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SHISA4 Gene

protein-coding   GIFtS: 43
GCID: GC01P201857

Shisa Family Member 4

(Previous names: chromosome 1 open reading frame 40, transmembrane protein...)
(Previous symbols: C1orf40, TMEM58)
  Search for SHISA4
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
Shisa Family Member 41 2     Chromosome 1 Open Reading Frame 401
Transmembrane Protein 581 2 3     Shisa Homolog 4 (Xenopus Laevis)1
C1orf401 2 3     Protein Shisa-42
TMEM581 2 3     Shisa Homolog 42

External Ids:    HGNC: 271391   Entrez Gene: 1493452   Ensembl: ENSG000001988927   UniProtKB: Q96DD73   

Export aliases for SHISA4 gene to outside databases

Previous GC identifers: GC01P200126 GC01P173023


(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 SHISA4 Gene:
SHISA4 (shisa family member 4) is a protein-coding gene.


(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_000001.11  NT_004487.20  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SHISA4 gene promoter:
         TBP   AP-1   p53   Pax-5   SREBP-1c   AP-4   SREBP-1b   SREBP-1a   GATA-6   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSHISA4 promoter sequence
   Search Chromatin IP Primers for SHISA4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SHISA4


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

Entrez Gene cytogenetic band: 1q32.1   Ensembl cytogenetic band:  1q32.1   HGNC cytogenetic band: 1q32.1

SHISA4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHISA4 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P201857:  view genomic region     (about GC identifiers)

Start:
201,857,797 bp from pter      End:
201,861,715 bp from pter
Size:
3,919 bases      Orientation:
plus strand

(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.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SHSA4_HUMAN, Q96DD7 (See protein sequence)
Recommended Name: Protein shisa-4 precursor  
Size: 197 amino acids; 21522 Da
Sequence caution: Sequence=AAH09558.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: B4DFI0 B7ZAJ7 Q5VUU1 Q6P711 Q6UWY7

Explore the universe of human proteins at neXtProt for SHISA4: NX_Q96DD7

Explore proteomics data for SHISA4 at MOPED


See SHISA4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_937792.2  
ENSEMBL proteins: 
 ENSP00000355064  

SHISA4 Human Recombinant Protein Products:

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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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HGNC Gene Families:
SHISA: Shisa homologs

1 InterPro protein domain:
 IPR026910 Shisa

Graphical View of Domain Structure for InterPro Entry Q96DD7

ProtoNet protein and cluster: Q96DD7

UniProtKB/Swiss-Prot: SHSA4_HUMAN, Q96DD7
Similarity: Belongs to the shisa family


SHISA4 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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Phenotypes:
     1 MGI mutant phenotype (inferred from 1 allele(MGI details for Shisa4):
 normal 

SHISA4 for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-out Shisa4tm1Sia for SHISA4

   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SHISA4
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miRNA
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hsa-mir-335-5p (MIRT018206)

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8 qRT-PCR Assays for microRNAs that regulate SHISA4:
hsa-miR-4283 hsa-miR-361-3p hsa-miR-922 hsa-miR-3151 hsa-miR-486-3p hsa-miR-548c-3p hsa-miR-3179 hsa-miR-150
SwitchGear 3'UTR luciferase reporter plasmidSHISA4 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat SHISA4

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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
SHSA4_HUMAN, Q96DD7: Membrane; Single-pass type I membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
plasma membrane2

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--

SHISA4 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 SHISA4
Interactions:

    Search GeneGlobe Interaction Network for SHISA4

(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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for SHISA4 (SHSA4)



(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 SHISA4 gene: 
NM_198149.2  

Unigene Cluster for SHISA4:

Shisa homolog 4 (Xenopus laevis)
Hs.632471  [show with all ESTs]
Unigene Representative Sequence: NM_198149
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000464117 ENST00000362011(uc021phk.1 uc001gxa.3) ENST00000481699

miRNA
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8 qRT-PCR Assays for microRNAs that regulate SHISA4:
hsa-miR-4283 hsa-miR-361-3p hsa-miR-922 hsa-miR-3151 hsa-miR-486-3p hsa-miR-548c-3p hsa-miR-3179 hsa-miR-150
SwitchGear 3'UTR luciferase reporter plasmidSHISA4 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat SHISA4
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Primer
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  QuantiTect SYBR Green Assays in human, mouse, rat SHISA4
  QuantiFast Probe-based Assays in human, mouse, rat SHISA4

Additional mRNA sequence: 

AK294106.1 AK316312.1 AY358589.1 BC009558.1 BC061908.1 BC104444.1 BC104445.1 BC111855.1 
NR_030775.1 

10 DOTS entries:

DT.100661984  DT.444192  DT.121416855  DT.102823138  DT.92421985  DT.92421982  DT.95195795  DT.95271096 
DT.97802459  DT.100786971 

Selected AceView cDNA sequences (see all 131):

BU738586 BE883522 BM714345 BF726572 AI740814 CR626801 AI624511 AI494502 
AI571396 AI366530 BM671894 AI361652 AI470980 CF127715 BC009558 BG151538 
AI473362 CK904415 BI753594 AI015586 BU726557 BQ084146 BM713135 AI167701 

GeneLoc Exon Structure


(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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SHISA4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TCTCTGCTGC
SHISA4 Expression
About this image

SHISA4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SHISA4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.632471
    Custom PCR Arrays for SHISA4
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SHISA4

(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 chordates.

