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Protein

Zinc transporter ZIP13

Gene

SLC39A13

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

Functioni

Acts as a zinc-influx transporter.1 Publication

GO - Molecular functioni

  • protein homodimerization activity Source: BHF-UCL
  • zinc ion transmembrane transporter activity Source: BHF-UCL

GO - Biological processi

  • cellular zinc ion homeostasis Source: BHF-UCL
  • connective tissue development Source: BHF-UCL
  • zinc II ion transmembrane transport Source: BHF-UCL
Complete GO annotation...

Keywords - Biological processi

Ion transport, Transport, Zinc transport

Keywords - Ligandi

Zinc

Protein family/group databases

TCDBi2.A.5.4.12. the zinc (zn(2+))-iron (fe(2+)) permease (zip) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Zinc transporter ZIP13
Alternative name(s):
LIV-1 subfamily of ZIP zinc transporter 9
Short name:
LZT-Hs9
Solute carrier family 39 member 13
Zrt- and Irt-like protein 13
Short name:
ZIP-13
Gene namesi
Name:SLC39A13
Synonyms:ZIP13
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:20859. SLC39A13.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 77LumenalSequence analysis
Transmembranei8 – 2821HelicalSequence analysisAdd
BLAST
Topological domaini29 – 6840CytoplasmicSequence analysisAdd
BLAST
Transmembranei69 – 8921HelicalSequence analysisAdd
BLAST
Topological domaini90 – 10819LumenalSequence analysisAdd
BLAST
Transmembranei109 – 12921HelicalSequence analysisAdd
BLAST
Topological domaini130 – 14920CytoplasmicSequence analysisAdd
BLAST
Transmembranei150 – 17021HelicalSequence analysisAdd
BLAST
Topological domaini171 – 23565LumenalSequence analysisAdd
BLAST
Transmembranei236 – 25621HelicalSequence analysisAdd
BLAST
Topological domaini257 – 27822CytoplasmicSequence analysisAdd
BLAST
Transmembranei279 – 29921HelicalSequence analysisAdd
BLAST
Topological domaini300 – 31617LumenalSequence analysisAdd
BLAST
Transmembranei317 – 33721HelicalSequence analysisAdd
BLAST
Topological domaini338 – 34912CytoplasmicSequence analysisAdd
BLAST
Transmembranei350 – 37021HelicalSequence analysisAdd
BLAST
Topological domaini371 – 3711LumenalSequence analysis

GO - Cellular componenti

  • Golgi apparatus Source: BHF-UCL
  • integral component of Golgi membrane Source: BHF-UCL
  • integral component of membrane Source: BHF-UCL
  • perinuclear region of cytoplasm Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Golgi apparatus, Membrane

Pathology & Biotechi

Involvement in diseasei

Ehlers-Danlos syndrome-like spondylocheirodysplasia (SCD-EDS)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionSpondylocheiro dysplastic form of Ehlers-Danlos syndrome. The syndrome consists of a generalized skeletal dysplasia involving mainly the spine (spondylo) and striking clinical abnormalities of the hands (cheiro) in addition to the EDS-like features. Clinical features included postnatal growth retardation, moderate short stature, protuberant eyes with bluish sclerae, hands with finely wrinkled palms, atrophy of the thenar muscles, and tapering fingers. Patients have thin, hyperelastic skin and hypermobile small joints consistent with an Ehlers-Danlos-like phenotype. Radiologic features included mild to moderate platyspondyly, mild to moderate osteopenia of the spine, small ileum, flat proximal femoral epiphyses, short, wide femoral necks, and broad metaphyses (elbows, knees, wrists, and interphalangeal joints).
See also OMIM:612350
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti162 – 1643Missing in SCD-EDS. 1 Publication
VAR_054127

Keywords - Diseasei

Ehlers-Danlos syndrome

Organism-specific databases

MalaCardsiSLC39A13.
MIMi612350. phenotype.
Orphaneti157965. Ehlers-Danlos syndrome, spondylocheirodysplastic type.
PharmGKBiPA134948414.

Polymorphism and mutation databases

BioMutaiSLC39A13.
DMDMi296452971.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 371371Zinc transporter ZIP13PRO_0000312309Add
BLAST

Proteomic databases

MaxQBiQ96H72.
PaxDbiQ96H72.
PRIDEiQ96H72.

PTM databases

iPTMnetiQ96H72.
PhosphoSiteiQ96H72.

Expressioni

Gene expression databases

BgeeiQ96H72.
CleanExiHS_SLC39A13.
ExpressionAtlasiQ96H72. baseline and differential.
GenevisibleiQ96H72. HS.

