Human Gene SMG5 (uc001foc.4) Description and Page Index
  Description: Homo sapiens smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans) (SMG5), mRNA.
RefSeq Summary (NM_015327): SMG5 is involved in nonsense-mediated mRNA decay (Ohnishi et al., 2003 [PubMed 14636577]).[supplied by OMIM, Mar 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC038296.1, SRR1803612.64849.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000361813.5/ ENSP00000355261.5 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:156,219,015-156,252,620 Size: 33,606 Total Exon Count: 22 Strand: -
Coding Region
   Position: hg19 chr1:156,220,378-156,252,471 Size: 32,094 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:156,219,015-156,252,620)mRNA (may differ from genome)Protein (1016 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SMG5_HUMAN
DESCRIPTION: RecName: Full=Protein SMG5; AltName: Full=EST1-like protein B; AltName: Full=LPTS-RP1; AltName: Full=LPTS-interacting protein; AltName: Full=SMG-5 homolog; Short=hSMG-5;
FUNCTION: Plays a role in nonsense-mediated mRNA decay. Does not have RNase activity by itself. Promotes dephosphorylation of UPF1. Together with SMG7 is thought to provide a link to the mRNA degradation machinery involving exonucleolytic pathways, and to serve as an adapter for UPF1 to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation. Necessary for TERT activity.
SUBUNIT: Interacts with TERT, PPP2CA and SMG1. Part of a complex that contains SMG1, SMG5, SMG7, PPP2CA, a short isoform of UPF3A (isoform UPF3AS, but not isoform UPF3AL) and phosphorylated UPF1. Not detected in complexes that contain unphosphorylated UPF1.
INTERACTION: Q92900-2:UPF1; NbExp=2; IntAct=EBI-3400861, EBI-373492;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Predominantly cytoplasmic, and nuclear. Shuttles between nucleus and cytoplasm. Detected in cytoplasmic mRNA decay bodies.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Contains 1 PINc domain.
SEQUENCE CAUTION: Sequence=BAA83041.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.08 RPKM in Pituitary
Total median expression: 1375.97 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -85.40149-0.573 Picture PostScript Text
3' UTR -640.601363-0.470 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
IPR018834 - DNA/RNA-bd_Est1-type
IPR019458 - EST1
IPR006596 - PINc_nuc-bd

Pfam Domains:
PF10373 - Est1 DNA/RNA binding domain
PF10374 - Telomerase activating protein Est1
PF13638 - PIN domain

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

2HWY
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9UPR3
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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 orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004540 ribonuclease activity
GO:0005515 protein binding
GO:0031625 ubiquitin protein ligase binding
GO:0042162 telomeric DNA binding
GO:0042826 histone deacetylase binding
GO:0043021 ribonucleoprotein complex binding
GO:0051721 protein phosphatase 2A binding
GO:0070034 telomerase RNA binding

Biological Process:
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0006406 mRNA export from nucleus
GO:0032204 regulation of telomere maintenance
GO:0032210 regulation of telomere maintenance via telomerase
GO:0035303 regulation of dephosphorylation
GO:0043487 regulation of RNA stability
GO:0090501 RNA phosphodiester bond hydrolysis

