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Protein

Synaptonemal complex protein 1

Gene

SYCP1

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

Functioni

Major component of the transverse filaments of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Required for normal assembly of the central element of the synaptonemal complexes. Required for normal centromere pairing during meiosis. Required for normal meiotic chromosome synapsis during oocyte and spermatocyte development and for normal male and female fertility.By similarity

GO - Molecular functioni

  • DNA binding Source: ProtInc

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Cell cycle, Cell division, Meiosis

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.

Names & Taxonomyi

Protein namesi
Recommended name:
Synaptonemal complex protein 1
Short name:
SCP-1
Alternative name(s):
Cancer/testis antigen 8
Short name:
CT8
Gene namesi
Name:SYCP1
Synonyms:SCP1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:11487. SYCP1.

Subcellular locationi

  • Nucleus By similarity
  • Chromosome By similarity
  • Chromosomecentromere By similarity

  • Note: In tripartite segments of synaptonemal complexes, between lateral elements in the nucleus. Its N-terminus is found towards the center of the synaptonemal complex while the C-terminus extends well into the lateral domain of the synaptonemal complex (By similarity). Only rarely detected at centromeres during leptotene and zygotene. Detected at centromeres during mid-diplotene, when it is no longer present along chromosome arms. No longer detected at centromeres at later stages of meiosis (By similarity).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA36269.

Polymorphism and mutation databases

BioMutaiSYCP1.
DMDMi209572682.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 976976Synaptonemal complex protein 1PRO_0000072362Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki295 – 295Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ15431.
MaxQBiQ15431.
PaxDbiQ15431.
PRIDEiQ15431.

PTM databases

iPTMnetiQ15431.
PhosphoSiteiQ15431.
SwissPalmiQ15431.

Expressioni

Tissue specificityi

Testis.1 Publication

Gene expression databases

BgeeiQ15431.
CleanExiHS_SYCP1.
ExpressionAtlasiQ15431. baseline and differential.
GenevisibleiQ15431. HS.

Organism-specific databases

HPAiHPA021083.

Interactioni

Subunit structurei

Homodimer (PubMed:26323297). Component of synaptonemal complexes. Found in a complex with SYCE1 and SYCE2. Interacts with SYCE1 and SYCE2 (By similarity).By similarity1 Publication

Protein-protein interaction databases

BioGridi112714. 3 interactions.
IntActiQ15431. 1 interaction.
STRINGi9606.ENSP00000358531.

Structurei

Secondary structure

1
976
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi675 – 72652Combined sources
Helixi728 – 76538Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4YTOX-ray2.00A/B662-801[»]
ProteinModelPortaliQ15431.
SMRiQ15431. Positions 745-783.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili107 – 798692Sequence analysisAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi117 – 1204Nuclear localization signalSequence analysis
Motifi679 – 6824Nuclear localization signalSequence analysis
Motifi880 – 8834Nuclear localization signalSequence analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi12 – 10089Asp/Glu-rich (acidic)Add
BLAST
Compositional biasi961 – 9699Arg/Lys-rich (basic)

Domaini

Consists of a predicted coiled coil region of 700 AA residues, flanked by N- and C-terminal globular domains. The C-terminal domain may have DNA-binding capacity.By similarity

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiENOG410IH3F. Eukaryota.
ENOG410XZPD. LUCA.
GeneTreeiENSGT00390000003368.
HOGENOMiHOG000154467.
HOVERGENiHBG059062.
InParanoidiQ15431.
KOiK19533.
OMAiQLNVYEI.
OrthoDBiEOG7KH9JR.
PhylomeDBiQ15431.
TreeFamiTF331737.

