id: A0A8B6BFL6 gene_symbol: A0A8B6BFL6 product_type: PROTEIN status: DRAFT taxon: id: NCBITaxon:29158 label: Mytilus galloprovincialis description: >- A0A8B6BFL6 (ORF MGAL_10B073878) is a predicted 612-residue protein of the Mediterranean mussel Mytilus galloprovincialis encoded by a DIRS-type (tyrosine recombinase) retrotransposon. It consists of a reverse transcriptase (RT) domain (residues ~174-349, with an intact YLDD polymerase motif C) followed by a DIRS1-type RNase H domain, preceded by an N-terminal region of unknown function. It belongs to PANTHER subfamily PTHR33050:SF7, together with the RT-RNase H protein encoded by ORF2 of the Dictyostelium DIRS-1 element, which it aligns with across both domains. It also shares more distant similarity with the hepadnavirus polymerases in the same subfamily. In DIRS elements, cDNA synthesis is carried out by the RT-RNase H protein, while integration is carried out by a separately encoded tyrosine recombinase. This protein contains no recombinase domain. Its expected role is therefore reverse transcription of the element RNA (RNA-directed DNA polymerase activity with associated RNase H degradation of the RNA template) during retrotransposition. No experimental characterisation of the mussel protein exists, and it is unknown whether the encoding element is intact or mobile. existing_annotations: - term: id: GO:0003964 label: RNA-directed DNA polymerase activity evidence_type: ISS review: summary: >- NEW: GOA has no annotations for this accession. RT activity is the defining function of the DIRS-type RT-RNase H protein. action: NEW reason: >- The Pfam RVT_1 domain (174-349) retains the YLDD polymerase motif C. The protein is in PTHR33050:SF7 with the Dictyostelium DIRS-1 ORF2 RT-RNase H and aligns with it across both domains (z=51.7 vs shuffled controls). The DIRS-1 RT is shown genetically to supply cDNA synthesis in trans. Inferred by sequence similarity (ISS) only, with no direct assay. supported_by: - reference_id: file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md supporting_text: "RT motif C (Y-x-D-D): `YLDD` at 300-303, inside the Pfam RVT_1 domain (174-349)." - reference_id: PMID:32170321 supporting_text: "indicated that the endogenous DIRS-1 reverse transcriptase can act in trans" - term: id: GO:0032197 label: retrotransposition evidence_type: ISS qualifier: involved_in review: summary: >- NEW: the RT-RNase H protein performs the cDNA-synthesis step of the element's retrotransposition cycle. action: NEW reason: >- This is participation, not necessity: the protein catalyses reverse transcription of the element RNA, which is a step of retrotransposition. DNA integration and DNA recombination are deliberately not proposed. In DIRS elements those steps are performed by the separately encoded tyrosine recombinase, and this protein has no similarity to it. supported_by: - reference_id: PMID:32170321 supporting_text: "indicated that the endogenous DIRS-1 reverse transcriptase can act in trans" - reference_id: file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md supporting_text: "The target aligns with DIRS-1 ORF2 continuously across both the RT and the RNase H regions" references: - id: file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-uniprot.txt title: UniProt entry A0A8B6BFL6 findings: - statement: >- Identifies the protein as a reverse transcriptase domain-containing protein with Pfam RVT_1 (PF00078) and CDD RNase_HI_RT_DIRS1 (cd09275) domains. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Source of the domain and family assignments (Pfam RVT_1 174-349, CDD cd09275, PANTHER PTHR33050:SF7). The record is unreviewed and PE 4, and the protein name is domain-derived. Only the classification lines are used as support. - id: file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-deep-research-falcon.md title: Deep research summary for A0A8B6BFL6 findings: - statement: >- Identifies the protein as a putative retrotransposon-associated reverse transcriptase with RNA-dependent DNA polymerase activity, involved in mobile element propagation in the M. galloprovincialis genome. - statement: >- Describes the M. galloprovincialis genome as repeat-rich with 43% repeat content and extensive structural variation, providing context for the abundance of retrotransposon-derived proteins. - statement: >- Reviews bivalve LINE diversity across 27 genomes, identifying 86,488 RT-containing elements from 12 distinct clades. reference_review: relevance: MEDIUM correctness: MISCITED review_notes: >- Its generic RT reasoning is sound, but it assumes a LINE/non-LTR element with target-primed reverse transcription and nucleo-cytoplasmic localisation by analogy to LINE-1. That contradicts the DIRS1-type RNase H (cd09275) and PTHR33050:SF7 placement, so its LINE-specific mechanism and localisation claims are not used in the 2026-10-21 re-review. - id: file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-protnlm-predictions-review.yaml title: ProtNLM2 predictions review for A0A8B6BFL6 findings: - statement: >- ProtNLM2 predicted DNA binding (GO:0003677, assessed as LSP), DNA recombination (GO:0006310, assessed as COR), and DNA integration (GO:0015074, assessed as COR) for this protein. - statement: >- The CDD RNase_HI_RT_DIRS1 domain (cd09275) identifies this protein as belonging to the DIRS1 retrotransposon class, which uses tyrosine recombinase-mediated recombination for integration rather than LINE-type target-primed reverse transcription. reference_review: relevance: NONE correctness: UNVERIFIED review_notes: >- Retained only for provenance. The 2026-10-21 full re-review was performed independently of ProtNLM2 output and does not use this file as support. Its claims of DNA integration