This term is obsolete.
The term 'RNA editing' (GO:0016547) was merged into 'RNA modification' (GO:0009451) on the basis of statements in the preface of Modification and Editing of RNA (ISBN:1555811337) that there is no clear distinction between modification and editing. Parallel changes were made for substrate (e.g. tRNA, rRNA, etc.) specific child terms of 'RNA editing'.

GO:0006400 JSON

tRNA modification

Biological Process

Definition (GO:0006400 GONUTS page)

The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.

Comments

The term 'RNA editing' (GO:0016547) was merged into 'RNA modification' (GO:0009451) on the basis of statements in the preface of Modification and Editing of RNA (ISBN:1555811337) that there is no clear distinction between modification and editing. Parallel changes were made for substrate (e.g. tRNA, rRNA, etc.) specific child terms of 'RNA editing'.

Secondary IDs

GO:0016549

2,581,734 annotations

Synonyms

Synonyms are alternative words or phrases closely related in meaning to the term name, with indication of the relationship between the name and synonym given by the synonym scope.

Synonym Type
tRNA editing narrow

Ancestor Chart

Ancestor chart for GO:0006400
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Ancestor chart

Child Terms

This table lists all terms that are direct descendants (child terms) of GO:0006400

Child Term Relationship to
GO:0006400
tRNA pseudouridine synthesis
is_a
tRNA methylthiolation
is_a
tRNA dihydrouridine synthesis
is_a
regulation of translational initiation by tRNA modification
is_a
wybutosine biosynthetic process
is_a
tRNA threonylcarbamoyladenosine modification
is_a
tRNA methylation
is_a
archaeosine-tRNA biosynthetic process
is_a
mitochondrial tRNA modification
is_a
tRNA-guanine transglycosylation
is_a

Annotation Blacklist

This list aims to correct incorrect annotations to UniProtKB accessions inferred from electronic annotation (IEA) methods that are supplied by the UniProt-GOA project to the GO Consortium:

Category Entity Type Entity ID Taxon ID Entity Name Ancestor GO ID Reason Rule/Method ID
NOT-qualified manual protein F4IL30 3702 POP1_ARATH GO:0008033 1 NOT-qualified manual annotation exists with evidence code ECO:0000315 from this reference: PMID:22549728
NOT-qualified manual protein O14133 284812 ATE1_SCHPO GO:0006399 1 NOT-qualified manual annotation exists with evidence code ECO:0000303 from this reference: GO_REF:0000051
NOT-qualified manual protein Q9SB36 3702 PP337_ARATH GO:0009451 1 NOT-qualified manual annotation exists with evidence code ECO:0000315 from this reference: PMID:21288264
NOT-qualified manual protein Q9ZW76 3702 POP4_ARATH GO:0008033 1 NOT-qualified manual annotation exists with evidence code ECO:0000315 from this reference: PMID:22549728

Cross-references

Database ID Description
InterPro IPR002616 tRNA-guanine(15) transglycosylase-like
InterPro IPR003358 tRNA (guanine-N-7) methyltransferase, Trmb type
InterPro IPR004520 tRNA modification GTPase MnmE
InterPro IPR004804 tRNA-guanine(15) transglycosylase
InterPro IPR005839 Methylthiotransferase
InterPro IPR005912 tRNA pseudouridine synthase, Pus10
InterPro IPR006463 tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB
InterPro IPR007537 tRNAHis guanylyltransferase Thg1
InterPro IPR010386 tRNA-hydroxylase MiaE
InterPro IPR022380 Glutamyl-Q tRNA(Asp) synthetase

Replaces

This term can be used instead of these obsolete terms:

GO Identifier GO Term Name Reason
GO:0002195 obsolete 2-methylthio-N-6-(cis-hydroxy)isopentenyl adenosine-tRNA biosynthesis consider GO:0006400

Co-occurring Terms

These tables show the number of times the term listed in the table has been co-annotated.

