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SYCP2L Gene

protein-coding   GIFtS: 39
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)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   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 Chromatin IP Primers for SYCP2L

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SYC2L_HUMAN, Q5T4T6 (See protein sequence)
Recommended Name: Synaptonemal complex protein 2-like  
Size: 812 amino acids; 93599 Da
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


See SYCP2L Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001035364.2  
ENSEMBL proteins: 
 ENSP00000340320   ENSP00000283141   ENSP00000417870   ENSP00000440676  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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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


Find genes that share domains with SYCP2L           About GenesLikeMe


(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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Phenotypes:
     1 GenomeRNAi human phenotype for SYCP2L:
 Decreased Wnt reporter activit 

Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SYCP2L
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miRNA
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miRTarBase miRNAs that target SYCP2L:
hsa-mir-335-5p (MIRT016704)

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
SYC2L_HUMAN, Q5T4T6: Nucleus. Note=Detected in nuclear granules and sizable aggregates
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5
cytosol2

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--

Find genes that share ontologies with SYCP2L           About GenesLikeMe


(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SYCP2L
Interactions:

    Search GeneGlobe Interaction Network for SYCP2L

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for 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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for SYCP2L gene (2 alternative transcripts): 
NM_194299.1  NM_001040274.2  

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)

miRNA
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22 AceView cDNA sequences:

BM750187 CD724012 AA782841 BX281631 AW183165 BX095003 AA115860 BF590345 
NM_194299 AW663048 AK128130 AA442215 AI027433 BC012225 AW674916 AA115861 
AA854950 D78862 BE541431 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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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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

SYCP2L Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SYCP2L Protein Expression

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)
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This gene was present in the common ancestor of chordates.

Orthologs for SYCP2L gene from Selected species (see all 12)    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 67.56(n)1
52.01(a)1
  13 (20.32 cM)5
6372771  XM_006516986.11  XP_006517049.11 
 411143075 
chicken
(Gallus gallus)
Aves SYCP2L1 synaptonemal complex protein 2-like 63.09(n)
54.19(a)
  771534  XM_004939660.1  XP_004939717.1 
lizard
(Anolis carolinensis)
Reptilia SYCP2L6
synaptonemal complex protein 2-like
24(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 sycp2l1 synaptonemal complex protein 2-like 50(n)
35.94(a)
  100149910  XM_005162578.1  XP_005162635.1 


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)
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Paralogs for SYCP2L gene
SYCP22  
1 SIMAP similar gene for SYCP2L using alignment to 3 protein entries:     SYC2L_HUMAN (see all proteins):
SYCP2

Find genes that share paralogs with SYCP2L           About GenesLikeMe



(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SYCP2L (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
----------
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
rs800668781,2
C--10885879(+) TATTG-/CTTCTTAT 1 -- us2k10--------

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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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Find genes that share disorders with SYCP2L           About GenesLikeMe

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)
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PubMed articles for SYCP2L gene, integrated from 10 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. (Nat. Genet. 2012)
  2. Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. (PubMed id 21829377)1, 4 Lemaitre R.N....Steffen L.M. (PLoS Genet. 2011)
  3. Genome-wide association studies identify loci associated with age at menarche and age at natural menopause. (PubMed id 19448621)1, 4 He C....Chasman D.I. (Nat. Genet. 2009)
  4. Diagnostic exome sequencing in persons with severe intellectual disability. (PubMed id 23033978)2 de Ligt J.... Vissers L.E. (N. Engl. J. Med. 2012)
  5. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
  6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 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. (BMC Med. Genet. 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. (J. Cell Sci. 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. (Genome Res. 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. (Genome Res. 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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)
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Entrez Gene: 221711 HGNC: 21537 AceView: LOC221711 Ensembl:ENSG00000153157 euGenes: HUgn221711
ECgene: SYCP2L H-InvDB: SYCP2L

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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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.)
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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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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