This gene encodes a member of the synaptonemal complex, which links homologous chromosomes during prophase I of meiosis. The tripartite structure of the complex is highly conserved amongst metazoans. It consists of two lateral elements and a central region formed by transverse elements and a central element. The protein encoded by this gene localizes to the central element and ... See more...

Aliases for SYCE1 Gene

Aliases for SYCE1 Gene

  • Synaptonemal Complex Central Element Protein 1 2 3 4 5
  • Cancer/Testis Antigen 76 2 3 4
  • CT76 2 3 4
  • C10orf94 3 4
  • Epididymis Secretory Sperm Binding Protein 3
  • Chromosome 10 Open Reading Frame 94 2
  • BA108K14.6 2
  • SPGF15 3
  • POF12 3
  • SYCE1 5

External Ids for SYCE1 Gene

Previous HGNC Symbols for SYCE1 Gene

  • C10orf94

Previous GeneCards Identifiers for SYCE1 Gene

  • GC10M135257
  • GC10M135217
  • GC10M135367
  • GC10M128909

Summaries for SYCE1 Gene

Entrez Gene Summary for SYCE1 Gene

  • This gene encodes a member of the synaptonemal complex, which links homologous chromosomes during prophase I of meiosis. The tripartite structure of the complex is highly conserved amongst metazoans. It consists of two lateral elements and a central region formed by transverse elements and a central element. The protein encoded by this gene localizes to the central element and is required for initiation and elongation of the synapsis. Allelic variants of this gene have been associated with premature ovarian failure and spermatogenic failure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

GeneCards Summary for SYCE1 Gene

SYCE1 (Synaptonemal Complex Central Element Protein 1) is a Protein Coding gene. Diseases associated with SYCE1 include Premature Ovarian Failure 12 and Spermatogenic Failure 15. Among its related pathways are Meiosis and Cell Cycle, Mitotic. An important paralog of this gene is SYCE1L.

UniProtKB/Swiss-Prot Summary for SYCE1 Gene

  • Major component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Requires SYCP1 in order to be incorporated into the central element. May have a role in the synaptonemal complex assembly, stabilization and recombination.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYCE1 Gene

Genomics for SYCE1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SYCE1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J133569 Promoter 0.8 EPDnew Ensembl 600.7 +0.6 634 1.2 EZH2 SYCE1 SPRNP1 lnc-SYCE1-1 ENSG00000288107 piR-58459 CYP2E1
GH10J133565 Promoter 0.6 EPDnew 600.7 +4.3 4261 0.1 YY1 NRF1 ZBTB33 ENSG00000288107 SYCE1 piR-58459 ENSG00000286789 CYP2E1
GH10J133622 Enhancer 0.3 Ensembl 6.6 -53.1 -53066 0.6 EZH2 MN298114-029 SYCE1 FRG2B ENSG00000288107
GH10J133541 Enhancer 0.2 Ensembl 10.4 +28.2 28179 0.6 ENSG00000286789 piR-36421-001 CYP2E1 SYCE1 ENSG00000278518
GH10J133516 Enhancer 0.4 FANTOM5 4.5 +53.4 53365 0.4 TEAD1 TEAD3 CYP2E1 SYCE1 LOC105378575 LOC107984284 SCART1 SPRN
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYCE1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYCE1

Top Transcription factor binding sites by QIAGEN in the SYCE1 gene promoter:
  • GR
  • GR-alpha
  • LyF-1
  • MIF-1
  • Nkx5-1
  • STAT3

Genomic Locations for SYCE1 Gene

Genomic Locations for SYCE1 Gene
chr10:133,553,900-133,569,835
(GRCh38/hg38)
Size:
15,936 bases
Orientation:
Minus strand
chr10:135,367,404-135,382,876
(GRCh37/hg19)
Size:
15,473 bases
Orientation:
Minus strand

Genomic View for SYCE1 Gene

Genes around SYCE1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYCE1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYCE1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYCE1 Gene

Proteins for SYCE1 Gene

  • Protein details for SYCE1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N0S2-SYCE1_HUMAN
    Recommended name:
    Synaptonemal complex central element protein 1
    Protein Accession:
    Q8N0S2
    Secondary Accessions:
    • B2RC80
    • Q9BWU3
    • Q9BWU4

    Protein attributes for SYCE1 Gene

    Size:
    351 amino acids
    Molecular mass:
    39699 Da
    Quaternary structure:
    • Homodimer. Found in a complex with SYCP1 and SYCE2. Interacts with SYCP1, SYCE2 and SYCE3. Interacts with SIX6OS1.
    SequenceCaution:
    • Sequence=AAH34821.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for SYCE1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYCE1 Gene

Post-translational modifications for SYCE1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYCE1 Gene

No data available for DME Specific Peptides for SYCE1 Gene

Domains & Families for SYCE1 Gene

Gene Families for SYCE1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SYCE1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYCE1 Gene

GenScript: Design optimal peptide antigens:
  • Cancer/testis antigen 76 (SYCE1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N0S2

UniProtKB/Swiss-Prot:

SYCE1_HUMAN :
  • Belongs to the SYCE family.
Family:
  • Belongs to the SYCE family.
genes like me logo Genes that share domains with SYCE1: view

Function for SYCE1 Gene

Molecular function for SYCE1 Gene

UniProtKB/Swiss-Prot Function:
Major component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Requires SYCP1 in order to be incorporated into the central element. May have a role in the synaptonemal complex assembly, stabilization and recombination.

