pcif1 encodes the cap-specific adenosine methyltransferase CAPAM, a nuclear enzyme that uses SAM to methylate the N6 position of the first transcribed adenosine of capped mRNAs, forming m6Am during mRNA processing. It binds the RNA polymerase II C-terminal domain, coupling the modification to transcription, and the resulting m6Am cap can influence mRNA translation and stability.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: nucleus (GO:0005634) is supported for zebrafish pcif1 and is coherent with the synthesized gene function. Reason: Pcif1/CAPAM is a nuclear mRNA cap methyltransferase. Supporting Evidence: file:DANRE/pcif1/pcif1-uniprot.txt SUBCELLULAR LOCATION: Nucleus file:DANRE/pcif1/pcif1-deep-research-falcon.md PCIF1 is described as primarily **nuclear** |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: nucleus (GO:0005634) is supported for zebrafish pcif1 and is coherent with the synthesized gene function. Reason: Pcif1/CAPAM is a nuclear mRNA cap methyltransferase. Supporting Evidence: file:DANRE/pcif1/pcif1-uniprot.txt SUBCELLULAR LOCATION: Nucleus file:DANRE/pcif1/pcif1-deep-research-falcon.md PCIF1 is described as primarily **nuclear** |
| GO:0016422 mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422) is supported for zebrafish pcif1 and is coherent with the synthesized gene function. Reason: This is the specific cap-adjacent mRNA methyltransferase activity established for PCIF1/CAPAM. Supporting Evidence: file:DANRE/pcif1/pcif1-uniprot.txt Cap-specific adenosine methyltransferase that catalyzes PMID:30467178 methyltransferase (CAPAM) responsible for N 6-methylation of m6Am file:DANRE/pcif1/pcif1-deep-research-falcon.md CAPAM/PCIF1 is the **cap-specific** methyltransferase that writes this **m6Am** mark at the transcription start nucleotide. |
| GO:0099122 RNA polymerase II C-terminal domain binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: RNA polymerase II C-terminal domain binding (GO:0099122) is supported or plausible for zebrafish pcif1, but it is not the most informative core function. Reason: RNA polymerase II CTD binding helps recruit/associate PCIF1 with transcription but is not the core catalytic activity. Supporting Evidence: PMID:30467178 interacts with the serine-5-phosphorylated PMID:30467178 carboxyl-terminal domain of RNA polymerase II file:DANRE/pcif1/pcif1-deep-research-falcon.md its WW domain binds the **Ser5-phosphorylated C-terminal domain (CTD)** of **RNA polymerase II**, consistent with recruitment to early transcription complexes and **co-transcriptional** installation of m6Am at transcription start sites. |
| GO:0005634 nucleus | ISS GO_REF:0000024 | ACCEPT | Summary: nucleus (GO:0005634) is supported for zebrafish pcif1 and is coherent with the synthesized gene function. Reason: Pcif1/CAPAM is a nuclear mRNA cap methyltransferase. Supporting Evidence: file:DANRE/pcif1/pcif1-uniprot.txt SUBCELLULAR LOCATION: Nucleus file:DANRE/pcif1/pcif1-deep-research-falcon.md PCIF1 is described as primarily **nuclear** |
| GO:0006397 mRNA processing | IDA PMID:30467178 Cap-specific terminal N (6)-methylation of RNA by an RNA pol... | ACCEPT | Summary: mRNA processing (GO:0006397) is supported for zebrafish pcif1 and is coherent with the synthesized gene function. Reason: mRNA processing captures the biological process supported by m6Am formation on capped mRNAs. Supporting Evidence: PMID:30467178 methyltransferase (CAPAM) responsible for N 6-methylation of m6Am file:DANRE/pcif1/pcif1-deep-research-falcon.md CAPAM/PCIF1 is the **cap-specific** methyltransferase that writes this **m6Am** mark at the transcription start nucleotide. |
| GO:0016422 mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity | IDA PMID:30467178 Cap-specific terminal N (6)-methylation of RNA by an RNA pol... | ACCEPT | Summary: mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422) is supported for zebrafish pcif1 and is coherent with the synthesized gene function. Reason: This is the specific cap-adjacent mRNA methyltransferase activity established for PCIF1/CAPAM. Supporting Evidence: file:DANRE/pcif1/pcif1-uniprot.txt Cap-specific adenosine methyltransferase that catalyzes PMID:30467178 methyltransferase (CAPAM) responsible for N 6-methylation of m6Am file:DANRE/pcif1/pcif1-deep-research-falcon.md CAPAM/PCIF1 is a **SAM-dependent N6-adenosine methyltransferase** that installs **m6Am** at the cap-adjacent nucleotide of mRNAs. |
| GO:0045727 positive regulation of translation | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: positive regulation of translation (GO:0045727) is supported or plausible for zebrafish pcif1, but it is not the most informative core function. Reason: Translation regulation is a downstream effect of m6Am installation, not the core writer activity, so this is kept as non-core. The DIRECTIONALITY of this ISS annotation is uncertain: while PMID:30467178 reported m6Am promoting translation, falcon (citing Jin 2024 and the UniProt CAUTION) summarizes m6Am effects on translation as context-dependent, with other studies reporting no clear effect or even inhibition. The positive direction should therefore be treated as one of several reported outcomes rather than an established zebrafish function. Supporting Evidence: PMID:30467178 cap-specific m6A writer promotes translation of mRNAs starting from m6Am file:DANRE/pcif1/pcif1-deep-research-falcon.md summarizes evidence for m6Am impacts on **splicing, stability, and translation** in different biological contexts |
| GO:0099122 RNA polymerase II C-terminal domain binding | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: RNA polymerase II C-terminal domain binding (GO:0099122) is supported or plausible for zebrafish pcif1, but it is not the most informative core function. Reason: RNA polymerase II CTD binding helps recruit/associate PCIF1 with transcription but is not the core catalytic activity. Supporting Evidence: PMID:30467178 interacts with the serine-5-phosphorylated PMID:30467178 carboxyl-terminal domain of RNA polymerase II file:DANRE/pcif1/pcif1-deep-research-falcon.md its WW domain binds the **Ser5-phosphorylated C-terminal domain (CTD)** of **RNA polymerase II**, consistent with recruitment to early transcription complexes and **co-transcriptional** installation of m6Am at transcription start sites. |
| GO:1904047 S-adenosyl-L-methionine binding | IDA PMID:30467178 Cap-specific terminal N (6)-methylation of RNA by an RNA pol... | KEEP AS NON CORE | Summary: S-adenosyl-L-methionine binding (GO:1904047) is supported or plausible for zebrafish pcif1, but it is not the most informative core function. Reason: SAM binding is a required cofactor interaction but is less informative than the methyltransferase activity. Supporting Evidence: file:DANRE/pcif1/pcif1-uniprot.txt S-adenosyl-L-methionine file:DANRE/pcif1/pcif1-deep-research-falcon.md CAPAM/PCIF1 is a **SAM-dependent N6-adenosine methyltransferase** that installs **m6Am** at the cap-adjacent nucleotide of mRNAs. |
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