Aliases for SPIN1 Gene

Aliases for SPIN1 Gene

  • Spindlin 1 2 3 5
  • Ovarian Cancer-Related Protein 3 4
  • Spindlin-1 3 4
  • Spindlin1 3 4
  • TDRD24 2 3
  • SPIN 3 4
  • Spindlin 2
  • SPIN1 5
  • OCR 4

External Ids for SPIN1 Gene

Previous HGNC Symbols for SPIN1 Gene

  • SPIN

Previous GeneCards Identifiers for SPIN1 Gene

  • GC16P028894
  • GC09P090194
  • GC09P091003
  • GC09P060869

Summaries for SPIN1 Gene

GeneCards Summary for SPIN1 Gene

SPIN1 (Spindlin 1) is a Protein Coding gene. Diseases associated with SPIN1 include Marcus Gunn Phenomenon and Hypertropia. Gene Ontology (GO) annotations related to this gene include methylated histone binding. An important paralog of this gene is SPIN3.

UniProtKB/Swiss-Prot Summary for SPIN1 Gene

  • Chromatin reader that specifically recognizes and binds histone H3 both trimethylated at 'Lys-4' and asymmetrically dimethylated at 'Arg-8' (H3K4me3 and H3R8me2a) and acts as an activator of Wnt signaling pathway downstream of PRMT2. In case of cancer, promotes cell cancer proliferation via activation of the Wnt signaling pathway (PubMed:24589551). Overexpression induces metaphase arrest and chromosomal instability. Localizes to active rDNA loci and promotes the expression of rRNA genes (PubMed:21960006). May play a role in cell-cycle regulation during the transition from gamete to embryo. Involved in oocyte meiotic resumption, a process that takes place before ovulation to resume meiosis of oocytes blocked in prophase I: may act by regulating maternal transcripts to control meiotic resumption.

Gene Wiki entry for SPIN1 Gene

Additional gene information for SPIN1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPIN1 Gene

Genomics for SPIN1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SPIN1 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
GH09J088386 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 611 +0.0 47 4 PRDM10 REST KDM1A CTCF BACH1 LARP7 PRDM1 ZNF143 RBFOX2 POLR2A SPIN1 ENSG00000287769 NXNL2
GH09J088410 Promoter 0.3 EPDnew 608.2 +21.7 21742 0.1 SPIN1 HNRNPA1P14 RF00017-7693 NXNL2
GH09J088528 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 15.1 +145.2 145228 10.1 CREB1 CTCF TEAD4 RFX1 RFX5 KDM1A ZNF692 TARDBP PRDM1 ZIC2 NXNL2 LOC105376134 lnc-SHC3-10 piR-57133-623 SPIN1
GH09J088434 Enhancer 0.9 Ensembl ENCODE 21.9 +47.4 47421 1.8 GATAD2A RCOR2 CEBPA SOX13 FOXA1 FOXA2 KDM6A HHEX CREM ZGPAT piR-55270-002 SPIN1 NXNL2 HNRNPA1P14
GH09J088475 Enhancer 0.9 Ensembl ENCODE 20.2 +89.4 89370 4.4 TCF12 IKZF2 TRIM22 PKNOX1 ARID3A DPF2 RELB CEBPB RUNX3 ZNF316 SPIN1 NXNL2 HSALNG0072545 piR-38463
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPIN1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPIN1

Top Transcription factor binding sites by QIAGEN in the SPIN1 gene promoter:
  • aMEF-2
  • En-1
  • FOXF2
  • FOXL1
  • FOXO3
  • FOXO3a
  • FOXO3b
  • HSF2
  • MEF-2A
  • Pbx1a

Genomic Locations for SPIN1 Gene

Genomic Locations for SPIN1 Gene
chr9:88,388,430-88,478,694
(GRCh38/hg38)
Size:
90,265 bases
Orientation:
Plus strand
chr9:91,003,297-91,093,623
(GRCh37/hg19)
Size:
90,327 bases
Orientation:
Plus strand

Genomic View for SPIN1 Gene

Genes around SPIN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPIN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPIN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPIN1 Gene

Proteins for SPIN1 Gene

  • Protein details for SPIN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y657-SPIN1_HUMAN
    Recommended name:
    Spindlin-1
    Protein Accession:
    Q9Y657
    Secondary Accessions:
    • A8K0X6
    • B3KRQ4
    • Q7KZJ8
    • Q9GZT2
    • Q9H0N7

