Aliases for VSTM2L Gene

Aliases for VSTM2L Gene

  • V-Set And Transmembrane Domain Containing 2 Like 2 3 5
  • V-Set And Transmembrane Domain-Containing Protein 2-Like Protein 3 4
  • DJ1118M15.2 2 3
  • C20orf102 3 4
  • Chromosome 20 Open Reading Frame 102 2
  • VSTM2L 5

External Ids for VSTM2L Gene

Previous HGNC Symbols for VSTM2L Gene

  • C20orf102

Previous GeneCards Identifiers for VSTM2L Gene

  • GC20P035965
  • GC20P036531
  • GC20P033266

Summaries for VSTM2L Gene

GeneCards Summary for VSTM2L Gene

VSTM2L (V-Set And Transmembrane Domain Containing 2 Like) is a Protein Coding gene. Diseases associated with VSTM2L include Spinocerebellar Ataxia 14. An important paralog of this gene is BSG.

Additional gene information for VSTM2L Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VSTM2L Gene

Genomics for VSTM2L Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VSTM2L 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
GH20J037902 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 609.5 +1.4 1397 3.8 HNRNPL CTCF ZNF629 KDM1A ZNF600 ZNF561 CBX3 ZBTB10 ZEB1 ZSCAN5C VSTM2L RPRD1B HSALNG0129929 TTI1
GH20J037903 Enhancer 0.8 ENCODE 600.7 -0.8 -770 0.2 CTCF ZBTB33 ZNF629 REST IKZF1 KDM1A ZNF143 MTA2 ZSCAN4 RAD21 VSTM2L HSALNG0129929 RF00017-3581 CTNNBL1
GH20J037840 Promoter 0.3 EPDnew 611 -63.0 -62974 0.1 VSTM2L lnc-TTI1-3 KR153225-007 CTNNBL1
GH20J038072 Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 25.4 +172.7 172697 6.8 GATAD2A CTCF ZNF7 FOXA1 ZNF143 ZIC2 RXRB REST RAD21 IRF2 TTI1 RPRD1B VSTM2L SNHG17 SNORA71A SNORA71C RBL1 RALGAPB RN7SKP173 TGM2
GH20J038031 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 15.7 +130.7 130656 3.7 RNF2 SP1 HNRNPL CREB1 GATAD2A PRDM10 REST ZNF629 TFE3 RFX1 TTI1 RPRD1B SNHG17 ACTR5 RALGAPB VSTM2L SNORA71C SNORA71A RN7SKP173 RBL1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VSTM2L on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VSTM2L

Top Transcription factor binding sites by QIAGEN in the VSTM2L gene promoter:
  • AhR
  • AML1a
  • CUTL1
  • NRF-2
  • p53
  • Spz1
  • STAT1
  • STAT1alpha
  • STAT1beta
  • TGIF

Genomic Locations for VSTM2L Gene

Genomic Locations for VSTM2L Gene
chr20:37,903,104-37,945,350
(GRCh38/hg38)
Size:
42,247 bases
Orientation:
Plus strand
chr20:36,531,499-36,573,752
(GRCh37/hg19)
Size:
42,254 bases
Orientation:
Plus strand

Genomic View for VSTM2L Gene

Genes around VSTM2L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VSTM2L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VSTM2L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VSTM2L Gene

Proteins for VSTM2L Gene

  • Protein details for VSTM2L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96N03-VTM2L_HUMAN
    Recommended name:
    V-set and transmembrane domain-containing protein 2-like protein
    Protein Accession:
    Q96N03
    Secondary Accessions:
    • E1P5V7
    • Q5JWZ4
    • Q5JWZ5
    • Q8ND45
    • Q9BR37

    Protein attributes for VSTM2L Gene

    Size:
    204 amino acids
    Molecular mass:
    22349 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for VSTM2L Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VSTM2L Gene

Post-translational modifications for VSTM2L Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VSTM2L Gene

No data available for DME Specific Peptides for VSTM2L Gene

Domains & Families for VSTM2L Gene

Gene Families for VSTM2L Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for VSTM2L Gene

InterPro:
Blocks:
  • Immunoglobulin subtype
ProtoNet:

Suggested Antigen Peptide Sequences for VSTM2L Gene

GenScript: Design optimal peptide antigens:
  • V-set and transmembrane domain-containing protein 2-like protein (VTM2L_HUMAN)
genes like me logo Genes that share domains with VSTM2L: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for VSTM2L Gene

Function for VSTM2L Gene

Phenotypes From GWAS Catalog for VSTM2L Gene

Gene Ontology (GO) - Molecular Function for VSTM2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16713569
GO:0098632 cell-cell adhesion mediator activity IBA 21873635
genes like me logo Genes that share ontologies with VSTM2L: view
genes like me logo Genes that share phenotypes with VSTM2L: view