Phenotypes From GWAS Catalog for SYCE1 Gene

Gene Ontology (GO) - Molecular Function for SYCE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SYCE1: view
genes like me logo Genes that share phenotypes with SYCE1: view

Human Phenotype Ontology for SYCE1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SYCE1 Gene

MGI Knock Outs for SYCE1:

Animal Model Products

CRISPR Products

miRNA for SYCE1 Gene

miRTarBase miRNAs that target SYCE1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYCE1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SYCE1 Gene

Localization for SYCE1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYCE1 Gene

Nucleus. Chromosome. Note=Associates with chromatin. In prophase I stage of meiosis, localizes in the transverse central elements of the central region between lateral elements of the synaptonemal complexes. Found only where the chromosome cores are synapsed. Colocalizes with SYCE2 in the central elements. {ECO:0000250 UniProtKB:Q9D495}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYCE1 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
cytoskeleton 1
mitochondrion 0
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Nucleoplasm (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYCE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000795 synaptonemal complex IBA 21873635
GO:0000801 central element ISS 15944401
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with SYCE1: view

Pathways & Interactions for SYCE1 Gene

PathCards logo

SuperPathways for SYCE1 Gene

SuperPathway Contained pathways
1 Meiosis
.73
2 Cell Cycle, Mitotic
genes like me logo Genes that share pathways with SYCE1: view

Pathways by source for SYCE1 Gene

3 Reactome pathways for SYCE1 Gene

Gene Ontology (GO) - Biological Process for SYCE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007049 cell cycle IEA --
GO:0007130 synaptonemal complex assembly IC 15944401
GO:0051301 cell division IEA --
GO:0051321 meiotic cell cycle IEA --
GO:0070193 synaptonemal complex organization IEA --
genes like me logo Genes that share ontologies with SYCE1: view

No data available for SIGNOR curated interactions for SYCE1 Gene

Drugs & Compounds for SYCE1 Gene

No Compound Related Data Available

Transcripts for SYCE1 Gene

mRNA/cDNA for SYCE1 Gene

4 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYCE1

Alternative Splicing Database (ASD) splice patterns (SP) for SYCE1 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4a · 4b · 4c · 4d ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16
SP1: - - - - - - - -
SP2: - - -
SP3: -
SP4: - - -
SP5:
SP6: -
SP7: -

Relevant External Links for SYCE1 Gene

GeneLoc Exon Structure for
SYCE1

Expression for SYCE1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYCE1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYCE1 Gene

This gene is overexpressed in Testis (x16.9).

Protein differential expression in normal tissues from HIPED for SYCE1 Gene

This gene is overexpressed in Synovial fluid (25.0), Lymph node (15.0), Testis (12.9), and Fetal ovary (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SYCE1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYCE1

SOURCE GeneReport for Unigene cluster for SYCE1 Gene:

Hs.553795

Evidence on tissue expression from TISSUES for SYCE1 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with SYCE1: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYCE1 Gene

Orthologs for SYCE1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYCE1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SYCE1 30 31
  • 98.96 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LOC480826 30
  • 83.6 (n)
SYCE1 31
  • 76 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SYCE1 30 31
  • 83.12 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Syce1 30 17 31
  • 76.57 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Syce1 30
  • 76.49 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 47 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 33 (a)
OneToMany
Species where no ortholog for SYCE1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for SYCE1 Gene

ENSEMBL:
Gene Tree for SYCE1 (if available)
TreeFam:
Gene Tree for SYCE1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYCE1: view image

Paralogs for SYCE1 Gene

Paralogs for SYCE1 Gene

(1) SIMAP similar genes for SYCE1 Gene using alignment to 1 proteins:

  • SYCE1_HUMAN
genes like me logo Genes that share paralogs with SYCE1: view

Variants for SYCE1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYCE1 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
643186 Pathogenic: not provided 133,557,074(-) GTC/G FRAMESHIFT_VARIANT
711062 Benign: not provided 133,559,335(-) C/T SYNONYMOUS_VARIANT
711322 Benign: not provided 133,555,402(-) G/C SYNONYMOUS_VARIANT
715410 Benign: not provided 133,557,853(-) GA/G INTRON_VARIANT
728677 Likely Benign: not provided 133,555,644(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SYCE1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SYCE1 Gene

