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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SYCP2L Gene

protein-coding   GIFtS: 40
GCID: GC06P010762

Synaptonemal Complex Protein 2-Like

(Previous name: chromosome 6 open reading frame 177)
(Previous symbol: C6orf177)
  Search for SYCP2L
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Synaptonemal Complex Protein 2-Like1 2     SCP-2-like2 3
C6orf1771 2 3     Chromosome 6 Open Reading Frame 1771
145 KDa Nucleolar Protein Homolog2 3     dJ62D2.12
NO1452 3     hsNO1453

External Ids:    HGNC: 215371   Entrez Gene: 2217112   Ensembl: ENSG000001531577   UniProtKB: Q5T4T63   

Export aliases for SYCP2L gene to outside databases

Previous GC identifers: GC06P010997 GC06P010887


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for SYCP2L Gene: 
SYCP2L (synaptonemal complex protein 2-like) is a protein-coding gene. An important paralog of this gene is SYCP2.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.2  NT_007592.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SYCP2L gene promoter:
         p53   Bach2   SREBP-1c   Pax-2   Pax-2a   GATA-1   SREBP-1b   SREBP-1a   POU2F1   POU2F1a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for SYCP2L

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SYCP2L


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p24.2   Ensembl cytogenetic band:  6p24.2   HGNC cytogenetic band: 6p24.2

SYCP2L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SYCP2L gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P010762:  view genomic region     (about GC identifiers)

Start:
10,748,027 bp from pter      End:
10,979,553 bp from pter
Size:
231,527 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SYC2L_HUMAN, Q5T4T6 (See protein sequence)
Recommended Name: Synaptonemal complex protein 2-like  
Size: 812 amino acids; 93599 Da
Subcellular location: Nucleus. Note=Detected in nuclear granules and sizable aggregates
Sequence caution: Sequence=CAI16226.1; Type=Erroneous gene model prediction; Sequence=CAI22075.1; Type=Erroneous
gene model prediction;
Secondary accessions: A6NDS5 Q08GK5 Q6ZRM2 Q96EJ2
Alternative splicing: 2 isoforms:  Q5T4T6-1   Q5T4T6-2   

Explore the universe of human proteins at neXtProt for SYCP2L: NX_Q5T4T6

Explore proteomics data for SYCP2L at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q5T4T6

  • SYCP2L Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SYCP2L Protein Expression
    REFSEQ proteins: NP_001035364.2  
    ENSEMBL proteins: 
     ENSP00000340320   ENSP00000283141   ENSP00000417870   ENSP00000440676  

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    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--

    SYCP2L for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR024835 SYCP2/SYCP2-like

    Graphical View of Domain Structure for InterPro Entry Q5T4T6

    ProtoNet protein and cluster: Q5T4T6

    UniProtKB/Swiss-Prot: SYC2L_HUMAN, Q5T4T6
    Similarity: Belongs to the SYCP2 family


    SYCP2L for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Phenotypes:
         1 GenomeRNAi human phenotype for SYCP2L:
     Decreased Wnt reporter activit 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for SYCP2L 
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SYCP2L

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SYCP2L (SYC2L)

    Search CenterWatch for drugs/clinical trials and news about SYCP2L / SYC2L

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SYCP2L gene (2 alternative transcripts): 
    NM_194299.1  NM_001040274.2  

    Unigene Cluster for SYCP2L:

    Synaptonemal complex protein 2-like
    Hs.729128  [show with all ESTs]
    Unigene Representative Sequence: NM_001040274
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000341041 ENST00000283141(uc003mzo.3 uc011din.1 uc010jow.3)
    ENST00000487561 ENST00000474197 ENST00000465872 ENST00000488191 ENST00000543878(uc011dim.1)

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    Additional mRNA sequence: 

    AM293674.1 BC012225.1 

    5 DOTS entries:

    DT.451722  DT.40118684  DT.428416  DT.101978998  DT.121397398 

    22 AceView cDNA sequences:

    BX281631 CD724012 BM750187 BX095003 AW183165 AA782841 AK128130 AA115860 
    AI027433 AA442215 BC012225 BF590345 NM_194299 AW663048 AW674916 D78862 
    AA115861 BE541431 AA854950 D78902 C17789 H75288 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SYCP2L expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGAAAGACCA
    SYCP2L Expression
    About this image


    See SYCP2L Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SYCP2L

    SOURCE GeneReport for Unigene cluster: Hs.729128

    UniProtKB/Swiss-Prot: SYC2L_HUMAN, Q5T4T6
    Tissue specificity: Expressed in the ovary (at protein level)

