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MAMDC4 Gene

protein-coding   GIFtS: 41
GCID: GC09P139745

MAM Domain Containing 4

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(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
MAM Domain Containing 41 2     Apical Early Endosomal Glycoprotein Precursor1
endotubin1 2     Apical Early Endosomal Glycoprotein2
AEGP2 3     Apical Endosomal Glycoprotein2
MAM Domain-Containing Protein 42 3     

External Ids:    HGNC: 240831   Entrez Gene: 1580562   Ensembl: ENSG000001779437   UniProtKB: Q6UXC13   
ORGUL members:         

Export aliases for MAMDC4 gene to outside databases

Previous GC identifers: GC09P137023 GC09P138866 GC09P109206


(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 MAMDC4 Gene:
MAMDC4 (MAM domain containing 4) is a protein-coding gene. An important paralog of this gene is MDGA2.

UniProtKB/Swiss-Prot: AEGP_HUMAN, Q6UXC1
Function: Probably involved in the sorting and selective transport of receptors and ligands across polarized
epithelia (By similarity)




(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 at NCBI GenBank:
NC_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the MAMDC4 gene promoter:
         E47   C/EBPalpha   Egr-2   RORalpha1   MEF-2A   AREB6   SEF-1 (1)   aMEF-2   NF-Y   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidMAMDC4 promoter sequence
   Search Chromatin IP Primers for MAMDC4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat MAMDC4


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

Entrez Gene cytogenetic band: 9q34.3   Ensembl cytogenetic band:  9q34.3   HGNC cytogenetic band: 9q34.3

MAMDC4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MAMDC4 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P139745:  view genomic region     (about GC identifiers)

Start:
139,745,395 bp from pter      End:
139,755,251 bp from pter
Size:
9,857 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: AEGP_HUMAN, Q6UXC1 (See protein sequence)
Recommended Name: Apical endosomal glycoprotein precursor  
Size: 1216 amino acids; 131499 Da
Secondary accessions: A2A3D4 B0QZ81 Q5T5S2 Q8NCX7
Alternative splicing: 3 isoforms:  Q6UXC1-1   Q6UXC1-2   Q6UXC1-3   (May be due to intron retention. No experimental confirmation available)

Explore the universe of human proteins at neXtProt for MAMDC4: NX_Q6UXC1

Explore proteomics data for MAMDC4 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn203, Asn281, Asn339, Asn583, Asn636, Asn835
  • Modification sites at PhosphoSitePlus

  • See MAMDC4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_996803.2  
    ENSEMBL proteins: 
     ENSP00000319388   ENSP00000435513   ENSP00000411339  

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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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    4 InterPro protein domains:
     IPR023415 LDLR_class-A_CS
     IPR002172 LDrepeatLR_classA_rpt
     IPR000998 MAM_dom
     IPR008985 ConA-like_lec_gl_sf

    Graphical View of Domain Structure for InterPro Entry Q6UXC1

    ProtoNet protein and cluster: Q6UXC1

    1 Blocks protein domain: IPB002172 Low density lipoprotein-receptor

    UniProtKB/Swiss-Prot: AEGP_HUMAN, Q6UXC1
    Similarity: Contains 3 LDL-receptor class A domains
    Similarity: Contains 6 MAM domains


    Find genes that share domains with MAMDC4           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: AEGP_HUMAN, Q6UXC1
    Function: Probably involved in the sorting and selective transport of receptors and ligands across polarized
    epithelia (By similarity)

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with MAMDC4           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for MAMDC4

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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
    AEGP_HUMAN, Q6UXC1: Membrane; Single-pass type I membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    plasma membrane3
    cytosol1
    nucleus1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with MAMDC4           About GenesLikeMe


    (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 MAMDC4
    Interactions:

        Search GeneGlobe Interaction Network for MAMDC4

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015031protein transport IEA--

    Find genes that share ontologies with MAMDC4           About GenesLikeMe



    (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
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    Browse Tocris compounds for MAMDC4 (AEGP)



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for MAMDC4 gene: 
    NM_206920.2  

    Unigene Cluster for MAMDC4:

    MAM domain containing 4
    Hs.376780  [show with all ESTs]
    Unigene Representative Sequence: AY358419
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000485732 ENST00000317446(uc004cjs.3) ENST00000481327 ENST00000479475
    ENST00000445819(uc011mej.2)
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      QuantiFast Probe-based Assays in human, mouse, rat MAMDC4

