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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

DisGeNETi6847.
OpenTargetsiENSG00000198765.
PharmGKBiPA36269.

Polymorphism and mutation databases

BioMutaiSYCP1.
DMDMi209572682.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000723621 – 976Synaptonemal complex protein 1Add BLAST976

Proteomic databases

EPDiQ15431.
MaxQBiQ15431.
PaxDbiQ15431.
PeptideAtlasiQ15431.
PRIDEiQ15431.

PTM databases

iPTMnetiQ15431.
PhosphoSitePlusiQ15431.
SwissPalmiQ15431.

Expressioni

Tissue specificityi

Testis.1 Publication

Gene expression databases

BgeeiENSG00000198765.
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 interactors.
IntActiQ15431. 1 interactor.
STRINGi9606.ENSP00000358531.

Structurei

Secondary structure

1976
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi675 – 726Combined sources52
Helixi728 – 765Combined sources38

3D structure databases

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

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili107 – 798Sequence analysisAdd BLAST692

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi117 – 120Nuclear localization signalSequence analysis4
Motifi679 – 682Nuclear localization signalSequence analysis4
Motifi880 – 883Nuclear localization signalSequence analysis4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi12 – 100Asp/Glu-rich (acidic)Add BLAST89
Compositional biasi961 – 969Arg/Lys-rich (basic)9

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.
OrthoDBiEOG091G0116.
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)DescriptionActionsGraphical viewLength
Sequence conflicti46F → L in CAA64956 (PubMed:9119375).Curated1
Sequence conflicti106Y → F in CAA64956 (PubMed:9119375).Curated1
Sequence conflicti153F → C in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti161K → T in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti168E → D in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti216N → S in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti225 – 226FE → HG in CAA64956 (PubMed:9119375).Curated2
Sequence conflicti350K → N in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti360E → D in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti400 – 401KN → NY in BAA22586 (PubMed:9371398).Curated2
Sequence conflicti406K → I in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti415K → T in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti449E → D in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti483 – 510IQLTA…LENEK → YSYCHYHKWTVLPKRGQRPK LSSKRE in BAA22586 (PubMed:9371398).CuratedAdd BLAST28
Sequence conflicti516 – 528LTSHC…SLENK → YFTLQQASPPPN in BAA22586 (PubMed:9371398).CuratedAdd BLAST13
Sequence conflicti549N → I in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti560K → T in BAA22586 (PubMed:9371398).Curated1
Sequence conflicti941S → P in CAA64956 (PubMed:9119375).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04699378E → D.Corresponds to variant rs12563933dbSNPEnsembl.1
Natural variantiVAR_046994805E → D.1 PublicationCorresponds to variant rs1053812dbSNPEnsembl.1

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.
XP_016857673.1. XM_017002184.1.
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.
XP_016857673.1. XM_017002184.1.
UniGeneiHs.112743.

3D structure databases

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

Protein-protein interaction databases

BioGridi112714. 3 interactors.
IntActiQ15431. 1 interactor.
STRINGi9606.ENSP00000358531.

PTM databases

iPTMnetiQ15431.
PhosphoSitePlusiQ15431.
SwissPalmiQ15431.

Polymorphism and mutation databases

BioMutaiSYCP1.
DMDMi209572682.

Proteomic databases

EPDiQ15431.
MaxQBiQ15431.
PaxDbiQ15431.
PeptideAtlasiQ15431.
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.
DisGeNETi6847.
GeneCardsiSYCP1.
H-InvDBHIX0028584.
HGNCiHGNC:11487. SYCP1.
HPAiHPA021083.
MIMi602162. gene.
neXtProtiNX_Q15431.
OpenTargetsiENSG00000198765.
PharmGKBiPA36269.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IH3F. Eukaryota.
ENOG410XZPD. LUCA.
GeneTreeiENSGT00390000003368.
HOGENOMiHOG000154467.
HOVERGENiHBG059062.
InParanoidiQ15431.
KOiK19533.
OMAiQLNVYEI.
OrthoDBiEOG091G0116.
PhylomeDBiQ15431.
TreeFamiTF331737.

Enzyme and pathway databases

ReactomeiR-HSA-1221632. Meiotic synapsis.

Miscellaneous databases

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

Gene expression databases

BgeeiENSG00000198765.
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...

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: November 30, 2016
This is version 133 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.