Organism-specific databases

HPAiHPA043971.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
RELQ048643EBI-10287091,EBI-307352
TCF4P158843EBI-10287091,EBI-533224

GO - Molecular functioni

  • protein homodimerization activity Source: BHF-UCL

Protein-protein interaction databases

BioGridi124808. 4 interactions.
IntActiQ96H72. 3 interactions.
STRINGi9606.ENSP00000354689.

Structurei

3D structure databases

ProteinModelPortaliQ96H72.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi257 – 2626XEXPHE-motif

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi146 – 1505Poly-Gln
Compositional biasi187 – 1915Poly-Ala
Compositional biasi353 – 3564Poly-Leu

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2694. Eukaryota.
COG0428. LUCA.
GeneTreeiENSGT00760000119115.
HOGENOMiHOG000185308.
HOVERGENiHBG001037.
InParanoidiQ96H72.
KOiK14719.
OMAiEEDDPWH.
PhylomeDBiQ96H72.
TreeFamiTF318470.

Family and domain databases

InterProiIPR003689. ZIP.
[Graphical view]
PfamiPF02535. Zip. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q96H72-1) [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
MPGCPCPGCG MAGPRLLFLT ALALELLERA GGSQPALRSR GTATACRLDN
60 70 80 90 100
KESESWGALL SGERLDTWIC SLLGSLMVGL SGVFPLLVIP LEMGTMLRSE
110 120 130 140 150
AGAWRLKQLL SFALGGLLGN VFLHLLPEAW AYTCSASPGG EGQSLQQQQQ
160 170 180 190 200
LGLWVIAGIL TFLALEKMFL DSKEEGTSQA PNKDPTAAAA ALNGGHCLAQ
210 220 230 240 250
PAAEPGLGAV VRSIKVSGYL NLLANTIDNF THGLAVAASF LVSKKIGLLT
260 270 280 290 300
TMAILLHEIP HEVGDFAILL RAGFDRWSAA KLQLSTALGG LLGAGFAICT
310 320 330 340 350
QSPKGVVGCS PAAEETAAWV LPFTSGGFLY IALVNVLPDL LEEEDPWRSL
360 370
QQLLLLCAGI VVMVLFSLFV D
Length:371
Mass (Da):39,011
Last modified:May 18, 2010 - v3
Checksum:iE3E9AF33A2EB4E42
GO
Isoform 2 (identifier: Q96H72-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     307-313: Missing.

Show »
Length:364
Mass (Da):38,425
Checksum:i7534E39568C15C7B
GO

Sequence cautioni

The sequence BAC05365.1 differs from that shown. Reason: Frameshift at position 314. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti28 – 281E → G.3 Publications
Corresponds to variant rs2010519 [ dbSNP | Ensembl ].
VAR_037484
Natural varianti162 – 1643Missing in SCD-EDS. 1 Publication
VAR_054127
Natural varianti346 – 3461P → L.
Corresponds to variant rs35978122 [ dbSNP | Ensembl ].
VAR_037485

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei307 – 3137Missing in isoform 2. 3 PublicationsVSP_029819

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK098651 mRNA. Translation: BAC05365.1. Frameshift.
AC090559 Genomic DNA. No translation available.
CH471064 Genomic DNA. Translation: EAW67918.1.
CH471064 Genomic DNA. Translation: EAW67919.1.
CH471064 Genomic DNA. Translation: EAW67920.1.
CH471064 Genomic DNA. Translation: EAW67921.1.
CH471064 Genomic DNA. Translation: EAW67922.1.
CH471064 Genomic DNA. Translation: EAW67923.1.
BC008853 mRNA. Translation: AAH08853.2.
BC019016 mRNA. Translation: AAH19016.1.
AL133581 mRNA. Translation: CAH56389.1.
CCDSiCCDS44592.1. [Q96H72-1]
CCDS7934.1. [Q96H72-2]
RefSeqiNP_001121697.1. NM_001128225.2.
NP_689477.2. NM_152264.4.
XP_011518769.1. XM_011520467.1. [Q96H72-1]
XP_011518770.1. XM_011520468.1. [Q96H72-1]
UniGeneiHs.523664.

