Human Gene SYCP2L (uc003mzo.3)
  Description: Homo sapiens synaptonemal complex protein 2-like (SYCP2L), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr6:10,887,064-10,974,541 Size: 87,478 Total Exon Count: 30 Strand: +
Coding Region
   Position: hg19 chr6:10,887,360-10,964,039 Size: 76,680 Coding Exon Count: 29 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:10,887,064-10,974,541)mRNA (may differ from genome)Protein (812 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYC2L_HUMAN
DESCRIPTION: RecName: Full=Synaptonemal complex protein 2-like; Short=SCP-2-like; AltName: Full=145 kDa nucleolar protein homolog; Short=hsNO145;
SUBCELLULAR LOCATION: Nucleus. Note=Detected in nuclear granules and sizable aggregates.
TISSUE SPECIFICITY: Expressed in the ovary (at protein level).
SIMILARITY: Belongs to the SYCP2 family.
SEQUENCE CAUTION: Sequence=CAI16226.1; Type=Erroneous gene model prediction; Sequence=CAI22075.1; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SYCP2L
CDC HuGE Published Literature: SYCP2L
Positive Disease Associations: Cholesterol, LDL , Menarche , menarche and menopause (age at onset) , Menopause , Phospholipids
Related Studies:
  1. Cholesterol, LDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  2. Menarche
    Chunyan He et al. Nature genetics 2009, Genome-wide association studies identify loci associated with age at menarche and age at natural menopause., Nature genetics. [PubMed 19448621]
  3. menarche and menopause (age at onset)
    He ,et al. 2009, Genome-wide association studies identify loci associated with age at menarche and age at natural menopause, Nature genetics 2009 . [PubMed 19448621]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.96 RPKM in Testis
Total median expression: 29.51 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -115.90296-0.392 Picture PostScript Text
3' UTR -100.61394-0.255 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR024835 - SYCP2/SYCP2-like

ModBase Predicted Comparative 3D Structure on Q5T4T6
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
      
      
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000780 condensed nuclear chromosome, centromeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome


-  Descriptions from all associated GenBank mRNAs
  AK294018 - Homo sapiens cDNA FLJ60468 complete cds, weakly similar to Synaptonemal complex protein 2.
AK128130 - Homo sapiens cDNA FLJ46251 fis, clone TESTI4021713, weakly similar to Homo sapiens synaptonemal complex protein 2 (SYCP2).
AM293674 - Homo sapiens mRNA for 145 kDa nucleolar protein (NO145 gene).
BC012225 - Homo sapiens synaptonemal complex protein 2-like, mRNA (cDNA clone IMAGE:3452587), partial cds.
JD330440 - Sequence 311464 from Patent EP1572962.
JD193561 - Sequence 174585 from Patent EP1572962.
JD064767 - Sequence 45791 from Patent EP1572962.
JD543063 - Sequence 524087 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NDS5, C6orf177, NM_001040274, NO145, NP_001035364, Q08GK5, Q5T4T6, Q6ZRM2, Q96EJ2, SYC2L_HUMAN
UCSC ID: uc003mzo.3
RefSeq Accession: NM_001040274
Protein: Q5T4T6 (aka SYC2L_HUMAN)
CCDS: CCDS43423.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001040274.2
exon count: 30CDS single in 3' UTR: no RNA size: 3139
ORF size: 2439CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4898.00frame shift in genome: no % Coverage: 99.68
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 1
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.