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    SYCE2 synaptonemal complex central element protein 2 [ Homo sapiens (human) ]

    Gene ID: 256126, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SYCE2provided by HGNC
    Official Full Name
    synaptonemal complex central element protein 2provided by HGNC
    Primary source
    HGNC:HGNC:27411
    See related
    Ensembl:ENSG00000161860 MIM:611487; AllianceGenome:HGNC:27411
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CESC1
    Summary
    The protein encoded by this gene is part of the synaptonemal complex formed between homologous chromosomes during meiotic prophase. The encoded protein associates with SYCP1 and SYCE1 and is found only where chromosome cores are synapsed. [provided by RefSeq, Dec 2012]
    Expression
    Broad expression in testis (RPKM 7.5), liver (RPKM 2.0) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYCE2 in Genome Data Viewer
    Location:
    19p13.13
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12898786..12919293, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13023239..13043759, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13009600..13030107, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CRISPRi-FlowFISH-validated PRDX2 and RAD23A regulatory element Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10180 Neighboring gene CRISPRi-FlowFISH-validated CALR, DHPS, JUNB, PRDX2, RAD23A, RNASEH2A and WDR83OS regulatory element Neighboring gene CRISPRi-FlowFISH-validated KLF1 regulatory element 2 Neighboring gene KLF transcription factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14090 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr19:13001481-13002118 and GRCh37_chr19:13002119-13002756 Neighboring gene glutaryl-CoA dehydrogenase Neighboring gene ribosomal protein S6 pseudogene 25 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:13010146-13011345 Neighboring gene CRISPRi-FlowFISH-validated KLF1 regulatory element 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:13021591-13021759 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:13022560-13023262 Neighboring gene Sharpr-MPRA regulatory region 4901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14092 Neighboring gene microRNA 5695 Neighboring gene phenylalanyl-tRNA synthetase subunit alpha Neighboring gene FARSA antisense RNA 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Structural analysis of the human SYCE2-TEX12 complex provides molecular insights into synaptonemal complex assembly. Davies OR, et al. Open Biol, 2012 Jul. PMID 22870393, Free PMC Article
    2. Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12. Dunce JM, et al. Nat Struct Mol Biol, 2021 Aug. PMID 34373646, Free PMC Article
    3. SYCE2 is required for synaptonemal complex assembly, double strand break repair, and homologous recombination. Bolcun-Filas E, et al. J Cell Biol, 2007 Mar 12. PMID 17339376, Free PMC Article
    4. Two novel proteins recruited by synaptonemal complex protein 1 (SYCP1) are at the centre of meiosis. Costa Y, et al. J Cell Sci, 2005 Jun 15. PMID 15944401
    5. The PSMA8 subunit of the spermatoproteasome is essential for proper meiotic exit and mouse fertility. Gómez-H L, et al. PLoS Genet, 2019 Aug. PMID 31437213, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12.
      Title: Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12.
    2. a model of chromosome synapsis driven by growth of SYCE2-TEX12 higher-order structures within the CE of the SC.
      Title: Structural analysis of the human SYCE2-TEX12 complex provides molecular insights into synaptonemal complex assembly.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
    EBI GWAS Catalog
    Seventy-five genetic loci influencing the human red blood cell.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptonemal complex assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in central element IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in central element ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    synaptonemal complex central element protein 2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_033049.1 RefSeqGene

      Range
      4980..25487
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001105578.2 → NP_001099048.1  synaptonemal complex central element protein 2

      See identical proteins and their annotated locations for NP_001099048.1

      Status: REVIEWED

      Source sequence(s)
      AC092069, AD000092, BC035819, DB449708
      Consensus CDS
      CCDS42509.1
      UniProtKB/Swiss-Prot
      B4DYD3, Q6PIF2
      Related
      ENSP00000293695.6, ENST00000293695.8
      Conserved Domains (2) summary
      pfam07307
      Location:48 → 116
      HEPPP_synt_1; Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1
      pfam16566
      Location:96 → 148
      CREPT; Cell-cycle alteration and expression-elevated protein in tumour

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      12898786..12919293 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011527882.3 → XP_011526184.1  synaptonemal complex central element protein 2 isoform X1

      Conserved Domains (2) summary
      pfam07307
      Location:48 → 116
      HEPPP_synt_1; Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1
      pfam16566
      Location:96 → 148
      CREPT; Cell-cycle alteration and expression-elevated protein in tumour

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      13023239..13043759 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320453.1 → XP_054176428.1  synaptonemal complex central element protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PIF2.2 GenPept UniProtKB/Swiss-Prot:Q6PIF2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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