EQUAS/BICDL1/BICDL1-uniprot.txt - genes/EQUAS/BICDL1/BICDL1-goa.tsv - genes/EQUAS/BICDL1/BICDL1-ai-review.yaml - genes/EQUAS/BICDL1__A0A9L0K8K5/BICDL1__A0A9L0K8K5-goa.tsv - genes/EQUAS/BICDL1__A0A9L0K8K5/BICDL1__A0A9L0K8K5-ai-review.yaml - genes/mouse/Bicdl1/Bicdl1-ai-review.yaml - genes/EQUAS/BICDL1/BICDL1-bioinformatics/human_Q6ZP65-uniprot.txt - genes/EQUAS/BICDL1/BICDL1-bioinformatics/RESULTS.md - genes/EQUAS/BICDL1/BICDL1-bioinformatics/RESULTS-rereview.md - projects/PROTNLM_EVALUATION/donkey40/donkey40-predictions.tsv predictions: - source_method: ProtNLM2 source_version: UniProt API snapshot 2026-10-14 predicted_term: id: GO:0034452 label: dynactin binding predicted_term_type: GO_MF review: assessment: UNC confidence_score: 1 summary: Dynactin binding is a true activity of the BICDL1 gene. Mouse BICDR-1 co-immunoprecipitates the major dynein and dynactin subunits, and in the cryo-EM structure of the dynein-dynactin-BICDR1 complex the BICDR1 coiled coil, modelled over mouse residues 105-392, lies along the dynactin filament. The term is already carried in GOA by the canonical product of the same donkey gene (A0A9L0K8K5), so it would not be novel. This accession, however, is a non-canonical splice form that lacks a 49-residue central coiled-coil segment (human Q6ZP65 residues 255-303, SEG_CORE) present in human, mouse and every other donkey product. That segment falls inside the coiled-coil stretch that contacts dynactin in the structure. The accession keeps the N-terminal CC1 box, but no experiment shows whether an adaptor with this shortened coiled coil still spans and binds dynactin. Whether this product retains the dynactin-binding interface is therefore unresolved. supported_by: - reference_id: PMID:20360680 supporting_text: Co-immunoprecipitation experiments from Hela cells transfected with GFP-BICDR-1 showed that BICDR-1 precipitates the major dynein/dynactin subunits, whereas no binding is seen with control GFP - reference_id: PMID:29420470 supporting_text: An approximate model for the BICDR1 coiled coil (residues 105-392) was generated by placing helices into density - reference_id: file:EQUAS/BICDL1/BICDL1-bioinformatics/RESULTS-rereview.md supporting_text: the benchmark product is the only donkey model that lacks SEG_CORE - reference_id: file:EQUAS/BICDL1/BICDL1-bioinformatics/RESULTS.md supporting_text: human residues 255-303 - reference_id: file:EQUAS/BICDL1/BICDL1-bioinformatics/RESULTS.md supporting_text: 'MOTIF (CC1 box): human [113, 114, 115, 116, 117] AARLG -> donkey [114, 115, 116, 117, 118] AARLG.' - source_method: ProtNLM2 source_version: UniProt API snapshot 2026-10-14 predicted_term: id: GO:0005813 label: centrosome predicted_term_type: GO_CC review: assessment: UNC confidence_score: 1 summary: Endogenous mouse BICDR-1 localizes around the gamma-tubulin-labelled centrosome, where it holds Rab6 secretory vesicles, and this localization depends on dynein and dynactin, since knockdown of either largely abolishes it. The term is already carried in GOA by the canonical donkey product A0A9L0K8K5, so it would not be novel. This accession is a non-canonical splice form that lacks the central coiled-coil segment (human Q6ZP65 residues 255-303, SEG_CORE) lying within the coiled coil that contacts dynactin. Because pericentrosomal targeting requires dynein-dynactin recruitment, and it is unresolved whether the shortened coiled coil of this product still engages dynactin, it cannot be determined whether this product localizes to the centrosome. supported_by: - reference_id: PMID:20360680 supporting_text: specifically localized around the γ-tubulin-labelled centrosome - reference_id: PMID:20360680 supporting_text: Quantification showed that only ∼15% of the dynein/dynactin knockdown cells showed BICDR-1 around the centrosome compared with ∼74% in control cells - reference_id: PMID:29420470 supporting_text: An approximate model for the BICDR1 coiled coil (residues 105-392) was generated by placing helices into density - reference_id: file:EQUAS/BICDL1/BICDL1-bioinformatics/RESULTS-rereview.md supporting_text: the benchmark product is the only donkey model that lacks SEG_CORE - source_method: ProtNLM2 source_version: UniProt API snapshot 2026-10-14 predicted_term: id: GO:0031267 label: small GTPase binding predicted_term_type: GO_MF review: assessment: CNN confidence_score: 2 summary: Mouse BICDR-1 is a Rab6 effector; full-length protein and its C-terminal region bind GTP-locked Rab6A but not GDP-locked Rab6A, and Lys512 is required for this binding. The donkey product is in the same PANTHER subfamily and keeps the C-terminal BICDL1/2-like region, so the transfer is a justified orthology inference. Small GTPase binding is the most specific applicable GO term used for this activity in the reviews. The term is already carried in GOA by the canonical donkey product A0A9L0K8K5 and is a core function of the target's gene review, so the prediction is correct but not novel. supported_by: - reference_id: PMID:20360680 supporting_text: Moreover, both full-length BICDR-1 and a C-terminal region of BICDR-1, amino acids 382–577, interact with constitutively active GTPase-deficient Rab6A-Q72R and not with GDP-locked inactive Rab6A-T27N in the yeast two-hybrid assay - reference_id: PMID:20360680 supporting_text: lysine 512 is required for binding to Rab6 - reference_id: file:EQUAS/BICDL1/BICDL1-bioinformatics/RESULTS-rereview.md supporting_text: It keeps the N-terminal CC1 box and the C-terminal region (the Rab6-binding region in mouse). - source_method: ProtNLM2 source_version: UniProt API snapshot 2026-10-14 predicted_term: id: GO:0031175 label: neuron projection development predicted_term_type: GO_BP review: assessment: NPI confidence_score: 0 error_type: CURATION_MISTAKE summary: The only experimental evidence linking BICDR-1 to neurites is an overexpression phenotype in cultured hippocampal neurons, where sustained BICDR-1 expression reduces neurite outgrowth by retaining Rab6 secretory vesicles in the pericentrosomal region; the authors conclude that BICDR-1 inhibits neuritogenesis early in differentiation. BICDL1 therefore does not perform neurite development; at most it negatively and indirectly regulates it through its vesicle-transport function. The positive process term matches the mouse IMP annotation that the mouse gene review modifies to negative regulation of neuron projection development, and the canonical donkey product's review marks the same term over-annotated on these grounds. The prediction reproduces that mis-signed source annotation rather than the supported role. supported_by: - reference_id: PMID:20360680 supporting_text: At 2, 3 and 4 days after transfection, BICDR-1-transfected neurons showed a marked reduction in neurite outgrowth compared with control cells transfected with an empty vector and β-galactosidase - reference_id: PMID:20360680 supporting_text: At early developmental stages, pericentrosomal BICDR-1 restricts secretory transport and inhibits neuritogenesis, whereas later during neuronal development the reduction in BICDR-1 expression permits anterograde transport required for neurite outgrowth. references: - id: PMID:20360680 title: Pericentrosomal targeting of Rab6 secretory vesicles by Bicaudal-D-related protein 1 (BICDR-1) regulates neuritogenesis. findings: [] - id: PMID:29420470 title: Cryo-EM shows how dynactin recruits two dyneins for faster movement. findings: [] - id: file:EQUAS/BICDL1/BICDL1-bioinformatics/RESULTS.md title: 'BICDL1: donkey-human sequence comparison' findings: [] - id: file:EQUAS/BICDL1/BICDL1-bioinformatics/RESULTS-rereview.md title: BICDL1 donkey gene-model comparison findings: []