Human Gene GEMIN5 (uc003lvx.3) Description and Page Index
  Description: Homo sapiens gem (nuclear organelle) associated protein 5 (GEMIN5), transcript variant 1, mRNA.
RefSeq Summary (NM_015465): This gene encodes a WD repeat protein that is a component of the survival of motor neurons (SMN) complex. The SMN complex plays a critical role in mRNA splicing through the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs), and may also mediate the assembly and transport of other classes of ribonucleoproteins. The encoded protein is the snRNA-binding component of the SMN complex. Dysregulation of this gene may play a role in alternative mRNA splicing and tumor cell motility. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011].
Transcript (Including UTRs)
   Position: hg19 chr5:154,266,976-154,317,776 Size: 50,801 Total Exon Count: 28 Strand: -
Coding Region
   Position: hg19 chr5:154,267,770-154,317,693 Size: 49,924 Coding Exon Count: 28 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:154,266,976-154,317,776)mRNA (may differ from genome)Protein (1508 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: GEMI5_HUMAN
DESCRIPTION: RecName: Full=Gem-associated protein 5; Short=Gemin5;
FUNCTION: The SMN complex plays an essential role in spliceosomal snRNP assembly in the cytoplasm and is required for pre-mRNA splicing in the nucleus. GEMIN5 acts as the snRNA-binding protein of the SMN complex.
SUBUNIT: Part of the core SMN complex that contains SMN1, SIP1/GEMIN2, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8 and STRAP/UNRIP. Interacts directly with SMN1, SNRPB, SNRPD1, SNRPD2, SNRPD3 and SNRPE.
INTERACTION: P06730:EIF4E; NbExp=3; IntAct=EBI-443630, EBI-73440; Q16637:SMN2; NbExp=7; IntAct=EBI-443630, EBI-395421; P62304:SNRPE; NbExp=2; IntAct=EBI-443630, EBI-348082;
SUBCELLULAR LOCATION: Nucleus, nucleoplasm. Nucleus, gem. Cytoplasm. Note=Found both in the nucleoplasm and in nuclear bodies called gems (Gemini of Cajal bodies) that are often in proximity to Cajal (coiled) bodies. Also found in the cytoplasm.
SIMILARITY: Belongs to the WD repeat gemin-5 family.
SIMILARITY: Contains 13 WD repeats.
SEQUENCE CAUTION: Sequence=BAB84892.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GEMIN5
CDC HuGE Published Literature: GEMIN5
Positive Disease Associations: Cholesterol, HDL , Respiratory Function Tests
Related Studies:
  1. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  2. Respiratory Function Tests
    Jemma B Wilk et al. BMC medical genetics 2007, Framingham Heart Study genome-wide association: results for pulmonary function measures., BMC medical genetics. [PubMed 17903307]
    GSTO2 and IL6R are credible candidate genes for association to pulmonary function identified by GWA. These and other observed associations warrant replication studies. This resource of GWA results for pulmonary function measures is publicly available at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite.

-  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: 10.11 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 219.21 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 -29.7083-0.358 Picture PostScript Text
3' UTR -198.62794-0.250 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
IPR020472 - G-protein_beta_WD-40_rep
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat
PF12894 - Anaphase-promoting complex subunit 4 WD40 domain

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q8TEQ6
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000340 RNA 7-methylguanosine cap binding
GO:0003723 RNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0005515 protein binding
GO:0017069 snRNA binding
GO:0030619 U1 snRNA binding
GO:0030621 U4 snRNA binding
GO:0030622 U4atac snRNA binding
GO:0043022 ribosome binding

Biological Process:
GO:0000387 spliceosomal snRNP assembly
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0006412 translation
GO:0006417 regulation of translation
GO:0008380 RNA splicing
GO:0051170 nuclear import
GO:0065003 macromolecular complex assembly

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0016604 nuclear body
GO:0032797 SMN complex
GO:0034718 SMN-Gemin2 complex
GO:0034719 SMN-Sm protein complex
GO:0097504 Gemini of coiled bodies
GO:0022625 cytosolic large ribosomal subunit


-  Descriptions from all associated GenBank mRNAs
  AL117665 - Homo sapiens mRNA; cDNA DKFZp586M1824 (from clone DKFZp586M1824).
AK074066 - Homo sapiens mRNA for FLJ00137 protein.
BC008776 - Homo sapiens gem (nuclear organelle) associated protein 5, mRNA (cDNA clone IMAGE:3143002), partial cds.
BC014147 - Homo sapiens gem (nuclear organelle) associated protein 5, mRNA (cDNA clone IMAGE:2989451), partial cds.
BC113614 - Homo sapiens gem (nuclear organelle) associated protein 5, mRNA (cDNA clone MGC:142174 IMAGE:8322666), complete cds.
BC143724 - Homo sapiens gem (nuclear organelle) associated protein 5, mRNA (cDNA clone MGC:177255 IMAGE:9052238), complete cds.
AY063750 - Homo sapiens WD repeat protein Gemin5 mRNA, complete cds.
AK315101 - Homo sapiens cDNA, FLJ96059.
AB385260 - Synthetic construct DNA, clone: pF1KF0137, Homo sapiens GEMIN5 gene for gem-associated protein 5, complete cds, without stop codon, in Flexi system.
BC036894 - Homo sapiens gem (nuclear organelle) associated protein 5, mRNA (cDNA clone IMAGE:5499572), partial cds.
BC040931 - Homo sapiens, clone IMAGE:4536624, mRNA.
AK022748 - Homo sapiens cDNA FLJ12686 fis, clone NT2RM4002527, weakly similar to VEGETATIBLE INCOMPATIBILITY PROTEIN HET-E-1.
JD022476 - Sequence 3500 from Patent EP1572962.
JD027915 - Sequence 8939 from Patent EP1572962.
JD051916 - Sequence 32940 from Patent EP1572962.
JD279125 - Sequence 260149 from Patent EP1572962.
JD262962 - Sequence 243986 from Patent EP1572962.

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

Protein Q8TEQ6 (Reactome details) participates in the following event(s):

R-HSA-191830 snRNP nuclear import and release
R-HSA-191790 Loading and methylation of Sm proteins onto SMN Complexes
R-HSA-191786 snRNP complex assembly
R-HSA-191763 snRNP:Snurportin complex formation
R-HSA-191784 snRNA Cap hypermethylation
R-HSA-191859 snRNP Assembly
R-HSA-194441 Metabolism of non-coding RNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: GEMI5_HUMAN, NM_015465, NP_056280, Q14CV0, Q8TEQ6, Q8WWV4, Q969W4, Q9H9K3, Q9UFI5
UCSC ID: uc003lvx.3
RefSeq Accession: NM_015465
Protein: Q8TEQ6 (aka GEMI5_HUMAN or GEM5_HUMAN)
CCDS: CCDS4330.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015465.4
exon count: 28CDS single in 3' UTR: no RNA size: 5404
ORF size: 4527CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9251.00frame shift in genome: no % Coverage: 100.00
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.