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SYCP2L

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for SYCP2L gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sycp2l1 , 5 synaptonemal complex protein 2-like1, 5 70.09(n)1
    56.51(a)1
      13 (20.32 cM)5
    6372771  XM_001472337.21  XP_001472387.21 
     411143075 
    chicken
    (Gallus gallus)
    Aves SYCP2L1 synaptonemal complex protein 2-like 53.33(n)
    43.79(a)
      771534  XM_001234802.2  XP_001234803.2 
    lizard
    (Anolis carolinensis)
    Reptilia SYCP2L6
    synaptonemal complex protein 2-like
    18(a)
    1 ↔ 1
    GL343209.1(2674713-2727553)
    African clawed frog
    (Xenopus laevis)
    Amphibia NO1452 NO145 protein 69.91(n)    AJ249963.2 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1001499101 similar to synaptonemal complex protein 2-like 47.4(n)
    33.19(a)
      100149910  XM_001923161.2  XP_001923196.2 


    ENSEMBL Gene Tree for SYCP2L (if available)
    TreeFam Gene Tree for SYCP2L (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SYCP2L gene
    SYCP22  
    1 SIMAP similar gene for SYCP2L using alignment to 3 protein entries:     SYC2L_HUMAN (see all proteins):
    SYCP2

    SYCP2L for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/2105 SNPs in SYCP2L are shown (see all 2105)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0694174
    ----see VAR_0694172 R W mis40--------
    rs1505066121,2
    --10885100(+) TCAAAC/TGGTCG 1 -- us2k10--------
    rs93487231,2
    C,F,H--10885216(+) TCCTGT/ATGATT 1 -- us2k17Minor allele frequency- A:0.15EA NS NA 542
    rs1998607961,2
    C--10885237(+) TTCGT-/TTGTT 
            
    TGTTT
    1 -- us2k10--------
    rs1826981661,2
    --10885290(+) AATTAC/TAGTAT 1 -- us2k10--------
    rs1148978921,2
    F--10885463(+) AGAGAG/AACCTG 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs1154634121,2
    C,F--10885586(+) TTTGAG/AAAGAA 1 -- us2k11Minor allele frequency- A:0.03NA 120
    rs64567361,2
    C,A,H--10885675(+) AAAAAC/ACAGAT 1 -- us2k1 tfbs35Minor allele frequency- A:0.02NS EA WA 508
    rs2006379441,2
    --10885675(+) AAAAA-/CCAGAT 1 -- us2k10--------
    rs778700921,2
    C,F--10885731(+) TTTGAA/GTGCAT 1 -- us2k11Minor allele frequency- G:0.12WA 118

    HapMap Linkage Disequilibrium report for SYCP2L (10748027 - 10979553 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for SYCP2L:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2506207CNV Insertion19546169
    nsv348982CNV Loss16902084
    nsv519302CNV Loss19592680
    nsv519009CNV Loss19592680

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SYCP2L for disorders           About MalaCards

    SYCP2L for disorders           About GeneDecksing

    Genetic Association Database (GAD): SYCP2L
    Human Genome Epidemiology (HuGE) Navigator: SYCP2L (1 document)

    Export disorders for SYCP2L gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SYCP2L gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with SYCP2L)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. (PubMed id 22267201)1, 4 Stolk L....Lunetta K.L. (2012)
    2. Genetic loci associated with plasma phospholipid n-3 f atty acids: a meta-analysis of genome-wide association studies from the CHARGE C onsortium. (PubMed id 21829377)1, 4 Lemaitre R.N....Steffen L.M. (2011)
    3. Genome-wide association studies identify loci associa ted with age at menarche and age at natural menopause. (PubMed id 19448621)1, 4 He C....Chasman D.I. (2009)
    4. Diagnostic exome sequencing in persons with severe intellectual disability. (PubMed id 23033978)2 de Ligt J.... Vissers L.E. (2012)
    5. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    7. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (2007)
    8. Regulatory mechanisms governing the oocyte-specific synthesis of the karyoskeletal protein NO145. (PubMed id 17374641)2 Voltmer-Irsch S.... Schmidt-Zachmann M.S. (2007)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 221711 HGNC: 21537 AceView: LOC221711 Ensembl:ENSG00000153157 euGenes: HUgn221711
    ECgene: SYCP2L H-InvDB: SYCP2L

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SYCP2L Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SYCP2L gene:
    Search GeneIP for patents involving SYCP2L

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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