    Additional mRNA sequence: 

    AY358419.1 BC144258.1 BC144259.1 

    3 DOTS entries:

    DT.100739467  DT.40316134  DT.101983584 

    Selected AceView cDNA sequences (see all 383):

    CD107634 BQ420364 BM716308 CD671496 BM979912 BQ270782 BC024648 BM983617 
    BQ640096 BM687094 BU173973 AI089700 CR614794 F26247 AL834531 AI198392 
    BU177309 BU727547 BM826004 BM919123 BM975420 CA433414 AL045051 AL137659 

    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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    MAMDC4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGGGCAGCCC
    MAMDC4 Expression
    About this image

    MAMDC4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    MAMDC4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.376780
        Custom PCR Arrays for MAMDC4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MAMDC4

    (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 MAMDC4 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Mamdc41 , 5 MAM domain containing 41, 5 78.33(n)1
    73.35(a)1
      2 (17.41 cM)5
    3813521  NM_001081199.11  NP_001074668.21 
     255631375 
    chicken
    (Gallus gallus)
    Aves MAMDC41 MAM domain containing 4 57.64(n)
    47.11(a)
      101751695  XM_004945715.1  XP_004945772.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    25(a)
    many ↔ many
    2(49222566-49289587)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia mamdc41 MAM domain containing 4 51.17(n)
    39.37(a)
      100497506  XM_002940739.2  XP_002940785.2 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC7971661 apical endosomal glycoprotein-like 47.57(n)
    37.97(a)
      797166  XM_001337588.4  XP_001337624.4 


    ENSEMBL Gene Tree for MAMDC4 (if available)
    TreeFam Gene Tree for MAMDC4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for MAMDC4 gene
    MDGA22  MDGA12  MALRD12  ENSG000002727812  MAMDC22  

    Find genes that share paralogs with MAMDC4           About GenesLikeMe



    (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 MAMDC4 (see all 513)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0357784
    A breast cancer sample4--see VAR_0357782 P T mis40--------
    VAR_0357794
    A breast cancer sample4--see VAR_0357792 R W mis40--------
    rs1919815751,2
    --139746122(+) CCAGAC/TGGGCA 1 -- us2k10--------
    rs1426200551,2
    C--139746254(+) AAAGAC/TCCTGC 1 -- us2k10--------
    rs1498619691,2
    C--139746290(+) AAACCA/GAAGTT 1 -- us2k10--------
    rs1458100291,2
    --139746332(+) CGGACA/GGCACC 1 -- us2k10--------
    rs1489685611,2
    --139746363(+) ATGACA/GGCGTG 1 -- us2k10--------
    rs1846267871,2
    --139746415(+) AGAACA/GCAGGG 1 -- us2k10--------
    rs1437677171,2
    --139746422(+) AGGGAA/CCAGCT 1 -- us2k10--------
    rs1382828611,2
    --139746743(+) CACTGA/GGTGGG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for MAMDC4 (139745395 - 139755251 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for MAMDC4 (see all 25):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2672706CNV Deletion23128226
    esv2422220CNV Deletion17116639
    nsv894483CNV Loss21882294
    dgv8414n71CNV Loss21882294
    dgv8421n71CNV Loss21882294
    dgv8416n71CNV Loss21882294
    dgv8420n71CNV Loss21882294
    nsv894491CNV Loss21882294
    nsv894469CNV Loss21882294
    dgv8418n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for MAMDC4

    (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.)
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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 MAMDC4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with MAMDC4)
        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 Clark H.F.... Gray A.M. (Genome Res. 2003)
    2. Molecular characterization of an apical early endosomal glycoprotein from developing rat intestinal epithelial cells. (PubMed id 7829488)1, 3 Speelman B.A....Wilson J.M. (J. Biol. Chem. 1995)
    3. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    4. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (Science 2006)
    5. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)
    6. 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: 158056 HGNC: 24083 AceView: PHPT1andAEGP Ensembl:ENSG00000177943 euGenes: HUgn158056
    ECgene: MAMDC4 H-InvDB: MAMDC4

    (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 MAMDC4 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 MAMDC4 gene:
    Search GeneIP for patents involving MAMDC4

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 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 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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