Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SPEF1 Gene

Aliases for SPEF1 Gene

  • Sperm Flagellar 1 2 3 5
  • C20orf28 3 4
  • Calponin-Homology And Microtubule-Associated Protein 3
  • CaLponin-Homology And Microtubule-Associated Protein 2
  • Chromosome 20 Open Reading Frame 28 2
  • Sperm Flagellar Protein 1 3
  • SPEF1A 3
  • CLAMP 3

External Ids for SPEF1 Gene

Previous HGNC Symbols for SPEF1 Gene

  • C20orf28

Previous GeneCards Identifiers for SPEF1 Gene

  • GC20M003707

Summaries for SPEF1 Gene

GeneCards Summary for SPEF1 Gene

SPEF1 (Sperm Flagellar 1) is a Protein Coding gene. An important paralog of this gene is SPATA4.

UniProtKB/Swiss-Prot for SPEF1 Gene

  • Microtubule-associated protein involved in the stabilization of microtubules along the axis of migration during radial intercalation. Promotes the establishment and stabilization of an axis of microtubules required for the active migration of cells into the outer epithelium (By similarity). Microtubule-associated protein that promotes microtubule bundling and stabilizes microtubules against depolymerization in response to cold shock (By similarity).

Gene Wiki entry for SPEF1 Gene

Additional gene information for SPEF1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SPEF1 Gene

Genomics for SPEF1 Gene

GeneHancer (GH) Regulatory Elements for SPEF1 Gene

Promoters and enhancers for SPEF1 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
GH20J003780 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 650.7 -2.7 -2704 6.7 HDGF PKNOX1 ZFP64 ARID4B SIN3A YBX1 YY1 SLC30A9 ZNF766 ZNF143 SPEF1 CDC25B VPS16 ENSG00000229539 UBOX5 PCED1A UBOX5-AS1 MAVS C20orf27 GC20M003787
GH20J003795 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.6 -20.6 -20588 14.1 CLOCK DMAP1 IRF4 YY1 ZNF213 ZNF143 SP3 NFYC ZNF610 GLIS1 CDC25B VPS16 ENSG00000229539 SPEF1 PTPRA UBOX5 ADAM33 PANK2 LINC01730 GC20P003786
GH20J003809 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 10.1 -30.5 -30521 4.7 HDGF PKNOX1 CLOCK FOXA2 ARNT MLX ZFP64 ARID4B NEUROD1 SIN3A GC20M003810 ENSG00000274949 VPS16 ENSG00000229539 MAVS PCED1A C20orf194 CDC25B PRNP SPEF1
GH20J004081 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 9.9 -302.4 -302399 5 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 RPL21P2 PANK2 SMOX ENSG00000229539 CDC25B CENPB SPEF1 MAVS RNF24 ENSG00000205300
GH20J004040 Enhancer 1.4 Ensembl ENCODE dbSUPER 10 -260.0 -259995 2.2 ATF1 FEZF1 ZNF121 GLIS2 E2F8 KLF7 FOS ATF7 SP3 TSHZ1 ENSG00000229539 PANK2 AP5S1 SPEF1 FTLP3 RPL21P2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPEF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SPEF1 gene promoter:
  • GR-alpha
  • GR
  • Nkx2-5
  • NF-kappaB1
  • ZID
  • STAT3

Genomic Locations for SPEF1 Gene

Genomic Locations for SPEF1 Gene
chr20:3,777,504-3,781,466
(GRCh38/hg38)
Size:
3,963 bases
Orientation:
Minus strand
chr20:3,758,151-3,762,102
(GRCh37/hg19)
Size:
3,952 bases
Orientation:
Minus strand

Genomic View for SPEF1 Gene

Genes around SPEF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPEF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPEF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPEF1 Gene

Proteins for SPEF1 Gene

  • Protein details for SPEF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y4P9-SPEF1_HUMAN
    Recommended name:
    Sperm flagellar protein 1
    Protein Accession:
    Q9Y4P9
    Secondary Accessions:
    • A5YM71
    • D3DVY0
    • Q5JX78

    Protein attributes for SPEF1 Gene

    Size:
    236 amino acids
    Molecular mass:
    26987 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Radial intercalation is a developmentally reiterated form of migration by which cells move in a direction orthogonal to the plane of the tissue from an inner layer to an outer layer.

    Three dimensional structures from OCA and Proteopedia for SPEF1 Gene

    Alternative splice isoforms for SPEF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPEF1 Gene

Post-translational modifications for SPEF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SPEF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SPEF1 Gene

Domains & Families for SPEF1 Gene

Gene Families for SPEF1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SPEF1 Gene

Suggested Antigen Peptide Sequences for SPEF1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SPEF1: view

No data available for UniProtKB/Swiss-Prot for SPEF1 Gene

Function for SPEF1 Gene

Molecular function for SPEF1 Gene

UniProtKB/Swiss-Prot Function:
Microtubule-associated protein involved in the stabilization of microtubules along the axis of migration during radial intercalation. Promotes the establishment and stabilization of an axis of microtubules required for the active migration of cells into the outer epithelium (By similarity). Microtubule-associated protein that promotes microtubule bundling and stabilizes microtubules against depolymerization in response to cold shock (By similarity).

