id: A0A9L0SWY1 gene_symbol: DYNLT2B product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9796 label: Equus caballus description: Dynein light chain Tctex-type 2B (DYNLT2B, also known as TCTEX1D2) is a small non-catalytic Tctex-1-fold light chain of the cytoplasmic dynein-2 motor that drives retrograde intraflagellar transport in cilia. By one-to-one orthology with human DYNLT2B (PANTHER subfamily PTHR21255:SF7, about 91-93% identity over the Tctex domain), the equine protein is expected to heterodimerize with DYNLT1 or DYNLT3 and bind the dynein-2 intermediate chain WDR60/DYNC2I1, contributing to retrograde ciliary protein trafficking; in mouse the orthologue is additionally required for sperm flagellum assembly. The equine locus (Ensembl ENSECAG00000015913, chromosome 19) is annotated with at least ten protein models that differ at the N- and C-termini. The A0A9L0SWY1 model (245 residues) carries an approximately 117-residue disordered N-terminal extension and ends after the fourth beta-strand, lacking the C-terminal beta-strand (human residues 128-142) that forms part of the Tctex fold, whereas other equine models (for example A0A9L0S150 and A0A9L0TLH8) encode the complete fold. No equine experimental characterization has been reported. suggested_questions: - question: Which equine DYNLT2B transcript is the predominant product in ciliated tissues and testis? The locus carries at least ten protein models; A0A9L0SWY1 combines an N-terminal disordered extension with a C-terminus that stops before the final Tctex beta-strand, while the Ensembl canonical model (A0A9L0S150) and A0A9L0TLH8 retain the human C-terminus, so transcript-level evidence is needed to decide whether the truncated form is expressed at all. experts: [] - question: Does the missing C-terminal region matter functionally? It covers most of the terminal beta-strand of the human Tctex fold, and human DYNLT2B works as a DYNLT2B-DYNLT1/DYNLT3 dimer bound to the WDR60 intermediate chain, so the question is whether this protein form can still dimerize and engage WDR60 at all. experts: [] - question: Given that mouse Tctex1d2 loss disrupts sperm flagellum assembly while leaving motile cilia normal, is the equine requirement for DYNLT2B likewise flagellum-biased, and is the long N-terminal extension expressed in testis? experts: [] suggested_experiments: - hypothesis: The equine DYNLT2B locus encodes a product matching the human light chain over its full length, and the N-terminal extension plus C-terminal truncation in A0A9L0SWY1 reflect a gene-model or translation-start discrepancy rather than equine biology. description: Long-read (Iso-Seq or targeted nanopore) sequencing of DYNLT2B transcripts from horse testis and a ciliated tissue, plus 5-prime RACE to fix the translation start; reassemble the ORF and re-run the paired comparison in DYNLT2B-bioinformatics on the corrected sequence. experiment_type: full-length transcript sequencing / gene-model validation - hypothesis: Loss of the C-terminal strand abolishes the DYNLT2B-DYNLT1 dimer and hence WDR60 binding, whereas the N-terminal extension is dispensable for both. description: Co-express the selected horse sequence, an N-terminally trimmed version, and a C-terminally restored version against DYNLT1/DYNLT3 and WDR60 in the visible-immunoprecipitation format used to map the human dynein-2 subcomplexes (PMID:29742051), scoring dimer formation and WDR60 recruitment with human TCTEX1D2 as the positive control. experiment_type: pairwise interaction mapping / co-immunoprecipitation - hypothesis: Whichever equine form is real, it supports retrograde ciliary protein trafficking as the human light chain does. description: Complement human TCTEX1D2-knockout cells with the selected horse sequence and with any transcript-verified full-length equine form, and score rescue of the retrograde trafficking defect (ciliary accumulation of IFT-B and GPCR cargo) against human TCTEX1D2 and empty vector. experiment_type: cross-species complementation in a knockout cell line references: - id: file:HORSE/DYNLT2B/DYNLT2B-uniprot.txt