    Protein attributes for SPIN1 Gene

    Size:
    262 amino acids
    Molecular mass:
    29601 Da
    Quaternary structure:
    • Homodimer; may form higher-order oligomers (PubMed:17082182). Interacts with TCF7L2/TCF4; the interaction is direct (PubMed:22258766, PubMed:24589551, PubMed:29061846). Interacts with HABP4 and SERBP1 (By similarity). Interacts with C11orf84/SPINDOC (PubMed:29061846).
    SequenceCaution:
    • Sequence=AAD43035.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAG38112.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAG48367.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=CAB66653.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305}; Sequence=CAG38515.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SPIN1 Gene

neXtProt entry for SPIN1 Gene

Post-translational modifications for SPIN1 Gene

Other Protein References for SPIN1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SPIN1 Gene

Domains & Families for SPIN1 Gene

Gene Families for SPIN1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SPIN1 Gene

InterPro:
Blocks:
  • Spindlin/spermiogenesis-specific protein
ProtoNet:

Suggested Antigen Peptide Sequences for SPIN1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ79503, highly similar to Spindlin-1 (A8K0X6_HUMAN)
  • Ovarian cancer-related protein (SPIN1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y657

UniProtKB/Swiss-Prot:

SPIN1_HUMAN :
  • The 3 tudor-like domains (also named Spin/Ssty repeats) specifically recognize and bind methylated histones (PubMed:23077255, PubMed:24589551). H3K4me3 and H3R8me2a are recognized by tudor-like domains 2 and 1, respectively (PubMed:24589551).
  • Belongs to the SPIN/STSY family.
Domain:
  • The 3 tudor-like domains (also named Spin/Ssty repeats) specifically recognize and bind methylated histones (PubMed:23077255, PubMed:24589551). H3K4me3 and H3R8me2a are recognized by tudor-like domains 2 and 1, respectively (PubMed:24589551).
Family:
  • Belongs to the SPIN/STSY family.
genes like me logo Genes that share domains with SPIN1: view

Function for SPIN1 Gene

Molecular function for SPIN1 Gene

UniProtKB/Swiss-Prot Function:
Chromatin reader that specifically recognizes and binds histone H3 both trimethylated at 'Lys-4' and asymmetrically dimethylated at 'Arg-8' (H3K4me3 and H3R8me2a) and acts as an activator of Wnt signaling pathway downstream of PRMT2. In case of cancer, promotes cell cancer proliferation via activation of the Wnt signaling pathway (PubMed:24589551). Overexpression induces metaphase arrest and chromosomal instability. Localizes to active rDNA loci and promotes the expression of rRNA genes (PubMed:21960006). May play a role in cell-cycle regulation during the transition from gamete to embryo. Involved in oocyte meiotic resumption, a process that takes place before ovulation to resume meiosis of oocytes blocked in prophase I: may act by regulating maternal transcripts to control meiotic resumption.

Phenotypes From GWAS Catalog for SPIN1 Gene

Gene Ontology (GO) - Molecular Function for SPIN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24589551
GO:0035064 methylated histone binding IBA,IDA 21029866
genes like me logo Genes that share ontologies with SPIN1: view
genes like me logo Genes that share phenotypes with SPIN1: view

Animal Models for SPIN1 Gene

MGI Knock Outs for SPIN1:
  • Spin1 Spin1<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPIN1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SPIN1 Gene

Localization for SPIN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPIN1 Gene

Nucleus. Nucleus, nucleolus.

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 SPIN1 gene
Compartment Confidence
nucleus 5
cytosol 4
cytoskeleton 3
mitochondrion 3
plasma membrane 2
extracellular 2
peroxisome 2
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SPIN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 29061846
GO:0005654 nucleoplasm IBA,IDA --
GO:0005730 nucleolus IEA,IDA 21960006
GO:0005819 spindle IEA --
GO:0005829 cytosol IBA,IDA --
genes like me logo Genes that share ontologies with SPIN1: view

Pathways & Interactions for SPIN1 Gene

PathCards logo

SuperPathways for SPIN1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SPIN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006355 regulation of transcription, DNA-templated IBA 21873635
GO:0007049 cell cycle IEA --
GO:0007275 multicellular organism development IEA --
GO:0007276 gamete generation IEA --
genes like me logo Genes that share ontologies with SPIN1: view

No data available for Pathways by source and SIGNOR curated interactions for SPIN1 Gene

Drugs & Compounds for SPIN1 Gene

No Compound Related Data Available

Transcripts for SPIN1 Gene

mRNA/cDNA for SPIN1 Gene

1 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
6 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 SPIN1

Alternative Splicing Database (ASD) splice patterns (SP) for SPIN1 Gene

No ASD Table

Relevant External Links for SPIN1 Gene

GeneLoc Exon Structure for
SPIN1

Expression for SPIN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPIN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SPIN1 Gene

This gene is overexpressed in Uterus (14.9), Fetal testis (11.4), Fetal Brain (9.7), and Fetal ovary (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPIN1 Gene



Protein tissue co-expression partners for SPIN1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPIN1

SOURCE GeneReport for Unigene cluster for SPIN1 Gene:

Hs.146804

mRNA Expression by UniProt/SwissProt for SPIN1 Gene:

Q9Y657-SPIN1_HUMAN
Tissue specificity: Highly expressed in ovarian cancer tissues.

