Aliases for SPIN3 Gene

Aliases for SPIN3 Gene

  • Spindlin Family Member 3 2 3 5
  • Spindlin-Like Protein 3 3 4
  • Spindlin-3 3 4
  • SPIN-3 3 4
  • Spindlin Family, Member 3 2
  • BA445O16.1 (DXF34) 3
  • BA445O16.1 3
  • TDRD27 3

External Ids for SPIN3 Gene

Previous GeneCards Identifiers for SPIN3 Gene

  • GC0XM056903
  • GC0XM057019
  • GC0XM054066

Summaries for SPIN3 Gene

GeneCards Summary for SPIN3 Gene

SPIN3 (Spindlin Family Member 3) is a Protein Coding gene. Diseases associated with SPIN3 include Patent Foramen Ovale. An important paralog of this gene is SPIN1.

UniProtKB/Swiss-Prot Summary for SPIN3 Gene

Additional gene information for SPIN3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPIN3 Gene

Genomics for SPIN3 Gene

GeneHancer (GH) Regulatory Elements for SPIN3 Gene

Promoters and enhancers for SPIN3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ056994 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.6 626 2.8 ZBTB40 NRF1 TCF12 MYC POLR2G POLR2A ZBTB25 TGIF2 TAF9B MXI1 SPIN3 lnc-NBDY-6
GH0XJ056802 Promoter/Enhancer 1.1 ENCODE CraniofacialAtlas dbSUPER 12 +192.4 192447 1.9 CTCF REST RAD21 SMC3 MXI1 ZNF384 YY1 MEF2B MAZ KLF5 SPIN2B SPIN3 lnc-SPIN3-2 RF00017-8473 lnc-NBDY-7 NBDY NONHSAG054609.2
GH0XJ056248 Enhancer 0.6 Ensembl 13.2 +747.2 747215 0.4 CTCF REST RAD21 TRIM22 SMC3 ZFHX2 ZNF654 EGR1 ZNF514 EGR2 SPIN3 RRAGB ENSG00000226310 NBDY RPL23AP83 lnc-SPIN3-6 KLF8 lnc-SPIN3-5
GH0XJ056807 Enhancer 0.2 Ensembl 12 +188.4 188426 0.4 SPIN3 lnc-SPIN3-2 RF00017-8473 lnc-NBDY-7 NBDY NONHSAG054609.2
GH0XJ056978 Enhancer 0.7 Ensembl ENCODE 0.4 +17.5 17496 0.4 CTCF REST RAD21 TRIM22 SMC3 DEK ZNF654 YY1 BCLAF1 ZNF143 ENSG00000224799 piR-48327-008 SPIN3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPIN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SPIN3 gene promoter:
  • COMP1
  • FOXL1
  • HSF2
  • Lhx3a
  • LHX3b
  • Pax-4a
  • POU2F2B
  • POU2F2C
  • RFX1
  • RP58

Genomic Locations for SPIN3 Gene

Genomic Locations for SPIN3 Gene
177,530 bases
Minus strand
19,186 bases
Minus strand

Genomic View for SPIN3 Gene

Genes around SPIN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPIN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPIN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPIN3 Gene

Proteins for SPIN3 Gene

  • Protein details for SPIN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2RUW3
    • B7Z8W2
    • Q8N5D9

    Protein attributes for SPIN3 Gene

    258 amino acids
    Molecular mass:
    29207 Da
    Quaternary structure:
    • Interacts with C11orf84/SPINDOC (PubMed:29061846).
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Three dimensional structures from OCA and Proteopedia for SPIN3 Gene

    Alternative splice isoforms for SPIN3 Gene


neXtProt entry for SPIN3 Gene

Post-translational modifications for SPIN3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SPIN3 Gene

Domains & Families for SPIN3 Gene

Gene Families for SPIN3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SPIN3 Gene

  • Spindlin/spermiogenesis-specific protein

Suggested Antigen Peptide Sequences for SPIN3 Gene

GenScript: Design optimal peptide antigens:
  • Spindlin-like protein 3 (SPIN3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SPIN/STSY family.
  • Belongs to the SPIN/STSY family.
genes like me logo Genes that share domains with SPIN3: view

Function for SPIN3 Gene

Molecular function for SPIN3 Gene

UniProtKB/Swiss-Prot Function:
Exhibits H3K4me3-binding activity.

