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Q7RTS9

- DYM_HUMAN

UniProt

Q7RTS9 - DYM_HUMAN

Protein

Dymeclin

Gene

DYM

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 89 (01 Oct 2014)
      Sequence version 1 (15 Dec 2003)
      Previous versions | rss
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    Functioni

    Necessary for correct organization of Golgi apparatus. Involved in bone development.1 Publication

    GO - Molecular functioni

    1. enzyme binding Source: UniProtKB
    2. protein binding Source: UniProtKB

    GO - Biological processi

    1. bone development Source: UniProtKB
    2. Golgi organization Source: UniProtKB

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dymeclin
    Alternative name(s):
    Dyggve-Melchior-Clausen syndrome protein
    Gene namesi
    Name:DYM
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 18

    Organism-specific databases

    HGNCiHGNC:21317. DYM.

    Subcellular locationi

    Cytoplasm. Golgi apparatus
    Note: Sequence analysis programs clearly predict 1 transmembrane region. However, PubMed:18996921 shows that it is not a stably anchored transmembrane protein but it weakly associates with the Golgi apparatus and shuttles between the Golgi and the cytosol.

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB
    2. Golgi apparatus Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm, Golgi apparatus

    Pathology & Biotechi

    Involvement in diseasei

    Dyggve-Melchior-Clausen syndrome (DMC) [MIM:223800]: A rare autosomal recessive disorder belonging to the group of spondyloepimetaphyseal dysplasias. DMC is characterized by progressive short stature with short trunk dwarfism, microcephaly, protruding sternum, and psychomotor retardation. Radiological features include a platyspondyly with double vertebral humps, an epiphyso-metaphyseal dysplasia and lacy pelvis iliac crests.2 Publications
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti469 – 4691N → Y in DMC; results in protein mis-localization and aggregation. 1 Publication
    VAR_054499
    Smith-McCort dysplasia 1 (SMC1) [MIM:607326]: A rare autosomal recessive osteochondrodysplasia with skeletal features identical to those of Dyggve-Melchior-Clausen syndrome, but with normal intelligence and no microcephaly. It is characterized by short limbs and trunk with barrel-shaped chest. The radiographic phenotype includes platyspondyly, generalized abnormalities of the epiphyses and metaphyses, and a distinctive lacy appearance of the iliac crest.2 Publications
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti87 – 871E → K in SMC1; does not affect protein localization. 1 Publication
    VAR_022740
    Natural varianti542 – 5421C → R in SMC1. 1 Publication
    VAR_065293

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi2 – 21G → A: Does not affect protein localization to Golgi apparatus. Prevents myristoylation in vitro. 1 Publication

    Keywords - Diseasei

    Disease mutation, Dwarfism

    Organism-specific databases

    MIMi223800. phenotype.
    607326. phenotype.
    Orphaneti239. Dyggve-Melchior-Clausen disease.
    178355. Smith-McCort dysplasia.
    PharmGKBiPA134879547.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedCurated
    Chaini2 – 669668DymeclinPRO_0000086883Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi2 – 21N-myristoyl glycine1 Publication

    Post-translational modificationi

    Myristoylated in vitro; myristoylation is not essential for protein targeting to Golgi compartment.1 Publication

    Keywords - PTMi

    Lipoprotein, Myristate

    Proteomic databases

    MaxQBiQ7RTS9.
    PaxDbiQ7RTS9.
    PRIDEiQ7RTS9.

    PTM databases

    PhosphoSiteiQ7RTS9.

    Expressioni

    Tissue specificityi

    Expressed in most embryo-fetal and adult tissues. Abundant in primary chondrocytes, osteoblasts, cerebellum, kidney, lung, stomach, heart, pancreas and fetal brain. Very low or no expression in the spleen, thymus, esophagus, bladder and thyroid gland.2 Publications

    Gene expression databases

    ArrayExpressiQ7RTS9.
    BgeeiQ7RTS9.
    CleanExiHS_DYM.
    GenevestigatoriQ7RTS9.

    Organism-specific databases

    HPAiHPA043551.
    HPA049187.

    Interactioni

    Subunit structurei

    Interacts with GOLM1 and PPIB.1 Publication

    Protein-protein interaction databases

    BioGridi120165. 1 interaction.
    IntActiQ7RTS9. 1 interaction.

    Structurei

    3D structure databases

    ProteinModelPortaliQ7RTS9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the dymeclin family.Curated

    Phylogenomic databases

    eggNOGiNOG308890.
    HOVERGENiHBG057356.
    InParanoidiQ7RTS9.
    OMAiNVRTYML.
    OrthoDBiEOG72ZCG2.
    PhylomeDBiQ7RTS9.
    TreeFamiTF314870.

