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SMDT1 Gene

protein-coding   GIFtS: 34
GCID: GC22P042476

Single-Pass Membrane Protein With Aspartate-Rich Tail 1

(Previous name: chromosome 22 open reading frame 32)
(Previous symbol: C22orf32)
  Search for SMDT1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Single-Pass Membrane Protein With Aspartate-Rich Tail 11 2     DDDD2
C22orf321 2 3 5     dJ186O1.12
EMRE2 3 5     Essential MCU Regulator, Mitochondrial2
Single-Pass Membrane Protein With Aspartate-Rich Tail 1, Mitochondrial2 3     UPF0466 Protein C22orf32, Mitochondrial2
Chromosome 22 Open Reading Frame 321     

External Ids:    HGNC: 250551   Entrez Gene: 916892   Ensembl: ENSG000001831727   OMIM: 6155885   UniProtKB: Q9H4I93   

Export aliases for SMDT1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SMDT1 Gene:
SMDT1 (single-pass membrane protein with aspartate-rich tail 1) is a protein-coding gene.

UniProtKB/Swiss-Prot: EMRE_HUMAN, Q9H4I9
Function: Essential regulatory subunit of the mitochondrial calcium uniporter complex (uniplex), a complex that
mediates calcium uptake into mitochondria. Required to bridge the calcium-sensing proteins MICU1 and MICU2 with
the calcium-conducting subunit MCU




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000022.11  NC_018933.2  NT_011520.13  NT_187682.1  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SMDT1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMDT1 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMDT1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 22q13.2   Ensembl cytogenetic band:  22q13.2   HGNC cytogenetic band: 22q13.2

SMDT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMDT1 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P042476:  view genomic region     (about GC identifiers)

Start:
42,475,695 bp from pter      End:
42,480,288 bp from pter
Size:
4,594 bases      Orientation:
plus strand

1 alternative location:
Chr22+,NW_003315971 1-2,325     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
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UniProtKB/Swiss-Prot: EMRE_HUMAN, Q9H4I9 (See protein sequence)
Recommended Name: Essential MCU regulator, mitochondrial precursor  
Size: 107 amino acids; 11441 Da
Subunit: Component of the uniplex complex, composed of MCU, MCUB, MICU1, MICU2 and EMRE/SMDT1
Secondary accessions: B2R5D1 Q8TAB9

Explore the universe of human proteins at neXtProt for SMDT1: NX_Q9H4I9

Explore proteomics data for SMDT1 at MOPED


See SMDT1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_201575.3  
ENSEMBL proteins: 
 ENSP00000402623   ENSP00000327467  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR018782 UPF0466

Graphical View of Domain Structure for InterPro Entry Q9H4I9

ProtoNet protein and cluster: Q9H4I9

UniProtKB/Swiss-Prot: EMRE_HUMAN, Q9H4I9
Similarity: Belongs to the SMDT1/EMRE family


SMDT1 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: EMRE_HUMAN, Q9H4I9
Function: Essential regulatory subunit of the mitochondrial calcium uniporter complex (uniplex), a complex that
mediates calcium uptake into mitochondria. Required to bridge the calcium-sensing proteins MICU1 and MICU2 with
the calcium-conducting subunit MCU

Phenotypes:
     1 GenomeRNAi human phenotype for SMDT1:

 Decreased viability with pacli 

     1 MGI phenotypic allele for 1500032L24Rik (no phenotypes)

SMDT1 for phenotypes           About GeneDecksing

Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
EMRE_HUMAN, Q9H4I9: Mitochondrion inner membrane; Single-pass membrane protein

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005739mitochondrion ----
GO:0016021integral component of membrane ----
GO:0031305integral component of mitochondrial inner membrane IDA--
GO:1990246uniplex complex IDA--

SMDT1 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SMDT1
Interactions:

    Search GeneGlobe Interaction Network for SMDT1

Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006851mitochondrial calcium ion transport IMP--
GO:0051560mitochondrial calcium ion homeostasis IMP--

SMDT1 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Tocris compounds for SMDT1 (EMRE)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for SMDT1 gene: 
NM_033318.4  

Unigene Cluster for SMDT1:

Single-pass membrane protein with aspartate-rich tail 1
Hs.306083  [show with all ESTs]
Unigene Representative Sequence: NM_033318
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000422252 ENST00000331479(uc003bca.3) ENST00000484235
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Additional mRNA sequence: 