Variant ID Type Subtype PubMed ID
dgv1000n100 CNV gain 25217958
dgv1001n100 CNV gain 25217958
dgv1003n100 CNV gain+loss 25217958
dgv1004n100 CNV loss 25217958
dgv1006n100 CNV gain 25217958
dgv1007n100 CNV gain 25217958
dgv123n27 CNV gain 19166990
dgv125n27 CNV gain 19166990
dgv126n27 CNV gain 19166990
dgv127n27 CNV gain 19166990
dgv128n27 CNV gain 19166990
dgv129n27 CNV gain 19166990
dgv1486n54 CNV gain 21841781
dgv1487n54 CNV gain 21841781
dgv1492n54 CNV loss 21841781
dgv1493n54 CNV gain 21841781
dgv1494n54 CNV gain+loss 21841781
dgv1495n54 CNV gain 21841781
dgv1496n54 CNV gain 21841781
dgv1497n54 CNV loss 21841781
dgv1498n54 CNV gain 21841781
dgv1499n54 CNV loss 21841781
dgv1500n54 CNV loss 21841781
dgv172e214 CNV gain 21293372
dgv174e214 CNV gain 21293372
dgv181e199 CNV deletion 23128226
dgv304e212 CNV gain 25503493
dgv305e212 CNV gain 25503493
dgv35e55 CNV gain 17911159
dgv36e55 CNV gain 17911159
dgv37e55 CNV gain 17911159
dgv8n64 CNV gain 17921354
dgv999n100 CNV gain 25217958
esv1354504 CNV deletion 17803354
esv2419070 CNV deletion 18987734
esv2421904 CNV duplication 20811451
esv2750853 CNV gain 17911159
esv2750875 CNV loss 17911159
esv2759793 CNV gain+loss 17122850
esv2760130 CNV gain+loss 21179565
esv2764146 CNV gain+loss 21179565
esv28562 CNV gain+loss 19812545
esv33719 CNV gain 17666407
esv3439276 CNV duplication 20981092
esv35157 CNV gain 17911159
esv3579237 CNV loss 25503493
esv3579239 CNV loss 25503493
esv3625046 CNV loss 21293372
esv3625052 CNV loss 21293372
esv3891902 CNV gain+loss 25118596
esv3891903 CNV gain 25118596
nsv1043323 CNV gain 25217958
nsv1052904 CNV gain 25217958
nsv1075825 CNV duplication 25765185
nsv1137976 CNV deletion 24896259
nsv1159789 CNV duplication 26073780
nsv428243 CNV gain 18775914
nsv436819 CNV insertion 17901297
nsv442594 CNV gain 18776908
nsv469597 CNV gain 16826518
nsv470981 CNV gain 18288195
nsv482151 CNV gain 20164927
nsv498746 CNV loss 21111241
nsv514545 CNV gain 21397061
nsv517180 CNV gain+loss 19592680
nsv528260 CNV loss 19592680
nsv552589 CNV gain 21841781
nsv552721 CNV gain 21841781
nsv552725 CNV gain 21841781
nsv552726 CNV gain 21841781
nsv552727 CNV gain 21841781
nsv552729 CNV gain 21841781
nsv552732 CNV gain 21841781
nsv552740 CNV loss 21841781
nsv7631 CNV deletion 18451855
nsv818790 CNV gain 17921354
nsv819137 CNV loss 19587683
nsv832042 CNV gain 17160897
nsv8752 CNV gain+loss 18304495
nsv952711 CNV deletion 24416366

Variation tolerance for SYCE1 Gene

Residual Variation Intolerance Score: 93.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.72; 83.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYCE1 Gene

Human Gene Mutation Database (HGMD)
SYCE1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYCE1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYCE1 Gene

Disorders for SYCE1 Gene

MalaCards: The human disease database

(13) MalaCards diseases for SYCE1 Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SYCE1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SYCE1_HUMAN
  • Premature ovarian failure 12 (POF12) [MIM:616947]: An ovarian disorder defined as the cessation of ovarian function under the age of 40 years. It is characterized by oligomenorrhea or amenorrhea, in the presence of elevated levels of serum gonadotropins and low estradiol. {ECO:0000269 PubMed:25062452}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Spermatogenic failure, 15 (SPGF15) [MIM:616950]: An infertility disorder caused by spermatogenesis defects and characterized by non-obstructive azoospermia due to complete meiotic maturation arrest. SPGF15 inheritance is autosomal recessive. {ECO:0000269 PubMed:25899990}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SYCE1

genes like me logo Genes that share disorders with SYCE1: view

No data available for Genatlas for SYCE1 Gene

Publications for SYCE1 Gene

  1. Genomic analysis of human chromosome 10q and 4q telomeres suggests a common origin. (PMID: 11829491) van Geel M … Hewitt JE (Genomics 2002) 2 3 4
  2. Deleterious mutation in SYCE1 is associated with non-obstructive azoospermia. (PMID: 25899990) Maor-Sagie E … Frumkin A (Journal of assisted reproduction and genetics 2015) 3 4
  3. Exome sequencing reveals SYCE1 mutation associated with autosomal recessive primary ovarian insufficiency. (PMID: 25062452) de Vries L … Basel-Vanagaite L (The Journal of clinical endocrinology and metabolism 2014) 3 4
  4. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P … Rogers J (Nature 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for SYCE1 Gene

Sources for SYCE1 Gene