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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

C22orf28 Gene

protein-coding   GIFtS: 47
GCID: GC22M032783

chromosome 22 open reading frame 28

 Explore 4 diseases affiliated with
C22orf28 via our new
 Human Malady Compendium 
Biological research products
for C22orf28
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Chromosome 22 Open Reading Frame 281 2     Ankyrin Repeat Domain 542
FAAP1 2     Focal Adhesion-Associated Protein2
HSPC1171     TRNA-Splicing Ligase RtcB Homolog2
DJ149A16.62     EC 6.5.1.33
RP1-149A16.62     

External Ids:    HGNC: 269351   Entrez Gene: 514932   Ensembl: ENSG000001002207   OMIM: 6139015   UniProtKB: Q9Y3I03   

Export aliases for C22orf28 gene to outside databases

Previous GC identifers: GC22M031113 GC22M015740


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: RTCB_HUMAN, Q9Y3I0
Function: Catalytic subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to
mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a
canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward
other RNAs




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000022.10  NC_018933.1  NT_011520.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C22orf28 gene promoter:
         NF-AT   NF-AT4   PPAR-gamma1   NF-AT2   SEF-1 (1)   FOXO1a   NF-AT3   PPAR-gamma2   FOXO1   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidC22orf28 promoter sequence
   Search SABiosciences Chromatin IP Primers for C22orf28

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C22orf28


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

Entrez Gene cytogenetic band: 22q12   Ensembl cytogenetic band:  22q12.3   HGNC cytogenetic band: 22q12.3

C22orf28 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C22orf28 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M032783:  view genomic region     (about GC identifiers)

Start:
32,783,562 bp from pter      End:
32,808,274 bp from pter
Size:
24,713 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: RTCB_HUMAN, Q9Y3I0 (See protein sequence)
Recommended Name: tRNA-splicing ligase RtcB homolog  
Size: 505 amino acids; 55210 Da
Subunit: Catalytic component of the tRNA-splicing ligase complex
Subcellular location: Cytoplasm (By similarity)
Sequence caution: Sequence=AAF29081.1; Type=Frameshift; Positions=295, 298; Sequence=AAF67477.1; Type=Frameshift;
Positions=173, 180;
Secondary accessions: B2R6A8 Q6IAI0 Q9BWL4 Q9NTH1 Q9P037 Q9P0J3

Explore the universe of human proteins at neXtProt for C22orf28: NX_Q9Y3I0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9Y3I0

  • C22orf28 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_055121.1  
    ENSEMBL proteins: 
     ENSP00000216038   ENSP00000413466  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for C22orf28

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0072669tRNA-splicing ligase complex IDA--


    C22orf28 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for C22orf28


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    C22orf28 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR001233 RtcB_family

    Graphical View of Domain Structure for InterPro Entry Q9Y3I0

    ProtoNet protein and cluster: Q9Y3I0

    1 Blocks protein family: IPB001233 Protein of unknown function UPF0027

    UniProtKB/Swiss-Prot: RTCB_HUMAN, Q9Y3I0
    Similarity: Belongs to the RtcB family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: RTCB_HUMAN, Q9Y3I0
    Function: Catalytic subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to
    mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a
    canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward
    other RNAs
    Catalytic activity: ATP + (ribonucleotide)(n) + (ribonucleotide)(m) = AMP + diphosphate + (ribonucleotide)(n+m)

    Enzyme Number (IUBMB): EC 6.5.1.31

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate C22orf28:
    hsa-miR-455-3p
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C22orf28

    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003972RNA ligase (ATP) activity IDA--
    GO:0005524ATP binding IEA--
    GO:0017166vinculin binding IPI15163412
    GO:0046872metal ion binding IEA--


    C22orf28 for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C22orf28

    STRING Interaction Network Preview (showing 5 interactants - click image to see 17)