AK312142.1 AL449243.1 BC024237.2 CR456453.1 

9 DOTS entries:

DT.415825  DT.95241308  DT.95375085  DT.100810411  DT.102836323  DT.120644859  DT.95253705  DT.91757809 
DT.99961342 

Selected AceView cDNA sequences (see all 262):

BQ184354 AI298371 F02766 BF507413 AW043630 BM767050 CR596524 BM704386 
AA042989 CR612282 H95219 F26599 CR597807 CA848372 BU726452 BU734488 
BQ217986 AI493681 AJ713576 AW025601 BU161537 AL449243 AI277646 CR617408 

GeneLoc Exon Structure

3 Alternative Splicing Database (ASD) splice patterns (SP) for SMDT1    About this scheme

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b
SP1:              -     -               
SP2:                    -               
SP3:                                    


ECgene alternative splicing isoforms for SMDT1

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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SMDT1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SMDT1 Expression
About this image

SMDT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SMDT1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.306083
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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for SMDT1 gene from Selected species (see all 14)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia 1500032L24Rik5
Smdt11
RIKEN cDNA 1500032L24 gene5
single-pass membrane protein with aspartate rich tail more1
85.15(n)1
80.2(a)1
  15 (38.56 cM)5
690291  NM_026914.11  NP_081190.11 
 823389595 
chicken
(Gallus gallus)
Aves C22ORF321 chromosome 1 open reading frame, human C22orf32 66.67(n)
75.58(a)
  770755  XM_001233648.3  XP_001233649.1 
lizard
(Anolis carolinensis)
Reptilia SMDT16
single-pass membrane protein with aspartate-rich t...
61(a)
1 ↔ 1
5(27093313-27095283)
African clawed frog
(Xenopus laevis)
Amphibia 480375402   -- 75.24(n)    48037540 
zebrafish
(Danio rerio)
Actinopterygii Dr.294722 Transcribed sequence with weak similarity to protein more 79.9(n)    CK395719.1 
fruit fly
(Drosophila melanogaster)
Insecta CG176806
--
43(a)
1 ↔ 1
2R(14034802-14035499)


ENSEMBL Gene Tree for SMDT1 (if available)
TreeFam Gene Tree for SMDT1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SMDT1 (see all 107)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1916015061,2
--42475948(+) GCCCAA/GACCGG 2 K R mis10--------
rs1825383231,2
C--42475971(+) TCCTCC/TTGGAG 1 -- int10--------
rs1857740811,2
C--42476004(+) AATCAC/TTGTGG 1 -- int10--------
rs1897371551,2
--42476224(+) CTGGAA/GTCAGA 1 -- int10--------
rs1181425711,2
F--42476307(+) TGAAAT/AATGAA 1 -- int11Minor allele frequency- A:0.01NA 120
rs738879201,2
C,F--42476415(+) TAGATG/ATGCAG 1 -- int12Minor allele frequency- A:0.07WA 120
rs1475776641,2
--42476429(+) ATTATG/TACAAT 1 -- int10--------
rs1824020521,2
--42476553(+) TTTTTC/GCAACA 1 -- int10--------
rs1887161841,2
--42476595(+) GGGAAA/TACGGA 1 -- int10--------
rs59961071,2
C,F,A,H--42476688(+) AAGCTA/GGTCTA 1 -- int18Minor allele frequency- G:0.10NS EA NA WA CSA 542

HapMap Linkage Disequilibrium report for SMDT1 (42475695 - 42480288 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SMDT1: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SMDT1
DNA2.0 Custom Variant and Variant Library Synthesis for SMDT1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 615588    OMIM disorders: --


SMDT1 for disorders           About GeneDecksing


Export disorders for SMDT1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for SMDT1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SMDT1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. EMRE is an essential component of the mitochondrial calcium uniporter complex. (PubMed id 24231807)1, 2 Sancak Y.... Mootha V.K. (Science 2013)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  6. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1 Collins J.E.... Dunham I. (Genome Biol. 2004)
  7. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. (PubMed id 12529303)2 Collins J.E.... Dunham I. (Genome Res. 2003)
  8. The DNA sequence of human chromosome 22. (PubMed id 10591208)2 Dunham I.... Wright H. (Nature 1999)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 91689 HGNC: 25055 AceView: LOC91689 Ensembl:ENSG00000183172 euGenes: HUgn91689
ECgene: SMDT1 H-InvDB: SMDT1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SMDT1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SMDT1 gene:
Search GeneIP for patents involving SMDT1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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