Format

Send to:

Choose Destination

TRNT1 tRNA nucleotidyl transferase 1 [ Homo sapiens (human) ]

Gene ID: 51095, updated on 5-Aug-2018

Summary

Official Symbol
TRNT1provided by HGNC
Official Full Name
tRNA nucleotidyl transferase 1provided by HGNC
Primary source
HGNC:HGNC:17341
See related
Ensembl:ENSG00000072756 MIM:612907; Vega:OTTHUMG00000090259
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CCA1; RPEM; SIFD; MtCCA; CGI-47
Summary
The protein encoded by this gene is a CCA-adding enzyme which belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. This essential enzyme functions by catalyzing the addition of the conserved nucleotide triplet CCA to the 3' terminus of tRNA molecules. Mutations in this gene result in sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Expression
Ubiquitous expression in prostate (RPKM 8.6), testis (RPKM 7.5) and 25 other tissues See more
Orthologs

Genomic context

See TRNT1 in Genome Data Viewer
Location:
3p26.2
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (3126916..3153435)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (3168600..3190919)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene contactin 4 Neighboring gene CNTN4 antisense RNA 1 Neighboring gene uncharacterized LOC107986006 Neighboring gene interleukin 5 receptor subunit alpha Neighboring gene cereblon Neighboring gene uncharacterized LOC100130207 Neighboring gene uncharacterized LOC107986007 Neighboring gene leucine rich repeat neuronal 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • RNA transport, organism-specific biosystem (from KEGG)
    RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • RNA transport, conserved biosystem (from KEGG)
    RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • tRNA processing, organism-specific biosystem (from REACTOME)
    tRNA processing, organism-specific biosystemGenes encoding transfer RNAs (tRNAs) are transcribed by RNA polymerase III in the nucleus and by mitochondrial RNA polymerase in the mitochondrion.In the nucleus transcription reactions produce precu...
  • tRNA processing in the mitochondrion, organism-specific biosystem (from REACTOME)
    tRNA processing in the mitochondrion, organism-specific biosystemEach strand of the circular mitochondrial genome is transcribed to yield long polycistronic transcripts, the heavy strand transcript and the light strand transcript, which are then cleaved to yield t...
  • tRNA processing in the nucleus, organism-specific biosystem (from REACTOME)
    tRNA processing in the nucleus, organism-specific biosystemGenes encoding transfer RNAs are transcribed in the nucleus by RNA polymerase III. (Distinct processes of transcription and processing also occur in mitochondria.) The initial transcripts, pre-tRNAs,...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
5'-3' RNA polymerase activity TAS
Traceable Author Statement
more info
 
ATP binding TAS
Traceable Author Statement
more info
PubMed 
ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
CTP:3'-cytidine-tRNA cytidylyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
CTP:tRNA cytidylyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
tRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
mitochondrial tRNA 3'-end processing IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial tRNA 3'-end processing TAS
Traceable Author Statement
more info
 
tRNA 3'-end processing TAS
Traceable Author Statement
more info
 
tRNA 3'-terminal CCA addition IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
intracellular IDA
Inferred from Direct Assay
more info
 
mitochondrial matrix TAS
Traceable Author Statement
more info
 
mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
CCA tRNA nucleotidyltransferase 1, mitochondrial
Names
ATP(CTP):tRNA nucleotidyltransferase
CCA-adding enzyme
mitochondrial CCA-adding tRNA-nucleotidyltransferase
mt CCA-adding enzyme
mt tRNA CCA-diphosphorylase
mt tRNA CCA-pyrophosphorylase
mt tRNA adenylyltransferase
tRNA CCA nucleotidyl transferase 1
tRNA nucleotidyl transferase, CCA-adding, 1
tRNA-nucleotidyltransferase 1, mitochondrial
NP_001289875.1
NP_886552.2
XP_011532078.1
XP_011532079.1
XP_011532080.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_041800.1 RefSeqGene

    Range
    5001..27108
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001302946.1NP_001289875.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform 2

    See identical proteins and their annotated locations for NP_001289875.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC024060, AL834397
    Consensus CDS
    CCDS77691.1
    UniProtKB/Swiss-Prot
    Q96Q11
    Related
    ENSP00000280591.6, OTTHUMP00000195199, ENST00000280591.10, OTTHUMT00000314016
    Conserved Domains (3) summary
    cd05398
    Location:42178
    NT_ClassII-CCAase; Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes
    COG0617
    Location:40316
    PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]
    pfam12627
    Location:216248
    PolyA_pol_RNAbd; Probable RNA and SrmB- binding site of polymerase A
  2. NM_182916.2NP_886552.2  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform 1

    See identical proteins and their annotated locations for NP_886552.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AB063105, AL834397, BQ722111, DA884423, DB032432, DB525237
    Consensus CDS
    CCDS2561.2
    UniProtKB/Swiss-Prot
    Q96Q11
    UniProtKB/TrEMBL
    A0A024R2H7
    Related
    ENSP00000251607.6, OTTHUMP00000206931, ENST00000251607.10, OTTHUMT00000337616
    Conserved Domains (3) summary
    cd05398
    Location:42178
    NT_ClassII-CCAase; Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes
    COG0617
    Location:40417
    PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]
    pfam12627
    Location:216270
    PolyA_pol_RNAbd; Probable RNA and SrmB- binding site of polymerase A

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    3126916..3153435
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533778.3XP_011532080.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_011532080.1

    UniProtKB/Swiss-Prot
    Q96Q11
    Conserved Domains (3) summary
    cd05398
    Location:42178
    NT_ClassII-CCAase; Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes
    COG0617
    Location:40417
    PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]
    pfam12627
    Location:216270
    PolyA_pol_RNAbd; Probable RNA and SrmB- binding site of polymerase A
  2. XM_011533777.2XP_011532079.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_011532079.1

    UniProtKB/Swiss-Prot
    Q96Q11
    Conserved Domains (3) summary
    cd05398
    Location:42178
    NT_ClassII-CCAase; Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes
    COG0617
    Location:40417
    PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]
    pfam12627
    Location:216270
    PolyA_pol_RNAbd; Probable RNA and SrmB- binding site of polymerase A
  3. XM_011533776.3XP_011532078.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_011532078.1

    UniProtKB/Swiss-Prot
    Q96Q11
    Conserved Domains (3) summary
    cd05398
    Location:42178
    NT_ClassII-CCAase; Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes
    COG0617
    Location:40417
    PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]
    pfam12627
    Location:216270
    PolyA_pol_RNAbd; Probable RNA and SrmB- binding site of polymerase A

RNA

  1. XR_001740169.2 RNA Sequence

  2. XR_940445.3 RNA Sequence

  3. XR_940446.3 RNA Sequence

  4. XR_001740168.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_016000.3: Suppressed sequence

    Description
    NM_016000.3: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Support Center