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Protein

Synapse differentiation-inducing gene protein 1

Gene

SYNDIG1

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

Functioni

May regulate AMPA receptor content at nascent synapses, and have a role in postsynaptic development and maturation.By similarity

GO - Molecular functioni

  1. glutamate receptor binding Source: UniProtKB
  2. protein homodimerization activity Source: UniProtKB

GO - Biological processi

  1. intracellular protein transport Source: UniProtKB
  2. positive regulation of synapse assembly Source: UniProtKB
  3. response to biotic stimulus Source: InterPro
  4. synaptic vesicle clustering Source: UniProtKB
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
Synapse differentiation-inducing gene protein 1
Short name:
SynDIG1
Alternative name(s):
Dispanin subfamily C member 2
Short name:
DSPC2
Transmembrane protein 90B
Gene namesi
Name:SYNDIG1
Synonyms:C20orf39, TMEM90B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:15885. SYNDIG1.

Subcellular locationi

  1. Cell membrane; Single-pass type II membrane protein
  2. Early endosome membrane By similarity; Single-pass type II membrane protein By similarity
  3. Cell junctionsynapsepostsynaptic cell membranepostsynaptic density By similarity
  4. Cell junctionsynapse By similarity
  5. Cell projectiondendrite By similarity
  6. Cell projectiondendritic spine By similarity

  7. Note: Shuttles between the cell surface and early endosome membrane.By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 181181CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei182 – 20221HelicalSequence AnalysisAdd
BLAST
Topological domaini203 – 22826ExtracellularSequence AnalysisAdd
BLAST
Intramembranei229 – 24921HelicalSequence AnalysisAdd
BLAST
Topological domaini250 – 2589ExtracellularSequence Analysis

GO - Cellular componenti

  1. cell body Source: UniProtKB
  2. cell junction Source: UniProtKB-KW
  3. dendritic shaft Source: UniProtKB
  4. dendritic spine Source: UniProtKB
  5. early endosome membrane Source: UniProtKB
  6. excitatory synapse Source: UniProtKB
  7. integral component of plasma membrane Source: UniProtKB
  8. postsynaptic density Source: UniProtKB
  9. postsynaptic membrane Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Cell projection, Endosome, Membrane, Postsynaptic cell membrane, Synapse

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA25752.

Polymorphism and mutation databases

DMDMi23813901.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 258258Synapse differentiation-inducing gene protein 1PRO_0000135696Add
BLAST

Proteomic databases

PaxDbiQ9H7V2.
PRIDEiQ9H7V2.

PTM databases

PhosphoSiteiQ9H7V2.

Expressioni

Gene expression databases

BgeeiQ9H7V2.
CleanExiHS_C20orf39.
GenevestigatoriQ9H7V2.

Organism-specific databases

HPAiHPA059267.

Interactioni

Subunit structurei

Homodimer. Interacts with GRIA1 and GRIA2 (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
FATE1Q969F03EBI-726331,EBI-743099

Protein-protein interaction databases

BioGridi123022. 1 interaction.
IntActiQ9H7V2. 2 interactions.
MINTiMINT-1378766.
STRINGi9606.ENSP00000366058.

Structurei

3D structure databases

ProteinModelPortaliQ9H7V2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi151 – 1555Poly-Glu

Sequence similaritiesi

Belongs to the CD225/Dispanin family.Curated

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG41838.
GeneTreeiENSGT00390000009914.
HOVERGENiHBG051163.
InParanoidiQ9H7V2.
OMAiRNEPVQQ.
OrthoDBiEOG7P5T2F.
PhylomeDBiQ9H7V2.
TreeFamiTF331357.