and DNA recombination were not carried forward, because in DIRS elements these steps belong to the separately encoded tyrosine recombinase, which this protein lacks. - id: PMID:32170321 title: DIRS retrotransposons amplify via linear, single-stranded cDNA intermediates. findings: - statement: >- DIRS elements are retrotransposons that use a tyrosine recombinase instead of an integrase or endonuclease. They encode GAG, RT, RNase H and YR functions. supporting_text: "These comprise, next to the name-giving YR, a putative GAG protein (GAG), a reverse transcriptase (RT) and an RNase H (RH)." - statement: >- Element-level genetics in Dictyostelium shows that the DIRS-1-encoded reverse transcriptase acts in trans to generate cDNA for retrotransposition. supporting_text: "indicated that the endogenous DIRS-1 reverse transcriptase can act in trans" reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Full text cached. It characterises the Dictyostelium DIRS-1 element, whose ORF2 RT-RNase H protein (O96849/Q23898) is in the same PANTHER subfamily (PTHR33050:SF7) as A0A8B6BFL6. It is evidence for the DIRS RT role and for the YR being a separate protein. It does not assay the mussel protein. - id: file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md title: Sequence comparison of A0A8B6BFL6 with PTHR33050:SF7 members findings: - statement: >- A0A8B6BFL6 aligns with DIRS-1 ORF2 (O96849) continuously across the RT and RNase H regions (z=51.7 vs shuffled controls). It aligns weakly with DHBV polymerase P (RT core only) and not at all with the DIRS-1 tyrosine recombinase. The RT motif C YLDD is retained. supporting_text: "The target aligns with DIRS-1 ORF2 continuously across both the RT and the RNase H regions" reference_review: relevance: HIGH correctness: VERIFIED review_notes: Reproducible script and raw output in the same folder. core_functions: - description: >- Reverse transcription of the DIRS-type element RNA. The RT domain (with intact YLDD motif C) synthesises cDNA on an RNA template, which is the copying step of the element's retrotransposition cycle. The function is inferred from domain architecture, an intact polymerase motif, and membership of PTHR33050:SF7 alongside the Dictyostelium DIRS-1 ORF2 RT, which element-level genetics shows supplies the RT activity for DIRS-1 mobility. Integration is not assigned to this protein, because DIRS elements perform it with a separately encoded tyrosine recombinase. molecular_function: id: GO:0003964 label: RNA-directed DNA polymerase activity directly_involved_in: - id: GO:0032197 label: retrotransposition supported_by: - reference_id: file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-uniprot.txt record_section: ["DR:Pfam"] supporting_text: "Pfam; PF00078; RVT_1; 1." - reference_id: file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-bioinformatics/RESULTS-rereview.md supporting_text: "RT motif C (Y-x-D-D): `YLDD` at 300-303, inside the Pfam RVT_1 domain (174-349)." - reference_id: PMID:32170321 supporting_text: "indicated that the endogenous DIRS-1 reverse transcriptase can act in trans" knowledge_gaps: - gap_statement: >- No biochemical assay has shown reverse transcriptase activity for this protein, and it is unknown whether the encoding mussel element is transcribed or mobile. boundary: >- Domain architecture, an intact YLDD motif and subfamily placement with DIRS-1 ORF2 support RT activity by homology only. gap_kind: - BIOLOGY - description: >- RNase H degradation of the RNA strand of the RNA-DNA hybrids formed during reverse transcription. This is inferred from the DIRS1-type RNase H domain (CDD cd09275), which aligns with the RNase H region of DIRS-1 ORF2 and has a candidate first catalytic carboxylate. It is weaker than the RT inference, because the catalytic DEDD set has not been mapped residue by residue. molecular_function: id: GO:0004523 label: RNA-DNA hybrid ribonuclease activity directly_involved_in: - id: GO:0032197 label: retrotransposition supported_by: - reference_id: file:MYTGA/A0A8B6BFL6/A0A8B6BFL6-uniprot.txt record_section: ["DR:CDD"] supporting_text: "CDD; cd09275; RNase_HI_RT_DIRS1; 1." - reference_id: PMID:32170321 supporting_text: "These comprise, next to the name-giving YR, a putative GAG protein (GAG), a reverse transcriptase (RT) and an RNase H (RH)." knowledge_gaps: - gap_statement: >- Whether the RNase H domain retains all catalytic carboxylates and is active is unknown. boundary: >- cd09275 assignment and alignment to the DIRS-1 RNase H region, with one candidate SDA motif at 463. gap_kind: - BIOLOGY suggested_questions: - question: >- Is this protein encoded by an intact DIRS-type element (with GAG and tyrosine recombinase ORFs and inverted terminal repeats at the locus), or by a degraded copy? - question: >- Should DIRS-type RT-RNase H proteins be separated from hepadnavirus polymerases at the subfamily level in PANTHER, given that PTHR33050:SF7 currently groups them together? - question: >- Is there evidence of recent retrotransposition activity for this element in the M. galloprovincialis population, such as polymorphic insertions? suggested_experiments: - description: >- Express and purify the RT-RNase H region and test RNA-dependent DNA polymerase and RNase H activities in vitro (primer extension on an RNA template; cleavage of a labelled RNA-DNA hybrid), with a YLDD-to-YLAA mutant as a control. - description: >- Perform RNA-seq across tissues and developmental stages to determine whether the encoding retrotransposon is transcriptionally active. - description: >- Annotate the genomic locus to test for companion GAG and tyrosine recombinase ORFs, and build a phylogeny of the RT domain with classified DIRS, PAT, Ngaro and VIPER elements.