Aliases for SYCP2L Gene

Aliases for SYCP2L Gene

  • Synaptonemal Complex Protein 2 Like 2 3 5
  • Synaptonemal Complex Protein 2-Like 2 3 4
  • 145 KDa Nucleolar Protein Homolog 3 4
  • SCP-2-Like 3 4
  • C6orf177 3 4
  • NO145 3 4
  • Chromosome 6 Open Reading Frame 177 2
  • DJ62D2.1 3
  • HsNO145 4

External Ids for SYCP2L Gene

Previous HGNC Symbols for SYCP2L Gene

  • C6orf177

Previous GeneCards Identifiers for SYCP2L Gene

  • GC06P010997
  • GC06P010762

Summaries for SYCP2L Gene

GeneCards Summary for SYCP2L Gene

SYCP2L (Synaptonemal Complex Protein 2 Like) is a Protein Coding gene. Diseases associated with SYCP2L include Orofacial Cleft 1. An important paralog of this gene is SYCP2.

UniProtKB/Swiss-Prot Summary for SYCP2L Gene

  • Oocyte-specific protein that localizes to centromeres at the dictyate stage and regulates the survival of primordial oocytes.

Additional gene information for SYCP2L Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYCP2L Gene

Genomics for SYCP2L Gene

GeneHancer (GH) Regulatory Elements for SYCP2L Gene

Promoters and enhancers for SYCP2L 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
GH06J010886 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 536.3 +0.3 270 2.2 CTCF ZSCAN5C TCF12 NRF1 USF1 GTF2E2 PHB2 ZNF639 ZIC2 ZBTB10 SYCP2L GCM2 piR-51819-022 ENSG00000272162
GH06J010910 Promoter 0.3 EPDnew 511.9 +23.3 23298 0.1 SYCP2L GCM2 ENSG00000235051 RF00017-5264 piR-35002-042 ENSG00000272162
GH06J010897 Promoter 0.3 EPDnew 500.4 +11.1 11146 0.1 SYCP2L piR-51819-022 RF00017-5264 ENSG00000272162
GH06J010907 Promoter 0.3 EPDnew 500.4 +20.7 20720 0.1 RF00017-5264 SYCP2L piR-35002-042 ENSG00000272162
GH06J011042 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 16.1 +156.9 156947 2.8 EP300 HNRNPK CTCF ZFX REST ZBTB10 ZBTB26 KLF7 ZNF662 CTBP1 ELOVL2-AS1 ELOVL2 piR-53111 TFAP2A-AS1 SYCP2L GCM2 ENSG00000235051 ERVFRD-1 RF00017-5266
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYCP2L on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYCP2L

Top Transcription factor binding sites by QIAGEN in the SYCP2L gene promoter:
  • Bach2
  • GATA-1
  • p53
  • Pax-2
  • Pax-2a
  • POU2F1
  • POU2F1a
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for SYCP2L Gene

Genomic Locations for SYCP2L Gene
chr6:10,886,831-10,979,320
(GRCh38/hg38)
Size:
92,490 bases
Orientation:
Plus strand
chr6:10,748,027-10,979,553
(GRCh37/hg19)
Size:
231,527 bases
Orientation:
Plus strand

Genomic View for SYCP2L Gene

Genes around SYCP2L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYCP2L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYCP2L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYCP2L Gene

Proteins for SYCP2L Gene

  • Protein details for SYCP2L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5T4T6-SYC2L_HUMAN
    Recommended name:
    Synaptonemal complex protein 2-like
    Protein Accession:
    Q5T4T6
    Secondary Accessions:
    • A6NDS5
    • Q08GK5
    • Q6ZRM2
    • Q96EJ2

    Protein attributes for SYCP2L Gene

    Size:
    812 amino acids
    Molecular mass:
    93599 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAI16226.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI22075.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for SYCP2L Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYCP2L Gene

Post-translational modifications for SYCP2L Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYCP2L Gene

No data available for DME Specific Peptides for SYCP2L Gene

Domains & Families for SYCP2L Gene

Gene Families for SYCP2L Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SYCP2L Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYCP2L Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60468, weakly similar to Synaptonemal complex protein 2 (B4DFB8_HUMAN)
  • 145 kDa nucleolar protein homolog (SYC2L_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q5T4T6

UniProtKB/Swiss-Prot:

SYC2L_HUMAN :
  • Belongs to the SYCP2 family.
Family:
  • Belongs to the SYCP2 family.
genes like me logo Genes that share domains with SYCP2L: view

Function for SYCP2L Gene

Molecular function for SYCP2L Gene

UniProtKB/Swiss-Prot Function:
Oocyte-specific protein that localizes to centromeres at the dictyate stage and regulates the survival of primordial oocytes.

Phenotypes From GWAS Catalog for SYCP2L Gene

genes like me logo Genes that share phenotypes with SYCP2L: view

Animal Models for SYCP2L Gene

MGI Knock Outs for SYCP2L:

Animal Model Products

CRISPR Products

miRNA for SYCP2L Gene

miRTarBase miRNAs that target SYCP2L

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SYCP2L Gene

Localization for SYCP2L Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYCP2L Gene

Nucleus. Chromosome, centromere. Note=Localized to the synaptonemal complex lateral elements in late diplotene oocytes, while it is absent on the synaptonemal complex of leptotene, zygotene, pachytene and early diplotene oocytes (By similarity). Localizes to centromeres in dictyate oocytes (By similarity). Detected in nuclear granules and sizable aggregates (PubMed:17374641). {ECO:0000250 UniProtKB:A0A0M3U1B0, ECO:0000269 PubMed:17374641}.