Genome annotation databases

EnsembliENST00000354884; ENSP00000346956; ENSG00000165915. [Q96H72-2]
ENST00000362021; ENSP00000354689; ENSG00000165915. [Q96H72-1]
GeneIDi91252.
KEGGihsa:91252.
UCSCiuc001nff.5. human. [Q96H72-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK098651 mRNA. Translation: BAC05365.1. Frameshift.
AC090559 Genomic DNA. No translation available.
CH471064 Genomic DNA. Translation: EAW67918.1.
CH471064 Genomic DNA. Translation: EAW67919.1.
CH471064 Genomic DNA. Translation: EAW67920.1.
CH471064 Genomic DNA. Translation: EAW67921.1.
CH471064 Genomic DNA. Translation: EAW67922.1.
CH471064 Genomic DNA. Translation: EAW67923.1.
BC008853 mRNA. Translation: AAH08853.2.
BC019016 mRNA. Translation: AAH19016.1.
AL133581 mRNA. Translation: CAH56389.1.
CCDSiCCDS44592.1. [Q96H72-1]
CCDS7934.1. [Q96H72-2]
RefSeqiNP_001121697.1. NM_001128225.2.
NP_689477.2. NM_152264.4.
XP_011518769.1. XM_011520467.1. [Q96H72-1]
XP_011518770.1. XM_011520468.1. [Q96H72-1]
UniGeneiHs.523664.

3D structure databases

ProteinModelPortaliQ96H72.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124808. 4 interactions.
IntActiQ96H72. 3 interactions.
STRINGi9606.ENSP00000354689.

Protein family/group databases

TCDBi2.A.5.4.12. the zinc (zn(2+))-iron (fe(2+)) permease (zip) family.

PTM databases

iPTMnetiQ96H72.
PhosphoSiteiQ96H72.

Polymorphism and mutation databases

BioMutaiSLC39A13.
DMDMi296452971.

Proteomic databases

MaxQBiQ96H72.
PaxDbiQ96H72.
PRIDEiQ96H72.

Protocols and materials databases

DNASUi91252.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000354884; ENSP00000346956; ENSG00000165915. [Q96H72-2]
ENST00000362021; ENSP00000354689; ENSG00000165915. [Q96H72-1]
GeneIDi91252.
KEGGihsa:91252.
UCSCiuc001nff.5. human. [Q96H72-1]

Organism-specific databases

CTDi91252.
GeneCardsiSLC39A13.
H-InvDBHIX0009615.
HGNCiHGNC:20859. SLC39A13.
HPAiHPA043971.
MalaCardsiSLC39A13.
MIMi608735. gene.
612350. phenotype.
neXtProtiNX_Q96H72.
Orphaneti157965. Ehlers-Danlos syndrome, spondylocheirodysplastic type.
PharmGKBiPA134948414.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2694. Eukaryota.
COG0428. LUCA.
GeneTreeiENSGT00760000119115.
HOGENOMiHOG000185308.
HOVERGENiHBG001037.
InParanoidiQ96H72.
KOiK14719.
OMAiEEDDPWH.
PhylomeDBiQ96H72.
TreeFamiTF318470.

Miscellaneous databases

ChiTaRSiSLC39A13. human.
GenomeRNAii91252.
PROiQ96H72.
SOURCEiSearch...

Gene expression databases

BgeeiQ96H72.
CleanExiHS_SLC39A13.
ExpressionAtlasiQ96H72. baseline and differential.
GenevisibleiQ96H72. HS.

Family and domain databases

InterProiIPR003689. ZIP.
[Graphical view]
PfamiPF02535. Zip. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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] (ISOFORM 2), VARIANT GLY-28.
    Tissue: Testis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  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] (ISOFORMS 1 AND 2), VARIANT GLY-28.
    Tissue: Brain.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 278-371 (ISOFORM 2), VARIANT GLY-28.
    Tissue: Testis.
  6. "Biochemical characterization of human ZIP13 protein: a homo-dimerized zinc transporter involved in the spondylocheiro dysplastic Ehlers-Danlos syndrome."
    Bin B.H., Fukada T., Hosaka T., Yamasaki S., Ohashi W., Hojyo S., Miyai T., Nishida K., Yokoyama S., Hirano T.
    J. Biol. Chem. 286:40255-40265(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, SUBUNIT.
  7. "Spondylocheiro dysplastic form of the Ehlers-Danlos syndrome -- an autosomal-recessive entity caused by mutations in the zinc transporter gene SLC39A13."
    Giunta C., Elcioglu N.H., Albrecht B., Eich G., Chambaz C., Janecke A.R., Yeowell H., Weis M., Eyre D.R., Kraenzlin M., Steinmann B.
    Am. J. Hum. Genet. 82:1290-1305(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT SCD-EDS 162-PHE--ALA-164 DEL.

Entry informationi

Entry nameiS39AD_HUMAN
AccessioniPrimary (citable) accession number: Q96H72
Secondary accession number(s): D3DQR6
, D3DQR7, E9PLY1, E9PQV3, Q659D9, Q8N7C9, Q8WV10
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 4, 2007
Last sequence update: May 18, 2010
Last modified: June 8, 2016
This is version 111 of the entry and version 3 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 11
    Human chromosome 11: 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.