Family and domain databases

InterProiIPR008827. SYCP1.
IPR024835. SYCP1/2.
[Graphical view]
PANTHERiPTHR15607. PTHR15607. 1 hit.
PfamiPF05483. SCP-1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q15431-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKQKPFALF VPPRSSSSQV SAVKPQTLGG DSTFFKSFNK CTEDDFEFPF
60 70 80 90 100
AKTNLSKNGE NIDSDPALQK VNFLPVLEQV GNSDCHYQEG LKDSDLENSE
110 120 130 140 150
GLSRVYSKLY KEAEKIKKWK VSTEAELRQK ESKLQENRKI IEAQRKAIQE
160 170 180 190 200
LQFGNEKVSL KLEEGIQENK DLIKENNATR HLCNLLKETC ARSAEKTKKY
210 220 230 240 250
EYEREETRQV YMDLNNNIEK MITAFEELRV QAENSRLEMH FKLKEDYEKI
260 270 280 290 300
QHLEQEYKKE INDKEKQVSL LLIQITEKEN KMKDLTFLLE ESRDKVNQLE
310 320 330 340 350
EKTKLQSENL KQSIEKQHHL TKELEDIKVS LQRSVSTQKA LEEDLQIATK
360 370 380 390 400
TICQLTEEKE TQMEESNKAR AAHSFVVTEF ETTVCSLEEL LRTEQQRLEK
410 420 430 440 450
NEDQLKILTM ELQKKSSELE EMTKLTNNKE VELEELKKVL GEKETLLYEN
460 470 480 490 500
KQFEKIAEEL KGTEQELIGL LQAREKEVHD LEIQLTAITT SEQYYSKEVK
510 520 530 540 550
DLKTELENEK LKNTELTSHC NKLSLENKEL TQETSDMTLE LKNQQEDINN
560 570 580 590 600
NKKQEERMLK QIENLQETET QLRNELEYVR EELKQKRDEV KCKLDKSEEN
610 620 630 640 650
CNNLRKQVEN KNKYIEELQQ ENKALKKKGT AESKQLNVYE IKVNKLELEL
660 670 680 690 700
ESAKQKFGEI TDTYQKEIED KKISEENLLE EVEKAKVIAD EAVKLQKEID
710 720 730 740 750
KRCQHKIAEM VALMEKHKHQ YDKIIEERDS ELGLYKSKEQ EQSSLRASLE
760 770 780 790 800
IELSNLKAEL LSVKKQLEIE REEKEKLKRE AKENTATLKE KKDKKTQTFL
810 820 830 840 850
LETPEIYWKL DSKAVPSQTV SRNFTSVDHG ISKDKRDYLW TSAKNTLSTP
860 870 880 890 900
LPKAYTVKTP TKPKLQQREN LNIPIEESKK KRKMAFEFDI NSDSSETTDL
910 920 930 940 950
LSMVSEEETL KTLYRNNNPP ASHLCVKTPK KAPSSLTTPG STLKFGAIRK
960 970
MREDRWAVIA KMDRKKKLKE AEKLFV
Length:976
Mass (Da):114,192
Last modified:October 14, 2008 - v2
Checksum:i43058F1A4B7F57E5
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti46 – 461F → L in CAA64956 (PubMed:9119375).Curated
Sequence conflicti106 – 1061Y → F in CAA64956 (PubMed:9119375).Curated
Sequence conflicti153 – 1531F → C in BAA22586 (PubMed:9371398).Curated
Sequence conflicti161 – 1611K → T in BAA22586 (PubMed:9371398).Curated
Sequence conflicti168 – 1681E → D in BAA22586 (PubMed:9371398).Curated
Sequence conflicti216 – 2161N → S in BAA22586 (PubMed:9371398).Curated
Sequence conflicti225 – 2262FE → HG in CAA64956 (PubMed:9119375).Curated
Sequence conflicti350 – 3501K → N in BAA22586 (PubMed:9371398).Curated
Sequence conflicti360 – 3601E → D in BAA22586 (PubMed:9371398).Curated
Sequence conflicti400 – 4012KN → NY in BAA22586 (PubMed:9371398).Curated
Sequence conflicti406 – 4061K → I in BAA22586 (PubMed:9371398).Curated
Sequence conflicti415 – 4151K → T in BAA22586 (PubMed:9371398).Curated
Sequence conflicti449 – 4491E → D in BAA22586 (PubMed:9371398).Curated
Sequence conflicti483 – 51028IQLTA…LENEK → YSYCHYHKWTVLPKRGQRPK LSSKRE in BAA22586 (PubMed:9371398).CuratedAdd
BLAST
Sequence conflicti516 – 52813LTSHC…SLENK → YFTLQQASPPPN in BAA22586 (PubMed:9371398).CuratedAdd
BLAST
Sequence conflicti549 – 5491N → I in BAA22586 (PubMed:9371398).Curated
Sequence conflicti560 – 5601K → T in BAA22586 (PubMed:9371398).Curated
Sequence conflicti941 – 9411S → P in CAA64956 (PubMed:9119375).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti78 – 781E → D.
Corresponds to variant rs12563933 [ dbSNP | Ensembl ].
VAR_046993
Natural varianti805 – 8051E → D.1 Publication
Corresponds to variant rs1053812 [ dbSNP | Ensembl ].
VAR_046994

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95654 mRNA. Translation: CAA64956.1.
D67035 mRNA. Translation: BAA22586.1.
AL645502, AL358372 Genomic DNA. Translation: CAH70064.1.
AL358372, AL645502 Genomic DNA. Translation: CAH72847.1.
CH471122 Genomic DNA. Translation: EAW56622.1.
BC126266 mRNA. Translation: AAI26267.1.
CCDSiCCDS879.1.
RefSeqiNP_001269470.1. NM_001282541.1.
NP_003167.2. NM_003176.3.
XP_006710922.1. XM_006710859.1.
UniGeneiHs.112743.

