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Q7RTS9

- DYM_HUMAN

UniProt

Q7RTS9 - DYM_HUMAN

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Protein

Dymeclin

Gene

DYM

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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

GO - Molecular functioni

  1. enzyme binding Source: UniProtKB

GO - Biological processi

  1. bone development Source: UniProtKB
  2. Golgi organization Source: UniProtKB
Complete GO annotation...

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
Complete GO annotation...

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

BgeeiQ7RTS9.
CleanExiHS_DYM.
ExpressionAtlasiQ7RTS9. baseline and differential.
GenevestigatoriQ7RTS9.

Organism-specific databases

HPAiHPA043551.
HPA049187.

Interactioni

Subunit structurei

Interacts with GOLM1 and PPIB.1 Publication

Protein-protein interaction databases

BioGridi120165. 6 interactions.
IntActiQ7RTS9. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliQ7RTS9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the dymeclin family.Curated

Phylogenomic databases

eggNOGiNOG308890.
GeneTreeiENSGT00390000008772.
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

        10         20         30         40         50
MGSNSSRIGD LPKNEYLKKL SGTESISEND PFWNQLLSFS FPAPTSSSEL
60 70 80 90 100
KLLEEATISV CRSLVENNPR TGNLGALIKV FLSRTKELKL SAECQNHIFI
110 120 130 140 150
WQTHNALFII CCLLKVFICQ MSEEELQLHF TYEEKSPGNY SSDSEDLLEE
160 170 180 190 200
LLCCLMQLIT DIPLLDITYE ISVEAISTMV VFLSCQLFHK EVLRQSISHK
210 220 230 240 250
YLMRGPCLPY TSKLVKTLLY NFIRQEKPPP PGAHVFPQQS DGGGLLYGLA
260 270 280 290 300
SGVATGLWTV FTLGGVGSKA AASPELSSPL ANQSLLLLLV LANLTDASDA
310 320 330 340 350
PNPYRQAIMS FKNTQDSSPF PSSIPHAFQI NFNSLYTALC EQQTSDQATL
360 370 380 390 400
LLYTLLHQNS NIRTYMLART DMENLVLPIL EILYHVEERN SHHVYMALII
410 420 430 440 450
LLILTEDDGF NRSIHEVILK NITWYSERVL TEISLGSLLI LVVIRTIQYN
460 470 480 490 500
MTRTRDKYLH TNCLAALANM SAQFRSLHQY AAQRIISLFS LLSKKHNKVL
510 520 530 540 550
EQATQSLRGS LSSNDVPLPD YAQDLNVIEE VIRMMLEIIN SCLTNSLHHN
560 570 580 590 600
PNLVYALLYK RDLFEQFRTH PSFQDIMQNI DLVISFFSSR LLQAGAELSV
610 620 630 640 650
ERVLEIIKQG VVALPKDRLK KFPELKFKYV EEEQPEEFFI PYVWSLVYNS
660
AVGLYWNPQD IQLFTMDSD
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. 6 interactions.
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.
GeneTreei ENSGT00390000008772.
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

Bgeei Q7RTS9.
CleanExi HS_DYM.
ExpressionAtlasi Q7RTS9. baseline and differential.
Genevestigatori Q7RTS9.

Family and domain databases

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

Publicationsi

« Hide 'large scale' publications
  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 29, 2014
This is version 90 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