Family and domain databases

InterProiIPR007593. CD225/Dispanin_fam.
[Graphical view]
PfamiPF04505. Dispanin. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9H7V2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDGIIEQKSM LVHSKISDAG KRNGLINTRN LMAESRDGLV SVYPAPQYQS
60 70 80 90 100
HRVGASTVPA SLDSSRSEPM QQLLDPNTLQ QSVESRYRPN IILYSEGVLR
110 120 130 140 150
SWGDGVAADC CETTFIEDRS PTKDSLEYPD GKFIDLSADD IKIHTLSYDV
160 170 180 190 200
EEEEEFQELE SDYSSDTESE DNFLMMPPRD HLGLSVFSML CCFWPLGIAA
210 220 230 240 250
FYLSHETNKA VAKGDLHQAS TSSRRALFLA VLSITIGTGV YVGVAVALIA

YLSKNNHL
Length:258
Mass (Da):28,551
Last modified:March 1, 2001 - v1
Checksum:i89EDF1AE382246A2
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti54 – 541G → R.
Corresponds to variant rs6083553 [ dbSNP | Ensembl ].
VAR_053733

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK024282 mRNA. Translation: BAB14872.1.
CR457325 mRNA. Translation: CAG33606.1.
AL049594, AL157413 Genomic DNA. Translation: CAI23040.1.
AL157413, AL049594 Genomic DNA. Translation: CAI15132.1.
BC030637 mRNA. Translation: AAH30637.1.
CCDSiCCDS13164.1.
RefSeqiNP_079169.1. NM_024893.2.
UniGeneiHs.124638.

Genome annotation databases

EnsembliENST00000376862; ENSP00000366058; ENSG00000101463.
GeneIDi79953.
KEGGihsa:79953.
UCSCiuc002wtw.1. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK024282 mRNA. Translation: BAB14872.1.
CR457325 mRNA. Translation: CAG33606.1.
AL049594, AL157413 Genomic DNA. Translation: CAI23040.1.
AL157413, AL049594 Genomic DNA. Translation: CAI15132.1.
BC030637 mRNA. Translation: AAH30637.1.
CCDSiCCDS13164.1.
RefSeqiNP_079169.1. NM_024893.2.
UniGeneiHs.124638.

3D structure databases

ProteinModelPortaliQ9H7V2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123022. 1 interaction.
IntActiQ9H7V2. 2 interactions.
MINTiMINT-1378766.
STRINGi9606.ENSP00000366058.

PTM databases

PhosphoSiteiQ9H7V2.

Polymorphism and mutation databases

DMDMi23813901.

Proteomic databases

PaxDbiQ9H7V2.
PRIDEiQ9H7V2.

Protocols and materials databases

DNASUi79953.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000376862; ENSP00000366058; ENSG00000101463.
GeneIDi79953.
KEGGihsa:79953.
UCSCiuc002wtw.1. human.

Organism-specific databases

CTDi79953.
GeneCardsiGC20P024451.
HGNCiHGNC:15885. SYNDIG1.
HPAiHPA059267.
MIMi614311. gene.
neXtProtiNX_Q9H7V2.
PharmGKBiPA25752.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG41838.
GeneTreeiENSGT00390000009914.
HOVERGENiHBG051163.
InParanoidiQ9H7V2.
OMAiRNEPVQQ.
OrthoDBiEOG7P5T2F.
PhylomeDBiQ9H7V2.
TreeFamiTF331357.

Miscellaneous databases

GenomeRNAii79953.
NextBioi69921.
PROiQ9H7V2.
SOURCEiSearch...

Gene expression databases

BgeeiQ9H7V2.
CleanExiHS_C20orf39.
GenevestigatoriQ9H7V2.

Family and domain databases

InterProiIPR007593. CD225/Dispanin_fam.
[Graphical view]
PfamiPF04505. Dispanin. 1 hit.
[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].
  2. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
    Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
    Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  3. "The DNA sequence and comparative analysis of human chromosome 20."
    Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E.
    , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
    Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
    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].
    Tissue: Hippocampus.
  5. "The dispanins: a novel gene family of ancient origin that contains 14 human members."
    Sallman Almen M., Bringeland N., Fredriksson R., Schioth H.B.
    PLoS ONE 7:E31961-E31961(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY.

Entry informationi

Entry nameiSYNG1_HUMAN
AccessioniPrimary (citable) accession number: Q9H7V2
Secondary accession number(s): Q6IA30, Q9H514
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: March 1, 2001
Last modified: April 29, 2015
This is version 100 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 20
    Human chromosome 20: 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

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 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.