id: Q9GF35 gene_symbol: matK product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:13288 label: Thlaspi arvense description: Maturase K (MatK) is the chloroplast-encoded intron maturase of field pennycress, typically encoded within the intron of the plastid trnK-UUU (lysine tRNA) gene. It is the only maturase retained in the plastid genome and acts as a trans-acting splicing factor that binds intron RNA and promotes excision of a conserved set of chloroplast group IIA introns (including its own trnK host intron and introns in trnA, trnI, trnV, atpF, rpl2 and rps12). It functions in the chloroplast stroma. MatK retains the maturase "domain X" and a degenerate reverse-transcriptase-like region but lacks the endonuclease/mobility domains of canonical bacterial intron-encoded proteins. The gene is also widely used as a plastid DNA barcode and phylogenetic marker. alternative_records: - id: A0A1U9RZH7 relationship: REFERENCE_PROTEOME_EQUIVALENT reference_proteome: UP000836841 reviewed_on: '2026-10-19' reason: Retain Q9GF35 as the primary Swiss-Prot accession. The leading full-length chloroplast maturase-K sequence has 98.21% global identity, eight substitutions and one gap column. Other hits are much shorter maturase fragments. This supports a qualified sequence-based counterpart while preserving the source sequence and documenting the differences. evidence: - type: PROTEOME_SEARCH description: MMseqs2 searched 26,379 sequences across UP000836841 at E <= 1e-5 and sensitivity 7.5, returning 6 hits. Every returned sequence was globally aligned using BLOSUM62 with gap-open -10 and extension -0.5. Scores and sequences for all 6 returned candidates are retained, with 6 detailed alignment files. The heuristic search does not establish genomic absence or unique locus identity. supported_by: - reference_id: file:THLAR/matK/matK-record-evidence.yaml supporting_text: 'target_sequence_count: 26379' - reference_id: file:THLAR/matK/matK-record-evidence.yaml supporting_text: 'candidate_count: 6' - type: SEQUENCE_COMPARISON description: 'A0A1U9RZH7: 495 identities across 504 global-alignment columns (98.2143% identity including gaps), 8 substitutions and 1 gap columns. Query coverage is 99.8016%; target coverage is 100.0%. Sequence similarity is interpreted in the manual rationale. Identity over paired residues is 98.4095% (495/503); gap columns are excluded from this denominator.' supported_by: - reference_id: file:THLAR/matK/matK-record-evidence.yaml supporting_text: |- query_length: 504 target_length: 503 alignment_columns: 504 identities: 495 mismatches: 8 gap_columns: 1 identity_percent: 98.2143 query_coverage_percent: 99.8016 target_coverage_percent: 100.0 - type: PROTEOME_MEMBERSHIP description: The primary accession is outside every searched exact-taxon reference proteome. Current UniProt records place A0A1U9RZH7 in UP000836841 and give it the same taxon as the primary. supported_by: - reference_id: file:THLAR/matK/matK-record-evidence.yaml supporting_text: 'primary_in_any_reference_proteome: false' - reference_id: file:THLAR/matK/matK-record-evidence.yaml supporting_text: 'alternative_in_reference_proteome: true' - reference_id: file:THLAR/matK/matK-record-evidence.yaml supporting_text: 'same_taxon: true' - type: RECORD_HISTORY description: 'Sampled UniSave observations: 07-JAN-2015, entry version 46.: no Proteomes cross-reference; 11-DEC-2019, entry version 51.: no Proteomes cross-reference; 22-FEB-2023, entry version 53.: no Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence, the exact change date, or UniProt''s motivation.' supported_by: - reference_id: file:THLAR/matK/matK-record-evidence.yaml supporting_text: |- entry_date: 07-JAN-2015, entry version 46. proteomes: [] - reference_id: file:THLAR/matK/matK-record-evidence.yaml supporting_text: |- entry_date: 11-DEC-2019, entry version 51. proteomes: [] - reference_id: file:THLAR/matK/matK-record-evidence.yaml supporting_text: |- entry_date: 22-FEB-2023, entry version 53. proteomes: [] existing_annotations: - term: id: GO:0005737 label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: located_in review: summary: Over-general and redundant. MatK is a plastid genome-encoded protein that localizes to the chloroplast stroma (soluble fraction in transplastomic tobacco); the generic cytoplasm term should