Human Gene ATAD3A (uc001aga.2)
  Description: Homo sapiens ATPase family, AAA domain containing 3A (ATAD3A), nuclear gene encoding mitochondrial protein, transcript variant 2, mRNA.
RefSeq Summary (NM_001170535): This gene encodes a ubiquitously expressed mitochondrial membrane protein that contributes to mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. This gene is a member of the ATPase family AAA-domain containing 3 gene family which, in humans, includes two other paralogs. Naturally occurring mutations in this gene are associated with distinct neurological syndromes including Harel-Yoon syndrome. High-level expression of this gene is associated with poor survival in breast cancer patients. A homozygous knockout of the orthologous gene in mice results in embryonic lethality at day 7.5 due to growth retardation and defective development of the trophoblast lineage. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017].
Transcript (Including UTRs)
   Position: hg19 chr1:1,447,523-1,470,067 Size: 22,545 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr1:1,447,649-1,469,452 Size: 21,804 Coding Exon Count: 16 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:1,447,523-1,470,067)mRNA (may differ from genome)Protein (586 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ATAD3A
CDC HuGE Published Literature: ATAD3A

-  MalaCards Disease Associations
  MalaCards Gene Search: ATAD3A
Diseases sorted by gene-association score: harel-yoon syndrome* (530), axonal neuropathy (15), dyskinetic cerebral palsy (12), branchiootic syndrome (8), giant axonal neuropathy (7)
* = 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: 17.74 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 484.05 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 -64.20126-0.510 Picture PostScript Text
3' UTR -313.13615-0.509 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
  Pfam Domains:
PF00004 - ATPase family associated with various cellular activities (AAA)
PF12037 - Domain of unknown function (DUF3523)

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q9NVI7-2
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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 orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Descriptions from all associated GenBank mRNAs
  AF343078 - Homo sapiens TOB3 mRNA, complete cds.
LF383937 - JP 2014500723-A/191440: Polycomb-Associated Non-Coding RNAs.
BC014101 - Homo sapiens ATPase family, AAA domain containing 3A, mRNA (cDNA clone MGC:20642 IMAGE:3503438), complete cds.
AK091144 - Homo sapiens cDNA FLJ33825 fis, clone CTONG2003375, moderately similar to Drosophila melanogaster AAA family protein Bor (bor) mRNA.
AX746805 - Sequence 330 from Patent EP1308459.
AK001571 - Homo sapiens cDNA FLJ10709 fis, clone NT2RP3000869.
BC011814 - Homo sapiens ATPase family, AAA domain containing 3A, mRNA (cDNA clone MGC:20264 IMAGE:3162989), complete cds.
BC033109 - Homo sapiens ATPase family, AAA domain containing 3A, mRNA (cDNA clone MGC:45699 IMAGE:4877449), complete cds.
BC007803 - Homo sapiens ATPase family, AAA domain containing 3A, mRNA (cDNA clone MGC:14291 IMAGE:4136170), complete cds.
BC063607 - Homo sapiens ATPase family, AAA domain containing 3A, mRNA (cDNA clone MGC:74860 IMAGE:4939339), complete cds.
LF210256 - JP 2014500723-A/17759: Polycomb-Associated Non-Coding RNAs.
GU189416 - Homo sapiens AAA domain containing 3A protein (ATAD3A) mRNA, complete cds.
KJ905491 - Synthetic construct Homo sapiens clone ccsbBroadEn_15089 ATAD3A gene, encodes complete protein.
LF336201 - JP 2014500723-A/143704: Polycomb-Associated Non-Coding RNAs.
LF357547 - JP 2014500723-A/165050: Polycomb-Associated Non-Coding RNAs.
AK056099 - Homo sapiens cDNA FLJ31537 fis, clone NT2RI2000704, highly similar to ATPase family AAA domain-containing protein 3A.
LF336202 - JP 2014500723-A/143705: Polycomb-Associated Non-Coding RNAs.
LF357545 - JP 2014500723-A/165048: Polycomb-Associated Non-Coding RNAs.