No co-occurrence statistics for GO:0006400 based on ALL annotations
The top 100 of 1,513 co-occurring terms
Co-occurring Term PR S% #Together #Compared
tRNA modification
300.62 100.00 659,163 659,163
tRNA processing
85.33 26.12 504,704 1,777,988
queuosine biosynthetic process
172.22 15.46 115,202 201,091
methylthiotransferase activity
281.65 12.53 83,293 88,901
tRNA wobble guanine modification
268.10 11.17 74,673 83,731
tRNA methylation
79.50 9.60 86,363 326,575
tRNA methylthiolation
240.58 8.36 56,287 70,332
tRNA dimethylallyltransferase activity
297.22 8.01 52,842 53,445
tRNA (guanine-N7)-methylation
299.24 6.81 44,883 45,089
mRNA pseudouridine synthesis
213.50 6.76 45,841 64,547
Totals 5300432 212374127
No co-occurrence statistics for GO:0006400 based on MANUAL annotations
The top 100 of 263 co-occurring terms
Co-occurring Term PR S% #Together #Compared
tRNA modification
1,180.21 100.00 1,196 1,196
tRNA dimethylallyltransferase activity
1,180.21 44.73 535 535
cytokinin biosynthetic process
513.42 23.11 395 908
tRNA methyltransferase complex
414.37 7.98 112 319
mRNA pseudouridine synthesis
251.59 7.45 123 577
elongator holoenzyme complex
204.81 6.02 101 582
pseudouridine synthase activity
86.56 4.47 123 1,677
AMP dimethylallyltransferase activity
1,008.89 4.40 53 62
tRNA-uridine aminocarboxypropyltransferase activity
1,180.21 3.68 44 44
tRNA binding
53.03 3.18 117 2,604
Totals 4484 435175

Change Log

Timestamp Action Category Detail
2024-12-05 Added XREF Reactome:R-HSA-6782315
2020-02-28 Deleted XREF MIPS_funcat:11.06.02
2019-05-04 Added XREF MIPS_funcat:11.06.02
2010-04-16 Deleted SYNONYM tRNA editing
2010-04-16 Added SYNONYM tRNA editing
2008-05-13 Added DEFINITION The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
2008-05-12 Deleted DEFINITION The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
2008-04-01 Updated RELATION is a GO:0008033 (tRNA processing)
2008-04-01 Updated RELATION is a GO:0009451 (RNA modification)
2007-08-09 Added SYNONYM tRNA editing
Timestamp Action Category Detail
2002-02-06 Updated TERM tRNA modification
2001-04-03 Updated TERM tRNA modification
2001-03-30 Added TERM tRNA modification
Timestamp Action Category Detail
2010-04-16 Deleted SYNONYM tRNA editing
2010-04-16 Added SYNONYM tRNA editing
2008-05-13 Added DEFINITION The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
2008-05-12 Deleted DEFINITION The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
2007-08-09 Added SYNONYM tRNA editing
2007-08-09 Deleted SYNONYM tRNA editing
2007-07-29 Added SYNONYM tRNA editing
2007-07-27 Updated DEFINITION The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
2006-03-15 Updated DEFINITION The covalent alteration of one or more nucleotides within tRNA, resulting in a change in the properties of the tRNA.
2002-11-27 Updated DEFINITION The enzymatic modification of the chemical structure of specific sites in tRNA.
2001-08-06 Added DEFINITION The enzymatic modification of the chemical structure of specific sites in tRNA.
Timestamp Action Category Detail
2008-04-01 Updated RELATION is a GO:0008033 (tRNA processing)
2008-04-01 Updated RELATION is a GO:0009451 (RNA modification)
Timestamp Action Category Detail
2024-12-05 Added XREF Reactome:R-HSA-6782315
2020-02-28 Deleted XREF MIPS_funcat:11.06.02
2019-05-04 Added XREF MIPS_funcat:11.06.02
Timestamp Action Category Detail
2007-07-29 Added SECONDARY GO:0016549 (tRNA editing)
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