    5/785 Interacting proteins for C22orf28 (Q9Y3I02, 3 ENSP000002160384) via UniProtKB, MINT, STRING, and/or I2D (see all 785)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NSFP464592, 3MINT-7945693 MINT-7947479 I2D: score=1 
    TLN1Q9Y4902, 3MINT-7945693 MINT-7947479 I2D: score=1 
    SQSTM1Q135012, 3MINT-7945693 I2D: score=1 
    CDC5LQ994592, ENSP000003605324MINT-7945693 MINT-7947479 STRING: ENSP00000360532
    YWHAZP631042, 3, ENSP000003095034MINT-3319822 I2D: score=1 STRING: ENSP00000309503
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001701in utero embryonic development IEA--
    GO:0001890placenta development IEA--
    GO:0006388tRNA splicing, via endonucleolytic cleavage and ligation IDA--
    GO:0007160cell-matrix adhesion NAS15163412
    GO:0034446substrate adhesion-dependent cell spreading NAS15163412


    C22orf28 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for C22orf28

    1 DrugBank Compound for C22orf28    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Sucrose-- 57-50-1target--10592235

    Search CenterWatch for drugs/clinical trials and news about C22orf28 / RTCB 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for C22orf28 gene: 
    NM_014306.4  

    Unigene Cluster for C22orf28:

    Chromosome 22 open reading frame 28
    Hs.474643  [show with all ESTs]
    Unigene Representative Sequence: NM_014306
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000216038(uc003amm.2 uc011ama.1) ENST00000498434 ENST00000476619
    ENST00000485373 ENST00000487704 ENST00000463455 ENST00000451746

    miRNA
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    hsa-miR-455-3p
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    Inhib. RNA
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    Additional cDNA sequence: 

    AF155658.1 AF161466.1 AK297826.1 AK297908.1 AK301945.1 AK312503.1 AL050255.1 AL137272.1 
    BC000151.1 BC002970.1 BC010308.1 BC016707.1 CR456450.1 CR457175.1 

    24/25 DOTS entries (see all 25):

    DT.454442  DT.100711914  DT.100655592  DT.91938790  DT.95166886  DT.100757849  DT.100761474  DT.95231806 
    DT.120641983  DT.75172190  DT.95166889  DT.100856047  DT.100861539  DT.120641967  DT.100859395  DT.100875038 
    DT.100655589  DT.100853424  DT.100866318  DT.100870752  DT.65285135  DT.100655590  DT.100863661  DT.120641920 

    24/735 AceView cDNA sequences (see all 735):

    CR591502 AW410128 BP374478 BQ064589 BM810678 AA303010 BM547176 BQ421026 
    CB145594 BE301527 BQ884068 AL711124 BU615565 BQ226199 BM549535 BQ888550 
    BQ880191 BI821046 BM999890 BM971902 CR602136 AU107681 BM827396 CA308568 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for C22orf28 (see all 6)    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
    SP1:                          -                                   -                                                   
    SP2:                          -           -     -                 -                                                   
    SP3:                          -                                                                                       
    SP4:                          -                                                                                       
    SP5:              -     -     -                                                                                       


    ECgene alternative splicing isoforms for C22orf28

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    C22orf28 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAGAAAGTTC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See C22orf28 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for C22orf28

    SOURCE GeneReport for Unigene cluster: Hs.474643
        SABiosciences Custom PCR Arrays for C22orf28
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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)
    About This Section

    This gene was present in the last universal common ancestor (LUCA).

    Orthologs for C22orf28 gene from 8/28 species (see all 28)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia D10Wsu52e1 , 5 DNA segment, Chr 10, Wayne State University 52, expressed1, 5 91.82(n)1
    99.41(a)1
      10 (41.81 cM)5
    280881  NM_145422.41  NP_663397.11 
     859386375 
    chicken
    (Gallus gallus)
    Aves C1H22orf281 chromosome 1 open reading frame, human C22orf28 83.23(n)
    97.43(a)
      418064  XM_416300.3  XP_416300.2 
    lizard
    (Anolis carolinensis)
    Reptilia C22orf286
    --
    96(a)
    1 ↔ 1
    5(19883949-19895515)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.60112 Xenopus laevis transcribed sequence with strong similarity more 78.64(n)    48016810 
    zebrafish
    (Danio rerio)
    Actinopterygii wufe02f022 Transcribed sequence with strong similarity to protein more 78.49(n)    BQ618446.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG99871 CG9987 72.1(n)
    85.49(a)
      35220  NM_136121.1  NP_609965.1 
    worm
    (Caenorhabditis elegans)
    Secernentea F16A11.21 Protein F16A11.2 66.6(n)
    73.07(a)
      184556  NM_060097.3  NP_492498.1 
    E. coli
    (Escherichia coli)
    Gamma proteobacteria rtcB6
    conserved protein
    26(a)
    1 ↔ 1
    Chromosome(3554875-3556101)