AK310572 - Homo sapiens cDNA, FLJ17614.
LF336203 - JP 2014500723-A/143706: Polycomb-Associated Non-Coding RNAs.
AK025865 - Homo sapiens cDNA: FLJ22212 fis, clone HRC01515.
JD328336 - Sequence 309360 from Patent EP1572962.
JD316198 - Sequence 297222 from Patent EP1572962.
LF336205 - JP 2014500723-A/143708: Polycomb-Associated Non-Coding RNAs.
LF357544 - JP 2014500723-A/165047: Polycomb-Associated Non-Coding RNAs.
LF336206 - JP 2014500723-A/143709: Polycomb-Associated Non-Coding RNAs.
LF357543 - JP 2014500723-A/165046: Polycomb-Associated Non-Coding RNAs.
AK092833 - Homo sapiens cDNA FLJ35514 fis, clone SPLEN2000537.
AX747755 - Sequence 1280 from Patent EP1308459.
JD195341 - Sequence 176365 from Patent EP1572962.
JD470713 - Sequence 451737 from Patent EP1572962.
JD206662 - Sequence 187686 from Patent EP1572962.
JD135337 - Sequence 116361 from Patent EP1572962.
JD426646 - Sequence 407670 from Patent EP1572962.
JD153179 - Sequence 134203 from Patent EP1572962.
JD137118 - Sequence 118142 from Patent EP1572962.
LF357542 - JP 2014500723-A/165045: Polycomb-Associated Non-Coding RNAs.
JD205268 - Sequence 186292 from Patent EP1572962.
JD159733 - Sequence 140757 from Patent EP1572962.
JD159732 - Sequence 140756 from Patent EP1572962.
JD054415 - Sequence 35439 from Patent EP1572962.
JD335944 - Sequence 316968 from Patent EP1572962.
JD392738 - Sequence 373762 from Patent EP1572962.
JD399501 - Sequence 380525 from Patent EP1572962.
JD389372 - Sequence 370396 from Patent EP1572962.
JD374285 - Sequence 355309 from Patent EP1572962.
JD169865 - Sequence 150889 from Patent EP1572962.
JD439827 - Sequence 420851 from Patent EP1572962.
JD195934 - Sequence 176958 from Patent EP1572962.
JD361485 - Sequence 342509 from Patent EP1572962.
MA619514 - JP 2018138019-A/191440: Polycomb-Associated Non-Coding RNAs.
MA445833 - JP 2018138019-A/17759: Polycomb-Associated Non-Coding RNAs.
MA571778 - JP 2018138019-A/143704: Polycomb-Associated Non-Coding RNAs.
MA593124 - JP 2018138019-A/165050: Polycomb-Associated Non-Coding RNAs.
MA571779 - JP 2018138019-A/143705: Polycomb-Associated Non-Coding RNAs.
MA593122 - JP 2018138019-A/165048: Polycomb-Associated Non-Coding RNAs.
MA571780 - JP 2018138019-A/143706: Polycomb-Associated Non-Coding RNAs.
MA571782 - JP 2018138019-A/143708: Polycomb-Associated Non-Coding RNAs.
MA593121 - JP 2018138019-A/165047: Polycomb-Associated Non-Coding RNAs.
MA571783 - JP 2018138019-A/143709: Polycomb-Associated Non-Coding RNAs.
MA593120 - JP 2018138019-A/165046: Polycomb-Associated Non-Coding RNAs.
MA593119 - JP 2018138019-A/165045: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001170535, NP_001164007, Q9NVI7-2
UCSC ID: uc001aga.2
RefSeq Accession: NM_001170535
Protein: Q9NVI7-2, splice isoform of Q9NVI7 CCDS: CCDS53259.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ATAD3A:
hsp (Hereditary Spastic Paraplegia Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001170535.1
exon count: 16CDS single in 3' UTR: no RNA size: 2512
ORF size: 1761CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3218.00frame shift in genome: no % Coverage: 99.60
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: 0# 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.