    Family and domain databases

    InterProiIPR019142. Dymeclin.
    [Graphical view]
    PfamiPF09742. Dymeclin. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q7RTS9-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL    50
    KLLEEATISV CRSLVENNPR TGNLGALIKV FLSRTKELKL SAECQNHIFI 100
    WQTHNALFII CCLLKVFICQ MSEEELQLHF TYEEKSPGNY SSDSEDLLEE 150
    LLCCLMQLIT DIPLLDITYE ISVEAISTMV VFLSCQLFHK EVLRQSISHK 200
    YLMRGPCLPY TSKLVKTLLY NFIRQEKPPP PGAHVFPQQS DGGGLLYGLA 250
    SGVATGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA 300
    PNPYRQAIMS FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL 350
    LLYTLLHQNS NIRTYMLART DMENLVLPIL EILYHVEERN SHHVYMALII 400
    LLILTEDDGF NRSIHEVILK NITWYSERVL TEISLGSLLI LVVIRTIQYN 450
    MTRTRDKYLH TNCLAALANM SAQFRSLHQY AAQRIISLFS LLSKKHNKVL 500
    EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN SCLTNSLHHN 550
    PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV 600
    ERVLEIIKQG VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS 650
    AVGLYWNPQD IQLFTMDSD 669
    Length:669
    Mass (Da):75,935
    Last modified:December 15, 2003 - v1
    Checksum:i7C8A216A09DBE43F
    GO
    Isoform 2 (identifier: Q7RTS9-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         65-65: V → A
         66-255: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:479
    Mass (Da):54,425
    Checksum:i1150D81BF01D76BC
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti66 – 661E → K in BAC11088. (PubMed:14702039)Curated
    Sequence conflicti249 – 2491L → P in BAC11088. (PubMed:14702039)Curated
    Sequence conflicti381 – 3811E → G in BAF83992. 1 PublicationCurated
    Sequence conflicti408 – 4081D → Y in AAH64394. (PubMed:15489334)Curated
    Sequence conflicti453 – 4531R → K in BAF83992. 1 PublicationCurated
    Sequence conflicti537 – 5371E → G in BAF83992. 1 PublicationCurated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti87 – 871E → K in SMC1; does not affect protein localization. 1 Publication
    VAR_022740
    Natural varianti469 – 4691N → Y in DMC; results in protein mis-localization and aggregation. 1 Publication
    VAR_054499
    Natural varianti542 – 5421C → R in SMC1. 1 Publication
    VAR_065293

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei65 – 651V → A in isoform 2. 1 PublicationVSP_036442
    Alternative sequencei66 – 255190Missing in isoform 2. 1 PublicationVSP_036443Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BK000950 Genomic DNA. Translation: DAA00396.1.
    AK074611 mRNA. Translation: BAC11088.1.
    AK091256 mRNA. Translation: BAG52319.1.
    AK291303 mRNA. Translation: BAF83992.1.
    AK296579 mRNA. Translation: BAG59199.1.
    AK315091 mRNA. Translation: BAG37556.1.
    CH471096 Genomic DNA. Translation: EAW62933.1.
    BC001252 mRNA. Translation: AAH01252.2.
    BC064394 mRNA. Translation: AAH64394.1.
    AY364250 mRNA. Translation: AAQ76809.1.
    AL390156 mRNA. Translation: CAB99092.1.
    CCDSiCCDS11937.1. [Q7RTS9-1]
    RefSeqiNP_060123.3. NM_017653.3. [Q7RTS9-1]
    XP_006722548.1. XM_006722485.1. [Q7RTS9-1]
    UniGeneiHs.162996.

    Genome annotation databases

    EnsembliENST00000269445; ENSP00000269445; ENSG00000141627. [Q7RTS9-1]
    ENST00000442713; ENSP00000395942; ENSG00000141627. [Q7RTS9-2]
    GeneIDi54808.
    KEGGihsa:54808.
    UCSCiuc002ldi.1. human. [Q7RTS9-1]
    uc010xdf.1. human. [Q7RTS9-2]

    Polymorphism databases

    DMDMi68565365.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BK000950 Genomic DNA. Translation: DAA00396.1 .
    AK074611 mRNA. Translation: BAC11088.1 .
    AK091256 mRNA. Translation: BAG52319.1 .
    AK291303 mRNA. Translation: BAF83992.1 .
    AK296579 mRNA. Translation: BAG59199.1 .
    AK315091 mRNA. Translation: BAG37556.1 .
    CH471096 Genomic DNA. Translation: EAW62933.1 .
    BC001252 mRNA. Translation: AAH01252.2 .
    BC064394 mRNA. Translation: AAH64394.1 .
    AY364250 mRNA. Translation: AAQ76809.1 .
    AL390156 mRNA. Translation: CAB99092.1 .
    CCDSi CCDS11937.1. [Q7RTS9-1 ]
    RefSeqi NP_060123.3. NM_017653.3. [Q7RTS9-1 ]
    XP_006722548.1. XM_006722485.1. [Q7RTS9-1 ]
    UniGenei Hs.162996.