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 SYCP2L gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SYCP2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000780 condensed nuclear chromosome, centromeric region IDA 26362258
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with SYCP2L: view

Pathways & Interactions for SYCP2L Gene

PathCards logo

SuperPathways for SYCP2L Gene

No Data Available

Interacting Proteins for SYCP2L Gene

STRING Interaction Network Preview (showing top 3 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000283141 Q5T4T6-SYC2L_HUMAN for SYCP2L Gene via STRING IID

;

Gene Ontology (GO) - Biological Process for SYCP2L Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SYCP2L Gene

Drugs & Compounds for SYCP2L Gene

No Compound Related Data Available

Transcripts for SYCP2L Gene

mRNA/cDNA for SYCP2L Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYCP2L Gene

No ASD Table

Relevant External Links for SYCP2L Gene

GeneLoc Exon Structure for
SYCP2L

Expression for SYCP2L Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYCP2L Gene

mRNA differential expression in normal tissues according to GTEx for SYCP2L Gene

This gene is overexpressed in Testis (x4.4).

Protein differential expression in normal tissues from HIPED for SYCP2L Gene

This gene is overexpressed in Neutrophil (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SYCP2L Gene



Protein tissue co-expression partners for SYCP2L Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYCP2L

SOURCE GeneReport for Unigene cluster for SYCP2L Gene:

Hs.729128

mRNA Expression by UniProt/SwissProt for SYCP2L Gene:

Q5T4T6-SYC2L_HUMAN
Tissue specificity: Expressed in the ovary (at protein level).
genes like me logo Genes that share expression patterns with SYCP2L: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYCP2L Gene

Orthologs for SYCP2L Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYCP2L Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYCP2L 31 30
  • 99.34 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SYCP2L 31 30
  • 80.34 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SYCP2L 31 30
  • 79 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Sycp2l 17 31 30
  • 67.56 (n)
rat
(Rattus norvegicus)
Mammalia Sycp2l 30
  • 63.36 (n)
oppossum
(Monodelphis domestica)
Mammalia SYCP2L 31
  • 61 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYCP2L 31
  • 54 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYCP2L 31 30
  • 63.09 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYCP2L 31
  • 24 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sycp2l 30
  • 56.49 (n)
African clawed frog
(Xenopus laevis)
Amphibia NO145 30
zebrafish
(Danio rerio)
Actinopterygii sycp2l 31 30
  • 50 (n)
OneToOne
Species where no ortholog for SYCP2L was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • 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 squirt (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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SYCP2L Gene

ENSEMBL:
Gene Tree for SYCP2L (if available)
TreeFam:
Gene Tree for SYCP2L (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYCP2L: view image

Paralogs for SYCP2L Gene

Paralogs for SYCP2L Gene

(1) SIMAP similar genes for SYCP2L Gene using alignment to 3 proteins:

  • SYC2L_HUMAN
  • B4DFB8_HUMAN
  • H7C4Q1_HUMAN
genes like me logo Genes that share paralogs with SYCP2L: view

Variants for SYCP2L Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYCP2L Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs1225746 - p.Pro672Ser
rs3798751 - p.Asn647Asp
rs6456746 - p.Val94Ile
rs905595849 - p.Arg291Trp

Additional dbSNP identifiers (rs#s) for SYCP2L Gene

Structural Variations from Database of Genomic Variants (DGV) for SYCP2L Gene

Variant ID Type Subtype PubMed ID
esv2506207 CNV insertion 19546169
nsv1124031 CNV deletion 24896259
nsv348982 CNV deletion 16902084
nsv519009 CNV loss 19592680
nsv519302 CNV loss 19592680

Variation tolerance for SYCP2L Gene

Residual Variation Intolerance Score: 56% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.63; 78.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYCP2L Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYCP2L

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYCP2L Gene

Disorders for SYCP2L Gene

MalaCards: The human disease database

(1) MalaCards diseases for SYCP2L Gene - From: DISEASES

Disorder Aliases PubMed IDs
orofacial cleft 1
  • ofc1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SYCP2L

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SYCP2L: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYCP2L Gene

Publications for SYCP2L Gene

  1. Accelerated reproductive aging in females lacking a novel centromere protein SYCP2L. (PMID: 26362258) Zhou J … Wang PJ (Human molecular genetics 2015) 3 4 54
  2. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. (PMID: 22267201) Stolk L … Lunetta KL (Nature genetics 2012) 3 41 54
  3. Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. (PMID: 21829377) Lemaitre RN … Steffen LM (PLoS genetics 2011) 3 41 54
  4. Genome-wide association studies identify loci associated with age at menarche and age at natural menopause. (PMID: 19448621) He C … Chasman DI (Nature genetics 2009) 3 41 54
  5. Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis. (PMID: 25085501) Bunyavanich S … Weiss ST (BMC medical genomics 2014) 3 54

Products for SYCP2L Gene

Sources for SYCP2L Gene