Orthologs for SHISA4 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Shisa41 , 5 shisa homolog 4 (Xenopus laevis)1, 5 90.74(n)1
91.11(a)1
  1 (58.58 cM)5
775521  NM_175259.41  NP_780468.11 
 1353710575 
lizard
(Anolis carolinensis)
Reptilia SHISA46
shisa family member 4
63(a)
1 ↔ 1
4(133635082-133645251)
tropical clawed frog
(Xenopus tropicalis)
Amphibia shisa41 shisa family member 4 60.2(n)
55.76(a)
  780140  NM_001079215.1  NP_001072683.1 
zebrafish
(Danio rerio)
Actinopterygii shisa41 shisa homolog 4 (Xenopus laevis) 58.33(n)
53.12(a)
  550567  NM_001017869.1  NP_001017869.1 


ENSEMBL Gene Tree for SHISA4 (if available)
TreeFam Gene Tree for SHISA4 (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 SHISA4 (see all 132)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1492392961,2
--201855874(+) CATTAC/TGGCGA 2 -- us2k10--------
rs1885492931,2
--201855898(+) CAGCTC/GTCCAT 2 -- us2k10--------
rs1812525391,2
--201856090(+) TGGTGC/TGTGCT 2 -- us2k10--------
rs1469365731,2
--201856149(+) GAGGGC/TGTGTC 2 -- us2k10--------
rs26441351,2
C,F,A,H--201856256(+) GTTTGG/CTTTGC 2 -- us2k112Minor allele frequency- C:0.28NA WA CSA EA 374
rs789975821,2
C,F--201856261(+) CTTTGC/GTTTGC 2 -- us2k12Minor allele frequency- G:0.10WA 120
rs1381728101,2
--201856288(+) GAGACA/TTGAGA 2 -- us2k10--------
rs1151647801,2
C,F--201856382(+) GTCAAG/CGGTAC 2 -- us2k11Minor allele frequency- C:0.04WA 118
rs1437358831,2
--201856389(+) GTACAC/TATGGG 2 -- us2k10--------
rs749639961,2
C,F--201856451(+) CAACAA/GTGACA 2 -- us2k11Minor allele frequency- G:0.07WA 118

HapMap Linkage Disequilibrium report for SHISA4 (201857797 - 201861715 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for SHISA4:    About this table    
Variant IDTypeSubtypePubMed ID
nsv521567CNV Loss19592680

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SHISA4
DNA2.0 Custom Variant and Variant Library Synthesis for SHISA4

(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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(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 SHISA4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SHISA4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2, 3 Clark H.F.... Gray A.M. (Genome Res. 2003)
  2. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  4. Mouse homologues of Shisa antagonistic to Wnt and Fgf signalings. (PubMed id 17481602)1 Furushima K....Aizawa S. (Dev. Biol. 2007)
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(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: 149345 HGNC: 27139 AceView: C1orf40 Ensembl:ENSG00000198892 euGenes: HUgn149345
ECgene: SHISA4 H-InvDB: SHISA4

(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 SHISA4 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 SHISA4 gene:
Search GeneIP for patents involving SHISA4

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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 Antibodies for SHISA4
 See all of Abcam's Antibodies, Kits and Proteins for SHISA4
 Custom Antibody / Protein Production Service
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 Abcam protocols and scientific support
 Browse ProSpec Recombinant Proteins
 Proteins for SHISA4
 Antibodies for SHISA4
 ELISAs for SHISA4
 CLIAs for SHISA4



 Browse ESI BIO Cell Lines and PureStem Progenitors for SHISA4
 Gene Synthesis
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 Variant Library Synthesis
 Codon Optimization
 Protein Production and Purification
 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SHISA4
 SwitchGear 3'UTR luciferase reporter plasmids for SHISA4
 SwitchGear Promoter luciferase reporter plasmids for SHISA4
 ThermoFisher Antibodies for SHISA4
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SHISA4
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SHISA4
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SHISA4
 LSBio Antibodies in human, mouse, rat for SHISA4
Customized transgenic rodents for:
 Humanization
 Biomarker expression
 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
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 Browse compounds at ApexBio
       
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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