    ENSEMBL Gene Tree for C22orf28 (if available)
    TreeFam Gene Tree for C22orf28 (if available) 

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

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/610 NCBI SNPs in C22orf28 are shown (see all 610    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs121657571,2
    --32783124(+) cggagC/Gttgca 1 -- int10--------
    rs1813714671,2
    --32783137(+) GAGCCA/GAGATT 1 -- int10--------
    rs1116025451,2
    C,--32783166(+) CTGGGC/TGACAG 1 -- int11Minor allele frequency- T:0.50NA 2
    rs1431643871,2
    C,--32783229(+) GTGTA-/GGAGGG 1 -- int10--------
    rs65187741,2
    C,F,A,H,--32783301(+) GTTCAC/TCCGGC 1 -- int118Minor allele frequency- T:0.05NS EA NA WA 2572
    rs1911016061,2
    --32783308(+) CGGCCC/TCATGG 1 -- int10--------
    rs1484418931,2
    --32783330(+) CTGCCA/GTGTAT 1 -- int10--------
    rs121658471,2
    C,F,H,--32783341(+) TTAGAA/GTAAGA 1 -- int18Minor allele frequency- G:0.02EA NS NA 544
    rs169903721,2
    C,F,H,--32783346(+) ATAAGA/GAAGGT 1 -- int18Minor allele frequency- G:0.03NA NS EA WA 660
    rs1810035301,2
    --32783377(+) GTCTTC/TTGGGC 1 -- int10--------

    HapMap Linkage Disequilibrium report for C22orf28 (32783562 - 32808274 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for C22orf28
         1 CNV: 5358

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    C22orf28 for disorders           About GeneDecksing

    OMIM gene information: 613901    OMIM disorders: --

    4 diseases for C22orf28:    About MalaCards
    cryptorchidism    tuberculosis    malaria    mycobacterium tuberculosis


    Export disorders for C22orf28 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)
    About This Section

    PubMed articles for C22orf28 gene, integrated from 9 sources (see all 32):
    (articles sorted by number of sources associating them with C22orf28)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. HSPC117 is the essential subunit of a human tRNA splicing ligase complex. (PubMed id 21311021)1, 2, 3 Popow J....Martinez J. (2011)
    2. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PubMed id 11042152)1, 2, 3 Zhang Q.-H.... Chen Z. (2000)
    3. Archaeal 3'-phosphate RNA splicing ligase characteriza tion identifies the missing component in tRNA maturation. (PubMed id 21209330)1, 3 Englert M....Soll D. (2011)
    4. Proteomic analysis of SUMO4 substrates in HEK293 cells under serum starvation-induced stress. (PubMed id 16236267)1, 2 Guo D.... Wang C.-Y. (2005)
    5. 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. (2004)
    6. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (2004)
    7. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. (PubMed id 12529303)1, 2 Collins J.E.... Dunham I. (2003)
    8. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PubMed id 10931946)1, 2 Hu R.-M.... Chen J.-L. (2000)
    9. The DNA sequence of human chromosome 22. (PubMed id 10591208)1, 2 Dunham I....O'Brien K.P. (1999)
    10. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 51493 HGNC: 26935 AceView: HSPC117 Ensembl:ENSG00000100220 euGenes: HUgn51493
    ECgene: C22orf28 H-InvDB: C22orf28

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for C22orf28 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for C22orf28 gene:
    Search GeneIP for patents involving C22orf28

    GeneCards and IP:
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