Genome annotation databases

EnsembliENST00000369518; ENSP00000358531; ENSG00000198765.
ENST00000369522; ENSP00000358535; ENSG00000198765.
ENST00000618516; ENSP00000480997; ENSG00000198765.
GeneIDi6847.
KEGGihsa:6847.
UCSCiuc001efq.5. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X95654 mRNA. Translation: CAA64956.1.
D67035 mRNA. Translation: BAA22586.1.
AL645502, AL358372 Genomic DNA. Translation: CAH70064.1.
AL358372, AL645502 Genomic DNA. Translation: CAH72847.1.
CH471122 Genomic DNA. Translation: EAW56622.1.
BC126266 mRNA. Translation: AAI26267.1.
CCDSiCCDS879.1.
RefSeqiNP_001269470.1. NM_001282541.1.
NP_003167.2. NM_003176.3.
XP_006710922.1. XM_006710859.1.
UniGeneiHs.112743.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4YTOX-ray2.00A/B662-801[»]
ProteinModelPortaliQ15431.
SMRiQ15431. Positions 745-783.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112714. 3 interactions.
IntActiQ15431. 1 interaction.
STRINGi9606.ENSP00000358531.

PTM databases

iPTMnetiQ15431.
PhosphoSiteiQ15431.
SwissPalmiQ15431.

Polymorphism and mutation databases

BioMutaiSYCP1.
DMDMi209572682.

Proteomic databases

EPDiQ15431.
MaxQBiQ15431.
PaxDbiQ15431.
PRIDEiQ15431.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000369518; ENSP00000358531; ENSG00000198765.
ENST00000369522; ENSP00000358535; ENSG00000198765.
ENST00000618516; ENSP00000480997; ENSG00000198765.
GeneIDi6847.
KEGGihsa:6847.
UCSCiuc001efq.5. human.

Organism-specific databases

CTDi6847.
GeneCardsiSYCP1.
H-InvDBHIX0028584.
HGNCiHGNC:11487. SYCP1.
HPAiHPA021083.
MIMi602162. gene.
neXtProtiNX_Q15431.
PharmGKBiPA36269.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IH3F. Eukaryota.
ENOG410XZPD. LUCA.
GeneTreeiENSGT00390000003368.
HOGENOMiHOG000154467.
HOVERGENiHBG059062.
InParanoidiQ15431.
KOiK19533.
OMAiQLNVYEI.
OrthoDBiEOG7KH9JR.
PhylomeDBiQ15431.
TreeFamiTF331737.

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.

Miscellaneous databases

ChiTaRSiSYCP1. human.
GeneWikiiSYCP1.
GenomeRNAii6847.
PROiQ15431.
SOURCEiSearch...

Gene expression databases

BgeeiQ15431.
CleanExiHS_SYCP1.
ExpressionAtlasiQ15431. baseline and differential.
GenevisibleiQ15431. HS.

Family and domain databases

InterProiIPR008827. SYCP1.
IPR024835. SYCP1/2.
[Graphical view]
PANTHERiPTHR15607. PTHR15607. 1 hit.
PfamiPF05483. SCP-1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Human synaptonemal complex protein 1 (SCP1): isolation and characterization of the cDNA and chromosomal localization of the gene."
    Meuwissen R.L.J., Meerts I., Hoovers J.M.N., Leschot N.J., Heyting C.
    Genomics 39:377-384(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT ASP-805.
    Tissue: Testis.
  2. "Assignment of synaptonemal complex protein 1 (SCP1) to human chromosome 1p13 by fluorescence in situ hybridization and its expression in the testis."
    Kondoh N., Nishina Y., Tsuchida J., Koga M., Tanaka H., Uchida K., Inazawa J., Taketo M., Nozaki M., Nojima H., Matsumiya K., Namiki M., Okuyama A., Nishimune Y.
    Cytogenet. Cell Genet. 78:103-104(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
    Tissue: Testis.
  3. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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: Testis.
  6. "Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry."
    Denis N.J., Vasilescu J., Lambert J.-P., Smith J.C., Figeys D.
    Proteomics 7:868-874(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-295.
    Tissue: Mammary cancer.
  7. "X-ray crystallographic studies of the middle part of the human synaptonemal complex protein 1 coiled-coil domain."
    Park H.H.
    Acta Crystallogr. F 71:1131-1134(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION, SUBUNIT.

Entry informationi

Entry nameiSYCP1_HUMAN
AccessioniPrimary (citable) accession number: Q15431
Secondary accession number(s): O14963, Q5VXJ6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: October 14, 2008
Last modified: June 8, 2016
This is version 128 of the entry and version 2 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

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.