title: 'UniProtKB A0A9L0SWY1: selected horse DYNLT2B protein model' findings: - statement: The horse DYNLT2B entry is an unreviewed 245-residue TrEMBL record whose protein name and gene symbol come solely from an Ensembl gene model, with no equine experimental characterization. record_section: ["DR:Ensembl"] supporting_text: Ensembl; ENSECAT00000143034.1; ENSECAP00000080542.1; ENSECAG00000015913.4. reference_section_type: DATABASE_ENTRY - statement: Domain signatures confirm a Tctex-1-like fold in the horse protein, which is what supports family identity independently of the length discrepancy. record_section: ["DR:InterPro"] supporting_text: 'InterPro; IPR005334; Tctex-1-like.' reference_section_type: DATABASE_ENTRY reference_review: relevance: HIGH correctness: VERIFIED review_notes: Source record for the reviewed protein form. Naming and domain assignment are computational (Ensembl/InterPro/Pfam); they establish family identity but no equine function, and they do not adjudicate the 245-versus-142-residue discrepancy. - id: file:HORSE/DYNLT2B/DYNLT2B-bioinformatics/RESULTS.md title: "DYNLT2B: horse\u2013human sequence comparison" findings: - statement: The conserved region is nearly identical to human DYNLT2B (91.41% over 128 residues) but covers only half the horse sequence, so family identity is secure while whole-protein equivalence is not. supporting_text: The horse sequence A0A9L0SWY1 (245 residues) aligns to human Q8WW35 (142 residues) with 91.41% identity across 128 paired residues. Paired coverage is 90.14% of the human sequence and 52.24% of the horse sequence. reference_section_type: RESULTS - statement: Mapping human secondary-structure features onto the alignment shows the human C-terminal strand (residues 128-140) has no horse counterpart beyond a single residue, localizing the discrepancy to a structural element rather than to a disordered tail. supporting_text: 'STRAND: human [128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140] DSLFCVVAAFGCF' reference_section_type: RESULTS - statement: The comparison explicitly declines to establish one-to-one orthology or to verify the sequence that was supplied to the prediction pipeline. supporting_text: This establishes sequence conservation between the selected pair; it does not independently establish one-to-one orthology or verify the sequence supplied to ProtNLM. reference_section_type: RESULTS reference_review: relevance: HIGH correctness: VERIFIED review_notes: Reproducible Biopython global alignment (BLOSUM62, gap open -10, extension -0.5) with retained sequence hashes and mapped human structural features; computed, not hardcoded. It localizes the model discrepancy to a specific beta-strand, which is why this review treats the alteration as consequential rather than as generic percentage-identity noise - while still not establishing a folding or binding defect. - id: file:HORSE/DYNLT2B/DYNLT2B-bioinformatics/RESULTS-rereview.md title: DYNLT2B horse gene models vs human Q8WW35 (re-review) findings: - statement: The equine DYNLT2B gene carries ten UniProt protein models; the Ensembl canonical transcript and the UniProt gene-centric entry are different models, and neither is A0A9L0SWY1. supporting_text: 'Ensembl canonical transcript of ENSECAG00000015913: ENSECAT00000082191. UniProt reference-proteome gene-centric entry: A0A9L0S9P8.' reference_section_type: RESULTS - statement: The benchmark model lacks the complete set of human Tctex-fold strands, whereas the Ensembl canonical model A0A9L0S150 covers the whole human sequence with all strands present. supporting_text: '| A0A9L0SWY1 (benchmark) | 245 | False | False | True | 91.41 | 90.14 | False | GVFMAARCFWDADTDNYTHDVFMNK |' reference_section_type: RESULTS - statement: The Ensembl canonical model A0A9L0S150 aligns over the full human length with all strands mapped and the human C-terminal sequence intact. supporting_text: '| A0A9L0S150 | 259 | True | False | True | 92.96 | 100.0 | True | DNYTHDVFMNDSLFCVVAAFGCFYY |' reference_section_type: RESULTS reference_review: relevance: HIGH correctness: VERIFIED