Phenotypes From GWAS Catalog for SPEF1 Gene

Gene Ontology (GO) - Molecular Function for SPEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IPI 25416956
GO:0008017 microtubule binding ISS,IEA --
genes like me logo Genes that share ontologies with SPEF1: view

Phenotypes for SPEF1 Gene

MGI mutant phenotypes for SPEF1:
inferred from 1 alleles
GenomeRNAi human phenotypes for SPEF1:
genes like me logo Genes that share phenotypes with SPEF1: view

Animal Models for SPEF1 Gene

MGI Knock Outs for SPEF1:
  • Spef1 Spef1<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPEF1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SPEF1 Gene

Localization for SPEF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPEF1 Gene

Cytoplasm. Cell projection, cilium, flagellum. Cytoplasm, cytoskeleton, cilium axoneme. Note=Present in the tails of developing and epididymal sperm, internal to the fibrous sheath and around the outer dense fibers of the sperm flagellum. Also found at the apical tip of cilia (By similarity). {ECO:0000250}.

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 SPEF1 gene
Compartment Confidence
cytoskeleton 4
nucleus 2
cytosol 2

Gene Ontology (GO) - Cellular Components for SPEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005737 cytoplasm IEA,IBA --
GO:0005856 cytoskeleton IEA --
GO:0005929 cilium IEA --
GO:0005930 axoneme ISS --
genes like me logo Genes that share ontologies with SPEF1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SPEF1 Gene

Pathways & Interactions for SPEF1 Gene

SuperPathways for SPEF1 Gene

No Data Available

Interacting Proteins for SPEF1 Gene

Gene Ontology (GO) - Biological Process for SPEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007026 negative regulation of microtubule depolymerization IEA,ISS --
GO:0008150 biological_process ND --
GO:0016477 cell migration ISS --
GO:0060285 cilium-dependent cell motility IBA --
genes like me logo Genes that share ontologies with SPEF1: view

No data available for Pathways by source and SIGNOR curated interactions for SPEF1 Gene

Drugs & Compounds for SPEF1 Gene

No Compound Related Data Available

Transcripts for SPEF1 Gene

mRNA/cDNA for SPEF1 Gene

(2) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(29) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SPEF1 Gene

Sperm flagellar 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPEF1

Alternative Splicing Database (ASD) splice patterns (SP) for SPEF1 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b
SP1: -
SP2: -
SP3:
SP4:

Relevant External Links for SPEF1 Gene

GeneLoc Exon Structure for
SPEF1
ECgene alternative splicing isoforms for
SPEF1

Expression for SPEF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SPEF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SPEF1 Gene

This gene is overexpressed in Brain - Putamen (basal ganglia) (x9.3), Brain - Caudate (basal ganglia) (x7.8), Brain - Nucleus accumbens (basal ganglia) (x7.5), and Testis (x4.4).

NURSA nuclear receptor signaling pathways regulating expression of SPEF1 Gene:

SPEF1

SOURCE GeneReport for Unigene cluster for SPEF1 Gene:

Hs.72620

Evidence on tissue expression from TISSUES for SPEF1 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with SPEF1: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPEF1 Gene

Orthologs for SPEF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SPEF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SPEF1 34 33
  • 99.29 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SPEF1 34 33
  • 89.27 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SPEF1 34 33
  • 88.98 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Spef1 33
  • 85.69 (n)
mouse
(Mus musculus)
Mammalia Spef1 16 34 33
  • 85.61 (n)
oppossum
(Monodelphis domestica)
Mammalia SPEF1 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves SPEF1 34
  • 47 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SPEF1 34
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia spef1 33
  • 62.03 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:66426 33
  • 51.6 (n)
SPEF1 34
  • 44 (a)
OneToOne
-- 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008402 33
  • 58.16 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG12395 34
  • 23 (a)
OneToMany
CG16719 34
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
OneToOne
Species where no ortholog for SPEF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 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 SPEF1 Gene

ENSEMBL:
Gene Tree for SPEF1 (if available)
TreeFam:
Gene Tree for SPEF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPEF1: view image

Paralogs for SPEF1 Gene

Paralogs for SPEF1 Gene

genes like me logo Genes that share paralogs with SPEF1: view

Variants for SPEF1 Gene

Sequence variations from dbSNP and Humsavar for SPEF1 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000082027 -- 3,783,217(-) G/A upstream_transcript_variant
rs1000947623 -- 3,781,791(-) C/T upstream_transcript_variant
rs1001121997 -- 3,777,679(-) G/ 3_prime_UTR_variant
rs1001508296 -- 3,777,958(-) A/G 3_prime_UTR_variant
rs1002144633 -- 3,779,358(-) G/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SPEF1 Gene

Variant ID Type Subtype PubMed ID
nsv585285 CNV loss 21841781
nsv585286 CNV loss 21841781
nsv828673 CNV gain 20364138
nsv833899 CNV loss 17160897

Variation tolerance for SPEF1 Gene

Residual Variation Intolerance Score: 75.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.38; 42.23% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPEF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPEF1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPEF1 Gene

Disorders for SPEF1 Gene

Additional Disease Information for SPEF1

No disorders were found for SPEF1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SPEF1 Gene

Publications for SPEF1 Gene

  1. Spef1, a conserved novel testis protein found in mouse sperm flagella. (PMID: 15979255) Chan SW … Kalitsis P (Gene 2005) 2 3 4 58
  2. Radial intercalation is regulated by the Par complex and the microtubule-stabilizing protein CLAMP/Spef1. (PMID: 25070955) Werner ME … Mitchell BJ (The Journal of cell biology 2014) 2 3 58
  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 58
  4. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4 58
  5. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4 58

Products for SPEF1 Gene

Sources for SPEF1 Gene

Content
Loading form....