Evidence on tissue expression from TISSUES for SPIN1 Gene

  • Nervous system(5)
  • Muscle(2.9)
  • Heart(2.8)
  • Skin(2.8)
  • Kidney(2.7)
  • Pancreas(2.6)
  • Lung(2.6)
  • Liver(2.5)
  • Intestine(2.4)
  • Blood(2.4)
  • Eye(2.4)
  • Thyroid gland(2.3)
  • Spleen(2.3)
  • Lymph node(2.2)
  • Bone marrow(2.1)
genes like me logo Genes that share expression patterns with SPIN1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPIN1 Gene

Orthologs for SPIN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SPIN1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SPIN1 30 31
  • 99.87 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 97 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia SPIN1 30 31
  • 95.04 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Spin1 30 17 31
  • 93 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SPIN1 30 31
  • 93 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC100363675 30
  • 92.24 (n)
Chicken
(Gallus gallus)
Aves SPINZ 30 31
  • 88.42 (n)
ManyToMany
SPINW 31
  • 83 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 96 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia spin1 30
  • 83.84 (n)
Str.20395 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.20083 30
Zebrafish
(Danio rerio)
Actinopterygii LOC792822 30
  • 75.57 (n)
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4056 30
Species where no ortholog for SPIN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 SPIN1 Gene

ENSEMBL:
Gene Tree for SPIN1 (if available)
TreeFam:
Gene Tree for SPIN1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPIN1: view image

Paralogs for SPIN1 Gene

Paralogs for SPIN1 Gene

(4) SIMAP similar genes for SPIN1 Gene using alignment to 1 proteins:

  • SPIN1_HUMAN
genes like me logo Genes that share paralogs with SPIN1: view

Variants for SPIN1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPIN1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs34794905 - p.Ala221Pro

Additional dbSNP identifiers (rs#s) for SPIN1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SPIN1 Gene

Variant ID Type Subtype PubMed ID
dgv12784n54 CNV gain+loss 21841781
dgv12785n54 CNV gain 21841781
esv23316 CNV loss 19812545
esv2658159 CNV deletion 23128226
esv2661430 CNV deletion 23128226
esv2667394 CNV deletion 23128226
esv3336546 CNV insertion 20981092
esv3621003 CNV loss 21293372
esv3621004 CNV loss 21293372
esv3621005 CNV loss 21293372
nsv1048043 CNV gain 25217958
nsv1076189 CNV deletion 25765185
nsv1137661 CNV deletion 24896259
nsv466432 CNV gain 19166990
nsv477124 CNV novel sequence insertion 20440878
nsv614798 CNV gain 21841781
nsv614799 CNV gain+loss 21841781
nsv614806 CNV loss 21841781
nsv614807 CNV gain 21841781
nsv831649 CNV loss 17160897
nsv972416 CNV duplication 23825009

Variation tolerance for SPIN1 Gene

Residual Variation Intolerance Score: 36.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.15; 3.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPIN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPIN1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPIN1 Gene

Disorders for SPIN1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SPIN1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
marcus gunn phenomenon
  • jaw-winking
hypertropia
tumoral calcinosis, hyperphosphatemic, familial, 1
  • hftc1
ovarian cancer
  • ovarian cancer, somatic
hypotrichosis 1
  • hhs
- elite association - COSMIC cancer census association via MalaCards
Search SPIN1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SPIN1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SPIN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPIN1 Gene

Publications for SPIN1 Gene

  1. Spindlin1, a novel nuclear protein with a role in the transformation of NIH3T3 cells. (PMID: 16098913) Gao Y … Pei X (Biochemical and biophysical research communications 2005) 2 3 4
  2. 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
  3. Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. (PMID: 24589551) Su X … Li H (Genes & development 2014) 3 4
  4. SPINDLIN1 promotes cancer cell proliferation through activation of WNT/TCF-4 signaling. (PMID: 22258766) Wang JX … Pei XT (Molecular cancer research : MCR 2012) 3 4
  5. Distinct mode of methylated lysine-4 of histone H3 recognition by tandem tudor-like domains of Spindlin1. (PMID: 23077255) Yang N … Xu RM (Proceedings of the National Academy of Sciences of the United States of America 2012) 3 4

Products for SPIN1 Gene

  • Signalway ELISA kits for SPIN1
  • Signalway Proteins for SPIN1

Sources for SPIN1 Gene