review_notes: Reproducible re-review script (compare_gene_models_rereview.py) that fetches all equine DYNLT2B UniProt entries, the Ensembl canonical flag and the UniProt reference-proteome gene-centric FASTA, and aligns each model to human Q8WW35. Establishes that A0A9L0SWY1 is one of several alternative gene models rather than the canonical product. Strand pairing counts aligned positions, not identity. - id: file:human/DYNLT2B/DYNLT2B-uniprot.txt title: 'UniProtKB Q8WW35: human DYNLT2B/TCTEX1D2 (curated reference ortholog)' findings: - statement: Human DYNLT2B is a non-catalytic accessory subunit of the cytoplasmic dynein-2 complex and is required for retrograde ciliary transport. record_section: ["CC:FUNCTION"] supporting_text: 'FUNCTION: Acts as one of several non-catalytic accessory components of' reference_section_type: DATABASE_ENTRY - statement: DYNLT2B is one of the light chains unique to dynein-2 rather than shared with dynein-1, so its loss is not buffered by the dynein-1 light-chain pool. record_section: ["CC:SUBUNIT"] supporting_text: intermediate chain (DYNC2LI1), and a light chain (DYNLT2B) are unique reference_section_type: DATABASE_ENTRY - statement: The functional unit is a dimer, and the dimer interface is what couples DYNLT2B to the intermediate chain - the reason the missing C-terminal strand in the horse model is a specific rather than a generic concern. record_section: ["CC:SUBUNIT"] supporting_text: DYNLT2B-DYNLT1/DYNLT3 interacts with DYNC2I1; this interaction is reference_section_type: DATABASE_ENTRY - statement: Biallelic human loss of function causes short-rib thoracic dysplasia with polydactyly (SRTD17), establishing the gene as ciliopathy-relevant in mammals. record_section: ["CC:DISEASE"] supporting_text: '(SRTD17) [MIM:617405]: A form of short-rib thoracic dysplasia, a group' reference_section_type: DATABASE_ENTRY reference_review: relevance: HIGH correctness: VERIFIED review_notes: Curated Swiss-Prot record for the human ortholog with experimental ECO codes. Used as the source of characterized mammalian biology under consideration for transfer; the dimer/intermediate-chain architecture is what makes the horse C-terminal difference worth flagging. - id: PMID:38454149 title: Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport. findings: - statement: DYNLT2B/TCTEX1D2 is one of four light chains in the reconstituted eight-subunit dynein-2 complex used for cryo-EM, alongside the heavy chain, two intermediate chains and the light intermediate chain. supporting_text: The subunits in the final construct are the dynein-2 heavy chain (DYNC2H1), two intermediate chains (WDR60/DYNC2I1 and WDR34/DYNC2I2), light intermediate chain (DYNC2LI1), and single isoforms of the four dynein-2 light chains (DYNLRB1, DYNLL1, DYNLT1, and DYNLT2B/TCTEX1D2). reference_section_type: RESULTS - statement: Even in this structure the stoichiometry of the DYNLT1/DYNLT2B pair within dynein-2 is left undefined, so the structural context of the horse model's altered C-terminus cannot be read off the complex architecture. supporting_text: Orange blur and question mark reflect undefined stoichiometry of DYNLT1 and DYNLT2B. reference_section_type: RESULTS reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text cached. The source of the structural context for the human Tctex fold referenced in the notes. Cited for complex composition and the explicit stoichiometry caveat, not for the WDR34/WDR60 tethering results, which concern the intermediate chains rather than DYNLT2B. - id: PMID:29742051 title: Interaction of WDR60 intermediate chain with TCTEX1D2 light chain of the dynein-2 complex is crucial for ciliary protein trafficking. findings: - statement: DYNLT2B/TCTEX1D2 sits in a defined dynein-2 subcomplex with WDR60 and DYNLT1/DYNLT3, mapped by visible immunoprecipitation - the interaction that the horse model's truncated dimer interface puts in question. supporting_text: The dynein-2 complex can be divided into three subcomplexes, namely DYNC2H1-DYNC2LI1, WDR34-DYNLL1/DYNLL2-DYNLRB1/DYNLRB2, and