Human Gene NMD3 (uc003feb.1) Description and Page Index
  Description: Homo sapiens NMD3 homolog (S. cerevisiae) (NMD3), mRNA.
RefSeq Summary (NM_015938): Ribosomal 40S and 60S subunits associate in the nucleolus and are exported to the cytoplasm. The protein encoded by this gene is involved in the passage of the 60S subunit through the nuclear pore complex and into the cytoplasm. Several transcript variants exist for this gene, but the full-length natures of only two have been described to date. [provided by RefSeq, Feb 2016].
Transcript (Including UTRs)
   Position: hg19 chr3:160,939,099-160,969,795 Size: 30,697 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr3:160,939,802-160,968,698 Size: 28,897 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:160,939,099-160,969,795)mRNA (may differ from genome)Protein (503 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
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neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: NMD3_HUMAN
DESCRIPTION: RecName: Full=60S ribosomal export protein NMD3; Short=hNMD3;
FUNCTION: Acts as an adapter for the XPO1/CRM1-mediated export of the 60S ribosomal subunit.
SUBUNIT: Found in a 60S ribosomal subunit export complex with RAN and XPO1. Interacts with XPO1. Associates with the 60S ribosomal subunit.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleoplasm. Nucleus, nucleolus. Note=Shuttles between the nucleus/nucleolus and the cytoplasm in a XPO1/CRM1-dependent manner.
SIMILARITY: Belongs to the NMD3 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NMD3
CDC HuGE Published Literature: NMD3
Positive Disease Associations: Body Weight
Related Studies:
  1. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.

-  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: 19.04 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 429.90 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 -44.60119-0.375 Picture PostScript Text
3' UTR -247.301097-0.225 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
IPR007064 - NMD3

Pfam Domains:
PF04981 - NMD3 family

ModBase Predicted Comparative 3D Structure on Q96D46
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0030674 protein binding, bridging
GO:0043023 ribosomal large subunit binding

Biological Process:
GO:0000055 ribosomal large subunit export from nucleus
GO:0015031 protein transport
GO:0032092 positive regulation of protein binding
GO:1902680 positive regulation of RNA biosynthetic process
GO:1904751 positive regulation of protein localization to nucleolus

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK225664 - Homo sapiens mRNA for NMD3 homolog, clone: STM05655.
AK308865 - Homo sapiens cDNA, FLJ98906.
BC013317 - Homo sapiens NMD3 homolog (S. cerevisiae), mRNA (cDNA clone MGC:13335 IMAGE:4291797), complete cds.
LF383796 - JP 2014500723-A/191299: Polycomb-Associated Non-Coding RNAs.
AF132941 - Homo sapiens CGI-07 protein mRNA, complete cds.
AK296710 - Homo sapiens cDNA FLJ57520 complete cds, highly similar to Homo sapiens NMD3 homolog (NMD3), mRNA.
AK094749 - Homo sapiens cDNA FLJ37430 fis, clone BRAWH2001679, highly similar to Homo sapiens NMD3 homolog (NMD3), mRNA.
EU832674 - Synthetic construct Homo sapiens clone HAIB:100067703; DKFZo008H0831 NMD3 homolog (S. cerevisiae) protein (NMD3) gene, encodes complete protein.
EU832753 - Synthetic construct Homo sapiens clone HAIB:100067782; DKFZo004H0832 NMD3 homolog (S. cerevisiae) protein (NMD3) gene, encodes complete protein.
KJ893795 - Synthetic construct Homo sapiens clone ccsbBroadEn_03189 NMD3 gene, encodes complete protein.
AK021775 - Homo sapiens cDNA FLJ11713 fis, clone HEMBA1005201, highly similar to Homo sapiens NMD3 homolog (NMD3), mRNA.
MA619373 - JP 2018138019-A/191299: Polycomb-Associated Non-Coding RNAs.
CU680564 - Synthetic construct Homo sapiens gateway clone IMAGE:100019705 5' read NMD3 mRNA.
LF351838 - JP 2014500723-A/159341: Polycomb-Associated Non-Coding RNAs.
LF351839 - JP 2014500723-A/159342: Polycomb-Associated Non-Coding RNAs.
LF351846 - JP 2014500723-A/159349: Polycomb-Associated Non-Coding RNAs.
MA587415 - JP 2018138019-A/159341: Polycomb-Associated Non-Coding RNAs.
MA587416 - JP 2018138019-A/159342: Polycomb-Associated Non-Coding RNAs.
MA587423 - JP 2018138019-A/159349: Polycomb-Associated Non-Coding RNAs.
LF351848 - JP 2014500723-A/159351: Polycomb-Associated Non-Coding RNAs.
LF351852 - JP 2014500723-A/159355: Polycomb-Associated Non-Coding RNAs.
AK024706 - Homo sapiens cDNA: FLJ21053 fis, clone CAS00524, highly similar to AF132941 Homo sapiens CGI-07 protein mRNA.
LF351853 - JP 2014500723-A/159356: Polycomb-Associated Non-Coding RNAs.
LF351854 - JP 2014500723-A/159357: Polycomb-Associated Non-Coding RNAs.
JD087278 - Sequence 68302 from Patent EP1572962.
JD536681 - Sequence 517705 from Patent EP1572962.
LF351855 - JP 2014500723-A/159358: Polycomb-Associated Non-Coding RNAs.
JD557576 - Sequence 538600 from Patent EP1572962.
LF351856 - JP 2014500723-A/159359: Polycomb-Associated Non-Coding RNAs.
JD501739 - Sequence 482763 from Patent EP1572962.
JD082490 - Sequence 63514 from Patent EP1572962.
JD088285 - Sequence 69309 from Patent EP1572962.
JD265793 - Sequence 246817 from Patent EP1572962.
MA587425 - JP 2018138019-A/159351: Polycomb-Associated Non-Coding RNAs.
MA587429 - JP 2018138019-A/159355: Polycomb-Associated Non-Coding RNAs.
MA587430 - JP 2018138019-A/159356: Polycomb-Associated Non-Coding RNAs.
MA587431 - JP 2018138019-A/159357: Polycomb-Associated Non-Coding RNAs.
MA587432 - JP 2018138019-A/159358: Polycomb-Associated Non-Coding RNAs.
MA587433 - JP 2018138019-A/159359: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: CGI-07, D3DNM7, NMD3_HUMAN, NM_015938, NP_057022, Q96D46, Q9Y2Z6
UCSC ID: uc003feb.1
RefSeq Accession: NM_015938
Protein: Q96D46 (aka NMD3_HUMAN)
CCDS: CCDS3194.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015938.3
exon count: 16CDS single in 3' UTR: no RNA size: 2758
ORF size: 1512CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2631.00frame shift in genome: no % Coverage: 98.91
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: 1117# 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.