    3D structure databases

    ProteinModelPortali Q7RTS9.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 120165. 1 interaction.
    IntActi Q7RTS9. 1 interaction.

    PTM databases

    PhosphoSitei Q7RTS9.

    Polymorphism databases

    DMDMi 68565365.

    Proteomic databases

    MaxQBi Q7RTS9.
    PaxDbi Q7RTS9.
    PRIDEi Q7RTS9.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000269445 ; ENSP00000269445 ; ENSG00000141627 . [Q7RTS9-1 ]
    ENST00000442713 ; ENSP00000395942 ; ENSG00000141627 . [Q7RTS9-2 ]
    GeneIDi 54808.
    KEGGi hsa:54808.
    UCSCi uc002ldi.1. human. [Q7RTS9-1 ]
    uc010xdf.1. human. [Q7RTS9-2 ]

    Organism-specific databases

    CTDi 54808.
    GeneCardsi GC18M046570.
    HGNCi HGNC:21317. DYM.
    HPAi HPA043551.
    HPA049187.
    MIMi 223800. phenotype.
    607326. phenotype.
    607461. gene.
    neXtProti NX_Q7RTS9.
    Orphaneti 239. Dyggve-Melchior-Clausen disease.
    178355. Smith-McCort dysplasia.
    PharmGKBi PA134879547.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG308890.
    HOVERGENi HBG057356.
    InParanoidi Q7RTS9.
    OMAi NVRTYML.
    OrthoDBi EOG72ZCG2.
    PhylomeDBi Q7RTS9.
    TreeFami TF314870.

    Miscellaneous databases

    ChiTaRSi DYM. human.
    GeneWikii DYM.
    GenomeRNAii 54808.
    NextBioi 57521.
    PROi Q7RTS9.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q7RTS9.
    Bgeei Q7RTS9.
    CleanExi HS_DYM.
    Genevestigatori Q7RTS9.

    Family and domain databases

    InterProi IPR019142. Dymeclin.
    [Graphical view ]
    Pfami PF09742. Dymeclin. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INVOLVEMENT IN DMC, TISSUE SPECIFICITY.
    2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
      Tissue: Cervix, Testis and Tongue.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Brain and Cervix.
    5. "Characterization of human proteins containing evolutionary conserved domains of unknown function."
      Kemmer D., Podowski R., Hodges E., Roth P., Lenhard B., Sonnhammer E.L.L., Wasserman W.W., Hoog C.
      Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-524 (ISOFORM 1).
    6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 446-669.
      Tissue: Melanoma.
    7. "The gene responsible for Dyggve-Melchior-Clausen syndrome encodes a novel peripheral membrane protein dynamically associated with the Golgi apparatus."
      Dimitrov A., Paupe V., Gueudry C., Sibarita J.-B., Raposo G., Vielemeyer O., Gilbert T., Csaba Z., Attie-Bitach T., Cormier-Daire V., Gressens P., Rustin P., Perez F., El Ghouzzi V.
      Hum. Mol. Genet. 18:440-453(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY, SUBCELLULAR LOCATION, MYRISTOYLATION AT GLY-2, MUTAGENESIS OF GLY-2, CHARACTERIZATION OF VARIANT SMC1 LYS-87, CHARACTERIZATION OF VARIANT DMC TYR-469.
    8. "Dymeclin, the gene underlying Dyggve-Melchior-Clausen syndrome, encodes a protein integral to extracellular matrix and Golgi organization and is associated with protein secretion pathways critical in bone development."
      Denais C., Dent C.L., Southgate L., Hoyle J., Dafou D., Trembath R.C., Machado R.D.
      Hum. Mutat. 32:231-239(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH GOLM1 AND PPIB, INVOLVEMENT IN DCM.
    9. "Mental retardation and abnormal skeletal development (Dyggve-Melchior-Clausen dysplasia) due to mutations in a novel, evolutionarily conserved gene."
      Cohn D.H., Ehtesham N., Krakow D., Unger S., Shanske A., Reinker K., Powell B.R., Rimoin D.L.
      Am. J. Hum. Genet. 72:419-428(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT DMC TYR-469, VARIANT SMC1 LYS-87.
    10. "Portuguese case of Smith-McCort syndrome caused by a new mutation in the dymeclin (FLJ20071) gene."
      Santos H.G., Fernandes H.C., Nunes J.L., Almeida M.R.
      Clin. Dysmorphol. 18:41-44(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT SMC1 ARG-542.

    Entry informationi

    Entry nameiDYM_HUMAN
    AccessioniPrimary (citable) accession number: Q7RTS9
    Secondary accession number(s): A8K5I8
    , B2RCF9, B4DKI7, Q3ZTS8, Q6P2P5, Q8N2M0, Q9BVE9, Q9NPU7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 5, 2005
    Last sequence update: December 15, 2003
    Last modified: October 1, 2014
    This is version 89 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 18
      Human chromosome 18: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3