be specialized to the chloroplast stroma, consistent with the separate chloroplast annotation. action: MODIFY proposed_replacement_terms: - id: GO:0009570 label: chloroplast stroma supported_by: - reference_id: file:THLAR/matK/matK-deep-research-falcon.md supporting_text: MatK is a chloroplast protein enriched in the soluble fraction (stroma) rather than membranes - term: id: GO:0006397 label: mRNA processing evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: summary: Acceptable. Several MatK splicing targets are group IIA introns within protein-coding (mRNA) transcripts, including atpF, rpl2 and rps12, so MatK does contribute to mRNA processing. The more precise activity is captured by the group II intron splicing annotation below. action: ACCEPT supported_by: - reference_id: file:THLAR/matK/matK-deep-research-falcon.md supporting_text: MatK-dependent group IIA introns include atpF, rpl2 and rps12 intron 2 - term: id: GO:0008380 label: RNA splicing evidence_type: IEA original_reference_id: GO_REF:0000104 qualifier: involved_in review: summary: Correct but can be made precise. MatK is specifically a group II intron maturase / splicing factor acting on chloroplast group IIA introns. The dedicated group II intron splicing term is more informative than the generic RNA splicing parent. action: MODIFY proposed_replacement_terms: - id: GO:0000373 label: Group II intron splicing supported_by: - reference_id: file:THLAR/matK/matK-deep-research-falcon.md supporting_text: MatK facilitates splicing (excision) of chloroplast group IIA introns as a trans-acting maturase - term: id: GO:0009507 label: chloroplast evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in review: summary: Correct. MatK is plastid genome-encoded and functions in the chloroplast. Consistent with the UniProt subcellular location (Plastid, chloroplast). action: ACCEPT supported_by: - reference_id: file:THLAR/matK/matK-deep-research-falcon.md supporting_text: chloroplast-encoded intron maturase localized to the chloroplast stroma - term: id: GO:0003723 label: RNA binding evidence_type: IEA review: summary: Proposed new molecular-function annotation. GOA currently lists no molecular function for MatK, but the protein is an RNA-binding intron maturase that binds its target group IIA introns to promote splicing; the conserved maturase domain X is an RNA-binding region. This is the core molecular function and should be added. action: NEW supported_by: - reference_id: file:THLAR/matK/matK-deep-research-falcon.md supporting_text: Maturases act as cofactors by binding intron RNA to stabilize the correct folded state and promote catalytic steps; MatK associates with multiple intron-containing transcripts in vivo core_functions: - description: MatK is a chloroplast-encoded, RNA-binding group II intron maturase that acts as a trans-acting splicing factor, promoting excision of a conserved set of chloroplast group IIA introns in the stroma. molecular_function: id: GO:0003723 label: RNA binding directly_involved_in: - id: GO:0000373 label: Group II intron splicing locations: - id: GO:0009570 label: chloroplast stroma supported_by: - reference_id: file:THLAR/matK/matK-deep-research-falcon.md supporting_text: trans-acting splicing cofactor for chloroplast group IIA introns (trnK, trnA, trnI, trnV, atpF, rpl2, rps12 intron 2), stroma-localized references: - id: file:THLAR/matK/matK-record-evidence.yaml title: Compact archived record and sequence evidence for Q9GF35 - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000104 title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features findings: [] - id: GO_REF:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: file:THLAR/matK/matK-deep-research-falcon.md title: Falcon/Edison deep research report for matK, Thlaspi arvense findings: - statement: MatK is the chloroplast-encoded group II intron maturase, a stroma-localized trans-acting splicing factor for a conserved set of chloroplast group IIA introns; the pennycress protein itself has not been directly assayed, so function is inferred from conserved land-plant MatK biology. reference_section_type: OTHER suggested_questions: - question: Which chloroplast group IIA introns does Thlaspi arvense MatK splice in vivo, and is MatK essential for plastid gene expression in pennycress as it is in tobacco?