WDR60-TCTEX1D2-DYNLT1/DYNLT3. reference_section_type: ABSTRACT - statement: TCTEX1D2 knockout cells are defective in retrograde ciliary protein trafficking, but less severely than WDR60 knockouts, placing TCTEX1D2 in an auxiliary rather than essential role within the complex. supporting_text: our results demonstrated that WDR60 plays a major role and TCTEX1D2 plays an auxiliary role in the dynein-2 complex to mediate retrograde ciliary protein trafficking. reference_section_type: ABSTRACT reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text cached. One of the two experimental sources behind the human FUNCTION annotation. The auxiliary-role conclusion is worth carrying forward, since it tempers how much phenotypic weight a divergent DYNLT2B form would be expected to carry. - id: PMID:25830415 title: Tctex1d2 associates with short-rib polydactyly syndrome proteins and is required for ciliogenesis. findings: - statement: Tctex1d2 associates with the dynein intermediate chains WDR34 and WDR60 and other dynein-1 and dynein-2 subunits, and localizes with WDR60 to the ciliary base; depletion of either causes ciliogenesis defects. supporting_text: Tctex1d2 and Wdr60 localize to the base of the cilium and their depletion causes defects in ciliogenesis. reference_section_type: ABSTRACT reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text cached. The original identification of TCTEX1D2 as a dynein light chain and the source of the ciliary-base localization claim. The localization is a separate observation from complex assembly and carries its own transfer limits, as the gene notes record. - id: PMID:39827215 title: TCTEX1D2 is essential for sperm flagellum formation in mice. findings: - statement: Mouse Tctex1d2 knockouts are male-infertile with dysplastic sperm flagella and disrupted axonemal structure, while their motile cilia remain normal - so the in vivo requirement is flagellum-biased rather than uniformly ciliary. supporting_text: Tctex1d2-/- mice generated in this study exhibited male infertility due to flagellar dysplasia, and the axonemal structures were disrupted inside the flagella. reference_section_type: ABSTRACT - statement: TCTEX1D2 acts in two distinct dynein complexes, interacting with cytoplasmic dynein-2 subunits (WDR34, WDR60, DYNLT1) and also with the inner-dynein-arm subunits WDR63 and WDR78 in testis. supporting_text: Furthermore, TCTEX1D2 also interacted with WDR63 and WDR78, subunits of inner dynein arm, which is axonemal dynein. reference_section_type: ABSTRACT reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text cached. Mouse in vivo evidence; cited for the tissue-restricted phenotype and the second (axonemal dynein) interaction set, both of which shape what an equine experiment should measure. Transfer to horse is not asserted. existing_annotations: [] core_functions: - description: Non-catalytic Tctex-type light chain of cytoplasmic dynein-2 that, as a heterodimer with DYNLT1/DYNLT3, binds the WDR60/DYNC2I1 intermediate chain and supports retrograde intraflagellar transport. Assigned to the equine gene by one-to-one orthology (PANTHER PTHR21255:SF7, the DYNLT2B-specific subfamily) to the experimentally characterized human protein. The A0A9L0SWY1 model specifically lacks the C-terminal beta-strand, so whether this particular protein form is competent for the function is unresolved. molecular_function: id: GO:0045505 label: dynein intermediate chain binding in_complex: id: GO:0005868 label: cytoplasmic dynein complex supported_by: - reference_id: PMID:29742051 supporting_text: The dynein-2 complex can be divided into three subcomplexes, namely DYNC2H1-DYNC2LI1, WDR34-DYNLL1/DYNLL2-DYNLRB1/DYNLRB2, and WDR60-TCTEX1D2-DYNLT1/DYNLT3. - reference_id: file:HORSE/DYNLT2B/DYNLT2B-bioinformatics/RESULTS.md supporting_text: The horse sequence A0A9L0SWY1 (245 residues) aligns to human Q8WW35 (142 residues) with 91.41% identity across 128 paired residues. - reference_id: file:HORSE/DYNLT2B/DYNLT2B-uniprot.txt record_section: ["DR:PANTHER"] supporting_text: PANTHER; PTHR21255:SF7; DYNEIN LIGHT CHAIN TCTEX-TYPE PROTEIN 2B; 1.