Phenotypes From GWAS Catalog for SPIN3 Gene

Gene Ontology (GO) - Molecular Function for SPIN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 29061846
GO:0035064 methylated histone binding IDA,IBA 29061846
genes like me logo Genes that share ontologies with SPIN3: view
genes like me logo Genes that share phenotypes with SPIN3: view

Animal Model Products

CRISPR Products

Clone Products

  • Addgene plasmids for SPIN3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SPIN3 Gene

Localization for SPIN3 Gene

Subcellular locations from

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 SPIN3 gene
Compartment Confidence
nucleus 4
cytosol 4
mitochondrion 3
plasma membrane 1
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SPIN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IBA 21873635
GO:0005829 cytosol IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SPIN3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SPIN3 Gene

Pathways & Interactions for SPIN3 Gene

PathCards logo

SuperPathways for SPIN3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SPIN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007276 gamete generation IEA --
genes like me logo Genes that share ontologies with SPIN3: view

No data available for Pathways by source and SIGNOR curated interactions for SPIN3 Gene

Drugs & Compounds for SPIN3 Gene

No Compound Related Data Available

Transcripts for SPIN3 Gene

mRNA/cDNA for SPIN3 Gene

12 NCBI additional mRNA sequence :
45 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for SPIN3

Alternative Splicing Database (ASD) splice patterns (SP) for SPIN3 Gene

No ASD Table

Relevant External Links for SPIN3 Gene

GeneLoc Exon Structure for

Expression for SPIN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPIN3 Gene

Protein differential expression in normal tissues from HIPED for SPIN3 Gene

This gene is overexpressed in Fetal testis (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPIN3 Gene

Protein tissue co-expression partners for SPIN3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPIN3

SOURCE GeneReport for Unigene cluster for SPIN3 Gene:


Evidence on tissue expression from TISSUES for SPIN3 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with SPIN3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPIN3 Gene

Orthologs for SPIN3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SPIN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SPIN3 30
  • 99.74 (n)
(Bos Taurus)
Mammalia SPIN3 30
  • 92.25 (n)
SPIN2 31
  • 70 (a)
(Monodelphis domestica)
Mammalia -- 31
  • 84 (a)
(Canis familiaris)
Mammalia SPIN3 31
  • 84 (a)
(Mus musculus)
Mammalia Gm21637 31
  • 56 (a)
(Gallus gallus)
Aves SPINZ 31
  • 83 (a)
  • 75 (a)
(Anolis carolinensis)
Reptilia -- 31
  • 84 (a)
Species where no ortholog for SPIN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for SPIN3 Gene

Gene Tree for SPIN3 (if available)
Gene Tree for SPIN3 (if available)
Evolutionary constrained regions (ECRs) for SPIN3: view image

Paralogs for SPIN3 Gene

Paralogs for SPIN3 Gene

(4) SIMAP similar genes for SPIN3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SPIN3: view

Variants for SPIN3 Gene

Additional dbSNP identifiers (rs#s) for SPIN3 Gene

Variation tolerance for SPIN3 Gene

Residual Variation Intolerance Score: 36.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.47; 10.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPIN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Structural Variations from Database of Genomic Variants (DGV) for SPIN3 Gene

Disorders for SPIN3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SPIN3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
patent foramen ovale
  • atrial septal defect within oval fossa
- elite association - COSMIC cancer census association via MalaCards
Search SPIN3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SPIN3

genes like me logo Genes that share disorders with SPIN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPIN3 Gene

Publications for SPIN3 Gene

  1. A transcriptional coregulator, SPIN·DOC, attenuates the coactivator activity of Spindlin1. (PMID: 29061846) Bae N … Bedford MT (The Journal of biological chemistry 2017) 3 4 54
  2. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 54
  3. 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 54
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54

Products for SPIN3 Gene

Sources for SPIN3 Gene