Cellular Component:
GO:0005634 nucleus
GO:0005697 telomerase holoenzyme complex
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC038296 - Homo sapiens Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans), mRNA (cDNA clone MGC:33341 IMAGE:4824487), complete cds.
AB085691 - Homo sapiens mRNA for SMG-5, complete cds.
AK092183 - Homo sapiens cDNA FLJ34864 fis, clone NT2NE2014028.
AX747396 - Sequence 921 from Patent EP1308459.
AB029012 - Homo sapiens KIAA1089 mRNA for KIAA1089 protein.
AY168922 - Homo sapiens Est1p-like protein B mRNA, complete cds.
AY336728 - Homo sapiens LPTS interacting protein (LPTSRP1) mRNA, complete cds.
KJ898480 - Synthetic construct Homo sapiens clone ccsbBroadEn_07874 SMG5 gene, encodes complete protein.
AB384108 - Synthetic construct DNA, clone: pF1KSDA1089, Homo sapiens SMG5 gene for Smg-5 homolog, nonsense mediated mRNA decay factor, complete cds, without stop codon, in Flexi system.
AK026395 - Homo sapiens cDNA: FLJ22742 fis, clone HUV00827.
AK025988 - Homo sapiens cDNA: FLJ22335 fis, clone HRC05856.
BC007292 - Homo sapiens Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans), mRNA (cDNA clone IMAGE:3349328).
AL137738 - Homo sapiens mRNA; cDNA DKFZp564M2163 (from clone DKFZp564M2163).
CR933677 - Homo sapiens mRNA; cDNA DKFZp781O0686 (from clone DKFZp781O0686).
BC007453 - Homo sapiens Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans), mRNA (cDNA clone IMAGE:3528110), partial cds.
AK027486 - Homo sapiens cDNA FLJ14580 fis, clone NT2RM4001204.
JD508958 - Sequence 489982 from Patent EP1572962.
JD178608 - Sequence 159632 from Patent EP1572962.
JD163483 - Sequence 144507 from Patent EP1572962.
JD338323 - Sequence 319347 from Patent EP1572962.
JD371669 - Sequence 352693 from Patent EP1572962.
JD515273 - Sequence 496297 from Patent EP1572962.
JD092261 - Sequence 73285 from Patent EP1572962.
JD233220 - Sequence 214244 from Patent EP1572962.
JD096178 - Sequence 77202 from Patent EP1572962.
JD218594 - Sequence 199618 from Patent EP1572962.
JD446619 - Sequence 427643 from Patent EP1572962.
JD396524 - Sequence 377548 from Patent EP1572962.
JD478992 - Sequence 460016 from Patent EP1572962.
JD498439 - Sequence 479463 from Patent EP1572962.
JD198927 - Sequence 179951 from Patent EP1572962.
JD479355 - Sequence 460379 from Patent EP1572962.
JD146888 - Sequence 127912 from Patent EP1572962.
JD485816 - Sequence 466840 from Patent EP1572962.
JD455193 - Sequence 436217 from Patent EP1572962.
JD269896 - Sequence 250920 from Patent EP1572962.
JD354104 - Sequence 335128 from Patent EP1572962.
JD282033 - Sequence 263057 from Patent EP1572962.
JD107123 - Sequence 88147 from Patent EP1572962.
JD153361 - Sequence 134385 from Patent EP1572962.
JD190656 - Sequence 171680 from Patent EP1572962.
JD270657 - Sequence 251681 from Patent EP1572962.
JD118691 - Sequence 99715 from Patent EP1572962.
JD151538 - Sequence 132562 from Patent EP1572962.
JD055967 - Sequence 36991 from Patent EP1572962.
JD444619 - Sequence 425643 from Patent EP1572962.
JD539838 - Sequence 520862 from Patent EP1572962.
JD309068 - Sequence 290092 from Patent EP1572962.
JD365313 - Sequence 346337 from Patent EP1572962.
JD317187 - Sequence 298211 from Patent EP1572962.
JD260420 - Sequence 241444 from Patent EP1572962.
JD432188 - Sequence 413212 from Patent EP1572962.
DQ589410 - Homo sapiens piRNA piR-56522, complete sequence.
JD475783 - Sequence 456807 from Patent EP1572962.
JD106179 - Sequence 87203 from Patent EP1572962.
JD341848 - Sequence 322872 from Patent EP1572962.
JD535861 - Sequence 516885 from Patent EP1572962.
JD414152 - Sequence 395176 from Patent EP1572962.
JD118921 - Sequence 99945 from Patent EP1572962.
JD200229 - Sequence 181253 from Patent EP1572962.

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

Protein Q9UPR3 (Reactome details) participates in the following event(s):

R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-927802 Nonsense-Mediated Decay (NMD)
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: D3DVB7, EST1B, KIAA1089, NM_015327, NP_056142, Q5QJE7, Q659C7, Q8IXC0, Q8IY09, Q96IJ7, Q9UPR3, SMG5_HUMAN
UCSC ID: uc001foc.4
RefSeq Accession: NM_015327
Protein: Q9UPR3 (aka SMG5_HUMAN)
CCDS: CCDS1137.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015327.2
exon count: 22CDS single in 3' UTR: no RNA size: 4577
ORF size: 3051CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6209.00frame shift in genome: no % Coverage: 99.69
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.