Human Gene TRNT1 (uc003bpp.4) Description and Page Index
  Description: Homo sapiens tRNA nucleotidyl transferase, CCA-adding, 1 (TRNT1), nuclear gene encoding mitochondrial protein, mRNA.
RefSeq Summary (NM_182916): 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].
Transcript (Including UTRs)
   Position: hg19 chr3:3,168,600-3,190,706 Size: 22,107 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr3:3,170,725-3,189,838 Size: 19,114 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:3,168,600-3,190,706)mRNA (may differ from genome)Protein (434 aa)
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UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: TRNT1_HUMAN
DESCRIPTION: RecName: Full=CCA tRNA nucleotidyltransferase 1, mitochondrial; EC=2.7.7.72; AltName: Full=Mitochondrial tRNA nucleotidyl transferase, CCA-adding; AltName: Full=mt CCA-adding enzyme; AltName: Full=mt tRNA CCA-diphosphorylase; AltName: Full=mt tRNA CCA-pyrophosphorylase; AltName: Full=mt tRNA adenylyltransferase; Flags: Precursor;
FUNCTION: Isoform 1: Adds and repairs the conserved 3'-CCA sequence necessary for the attachment of amino acids to the 3' terminus of tRNA molecules, using CTP and ATP as substrates.
FUNCTION: Isoform 2: Adds 2 C residues (CC-) to the 3' terminus of tRNA molecules instead of a complete CCA end as isoform 1 does (in vitro).
CATALYTIC ACTIVITY: A tRNA precursor + 2 CTP + ATP = a tRNA with a 3' CCA end + 3 diphosphate.
COFACTOR: Magnesium (Probable).
SUBUNIT: Monomer, and homodimer; disulfide-linked.
SUBCELLULAR LOCATION: Mitochondrion.
SIMILARITY: Belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family.
SEQUENCE CAUTION: Sequence=AAD34042.1; Type=Frameshift; Positions=16; Sequence=AAH12537.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TRNT1
CDC HuGE Published Literature: TRNT1

-  MalaCards Disease Associations
  MalaCards Gene Search: TRNT1
Diseases sorted by gene-association score: sideroblastic anemia with b-cell immunodeficiency, periodic fevers, and developmental delay* (1694), retinitis pigmentosa and erythrocytic microcytosis* (920), sideroblastic anemia (33), cataract 7 (13), lens disease (4), retinitis pigmentosa (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.16 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 161.07 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -45.20102-0.443 Picture PostScript Text
3' UTR -206.90868-0.238 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002646 - PolA_pol_head_dom
IPR026973 - Trnt1

Pfam Domains:
PF01743 - Poly A polymerase head domain
PF12627 - Probable RNA and SrmB- binding site of polymerase A

SCOP Domains:
81891 - Poly A polymerase C-terminal region-like
81301 - Nucleotidyltransferase

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1OU5
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96Q11
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0052927 CTP:tRNA cytidylyltransferase activity
GO:0052928 CTP:3'-cytidine-tRNA cytidylyltransferase activity
GO:0052929 ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity

Biological Process:
GO:0001680 tRNA 3'-terminal CCA addition
GO:0006396 RNA processing
GO:0008033 tRNA processing
GO:0042780 tRNA 3'-end processing
GO:1990180 mitochondrial tRNA 3'-end processing

Cellular Component:
GO:0005622 intracellular
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  BC005184 - Homo sapiens tRNA nucleotidyl transferase, CCA-adding, 1, mRNA (cDNA clone IMAGE:3686608), complete cds.
AK290411 - Homo sapiens cDNA FLJ75300 complete cds, highly similar to Homo sapiens hMtCCA mRNA for tRNA-nucleotidyltransferase.
AL834397 - Homo sapiens mRNA; cDNA DKFZp547J2110 (from clone DKFZp547J2110).
BC012537 - Homo sapiens tRNA nucleotidyl transferase, CCA-adding, 1, mRNA (cDNA clone MGC:13334 IMAGE:4097092), complete cds.
AB063105 - Homo sapiens hMtCCA mRNA for tRNA-nucleotidyltransferase, complete cds.
AF151805 - Homo sapiens CGI-47 protein mRNA, complete cds.
AK124137 - Homo sapiens cDNA FLJ42143 fis, clone TESTI2046100.
JD183149 - Sequence 164173 from Patent EP1572962.
JD232241 - Sequence 213265 from Patent EP1572962.
KJ902554 - Synthetic construct Homo sapiens clone ccsbBroadEn_11948 TRNT1 gene, encodes complete protein.
AB385188 - Synthetic construct DNA, clone: pF1KB9025, Homo sapiens TRNT1 gene for tRNA-nucleotidyltransferase 1, complete cds, without stop codon, in Flexi system.
AM392669 - Synthetic construct Homo sapiens clone IMAGE:100001905 for hypothetical protein (TRNT1 gene).
AM393260 - Synthetic construct Homo sapiens clone IMAGE:100001912 for hypothetical protein (TRNT1 gene).
EU832347 - Synthetic construct Homo sapiens clone HAIB:100067376; DKFZo008H0127 tRNA nucleotidyl transferase, CCA-adding, 1 protein (TRNT1) gene, encodes complete protein.
EU832432 - Synthetic construct Homo sapiens clone HAIB:100067461; DKFZo004H0128 tRNA nucleotidyl transferase, CCA-adding, 1 protein (TRNT1) gene, encodes complete protein.
JD079085 - Sequence 60109 from Patent EP1572962.
JD230699 - Sequence 211723 from Patent EP1572962.
JD274626 - Sequence 255650 from Patent EP1572962.
JD098530 - Sequence 79554 from Patent EP1572962.
CU680352 - Synthetic construct Homo sapiens gateway clone IMAGE:100018231 5' read TRNT1 mRNA.
KJ902555 - Synthetic construct Homo sapiens clone ccsbBroadEn_11949 TRNT1 gene, encodes complete protein.
JD020947 - Sequence 1971 from Patent EP1572962.
JD035159 - Sequence 16183 from Patent EP1572962.
LF207322 - JP 2014500723-A/14825: Polycomb-Associated Non-Coding RNAs.
LF364671 - JP 2014500723-A/172174: Polycomb-Associated Non-Coding RNAs.
LF364673 - JP 2014500723-A/172176: Polycomb-Associated Non-Coding RNAs.
MA600248 - JP 2018138019-A/172174: Polycomb-Associated Non-Coding RNAs.
MA600250 - JP 2018138019-A/172176: Polycomb-Associated Non-Coding RNAs.
MA442899 - JP 2018138019-A/14825: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96Q11 (Reactome details) participates in the following event(s):

R-HSA-5696807 TRNT1 polymerizes CCA at the 3' end of pre-tRNA
R-HSA-6786881 TRNT1 polymerizes CCA at the 3' end of pre-tRNA
R-HSA-6784531 tRNA processing in the nucleus
R-HSA-6785470 tRNA processing in the mitochondrion
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8K2Z6, B7WP13, C9JKA2, CGI-47, NM_182916, NP_886552, Q8ND57, Q96Q11, Q9BS97, Q9Y362, TRNT1_HUMAN
UCSC ID: uc003bpp.4
RefSeq Accession: NM_182916
Protein: Q96Q11 (aka TRNT1_HUMAN or CCA1_HUMAN)
CCDS: CCDS2561.2

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TRNT1:
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_182916.2
exon count: 8CDS single in 3' UTR: no RNA size: 2291
ORF size: 1305CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 2701.50frame shift in genome: no % Coverage: 99.30
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 835# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.