Animal Model Products

  • Taconic Biosciences Mouse Models for VSTM2L

CRISPR Products

miRNA for VSTM2L Gene

miRTarBase miRNAs that target VSTM2L

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VSTM2L

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VSTM2L Gene

Localization for VSTM2L Gene

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 VSTM2L gene
Compartment Confidence
extracellular 5
plasma membrane 3
nucleus 2
cytoskeleton 1
mitochondrion 1
cytosol 1
lysosome 0

Gene Ontology (GO) - Cellular Components for VSTM2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IDA 21393573
GO:0005737 cytoplasm IDA 21393573
GO:0005886 plasma membrane IBA 21873635
GO:0030424 axon IBA 21873635
genes like me logo Genes that share ontologies with VSTM2L: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for VSTM2L Gene

Pathways & Interactions for VSTM2L Gene

PathCards logo

SuperPathways for VSTM2L Gene

No Data Available

Gene Ontology (GO) - Biological Process for VSTM2L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IBA 21873635
GO:0007411 axon guidance IBA 21873635
GO:0043524 negative regulation of neuron apoptotic process IDA 21393573
GO:0070593 dendrite self-avoidance IBA 21873635
genes like me logo Genes that share ontologies with VSTM2L: view

No data available for Pathways by source and SIGNOR curated interactions for VSTM2L Gene

Drugs & Compounds for VSTM2L Gene

No Compound Related Data Available

Transcripts for VSTM2L Gene

mRNA/cDNA for VSTM2L Gene

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VSTM2L

Alternative Splicing Database (ASD) splice patterns (SP) for VSTM2L Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b · 5c
SP1: -
SP2: - -
SP3:
SP4: - -
SP5: - - - - -

Relevant External Links for VSTM2L Gene

GeneLoc Exon Structure for
VSTM2L

Expression for VSTM2L Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VSTM2L Gene

mRNA differential expression in normal tissues according to GTEx for VSTM2L Gene

This gene is overexpressed in Brain - Cortex (x6.6), Brain - Frontal Cortex (BA9) (x5.4), Heart - Atrial Appendage (x5.0), Brain - Hippocampus (x5.0), Brain - Anterior cingulate cortex (BA24) (x4.6), and Brain - Amygdala (x4.4).

Protein differential expression in normal tissues from HIPED for VSTM2L Gene

This gene is overexpressed in Liver (68.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VSTM2L Gene



Protein tissue co-expression partners for VSTM2L Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VSTM2L

SOURCE GeneReport for Unigene cluster for VSTM2L Gene:

Hs.517029

Evidence on tissue expression from TISSUES for VSTM2L Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with VSTM2L: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VSTM2L Gene

Orthologs for VSTM2L Gene

This gene was present in the common ancestor of chordates.

Orthologs for VSTM2L Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia VSTM2L 30 31
  • 99.18 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia VSTM2L 30 31
  • 95.42 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia VSTM2L 30 31
  • 95.26 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia RGD1305725 30
  • 89.27 (n)
Mouse
(Mus musculus)
Mammalia Vstm2l 30 17 31
  • 88.45 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia VSTM2L 31
  • 74 (a)
OneToOne
Chicken
(Gallus gallus)
Aves VSTM2L 30 31
  • 84.75 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia VSTM2L 31
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia vstm2l 30
  • 68.12 (n)
Str.19138 30
Zebrafish
(Danio rerio)
Actinopterygii vstm2l 30 31
  • 65.53 (n)
OneToOne
zgc66133 30
Species where no ortholog for VSTM2L was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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 VSTM2L Gene

ENSEMBL:
Gene Tree for VSTM2L (if available)
TreeFam:
Gene Tree for VSTM2L (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VSTM2L: view image

Paralogs for VSTM2L Gene

Paralogs for VSTM2L Gene

(2) SIMAP similar genes for VSTM2L Gene using alignment to 2 proteins:

  • VTM2L_HUMAN
  • F2Z3I3_HUMAN
genes like me logo Genes that share paralogs with VSTM2L: view

Variants for VSTM2L Gene

Additional dbSNP identifiers (rs#s) for VSTM2L Gene

Structural Variations from Database of Genomic Variants (DGV) for VSTM2L Gene

Variant ID Type Subtype PubMed ID
esv2633566 CNV insertion 19546169
nsv1057334 CNV loss 25217958
nsv1066778 CNV gain 25217958
nsv833970 CNV gain 17160897
nsv833971 CNV gain 17160897

Variation tolerance for VSTM2L Gene

Residual Variation Intolerance Score: 81.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.57; 65.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VSTM2L Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VSTM2L

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VSTM2L Gene

Disorders for VSTM2L Gene

MalaCards: The human disease database

(1) MalaCards diseases for VSTM2L Gene - From: DISEASES

Disorder Aliases PubMed IDs
spinocerebellar ataxia 14
  • sca14
- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with VSTM2L: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VSTM2L Gene

Publications for VSTM2L Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4
  4. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. (PMID: 28611215) Fei T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2017) 3
  5. SR protein kinases promote splicing of nonconsensus introns. (PMID: 26167880) Lipp JJ … Guthrie C (Nature structural & molecular biology 2015) 3

Products for VSTM2L Gene

Sources for VSTM2L Gene