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Aliases for NIPSNAP3A Gene

Aliases for NIPSNAP3A Gene

  • Nipsnap Homolog 3A 2 3 5
  • Target For Salmonella Secreted Protein C 3 4
  • Protein NipSnap Homolog 4 3 4
  • NIPSNAP4 3 4
  • TASSC 3 4
  • Nipsnap Homolog 3A (C. Elegans) 2
  • Protein NipSnap Homolog 3A 3
  • NipSnap3A 4
  • HSPC299 3

External Ids for NIPSNAP3A Gene

Previous GeneCards Identifiers for NIPSNAP3A Gene

  • GC09P102889
  • GC09P104589
  • GC09P106549
  • GC09P107509
  • GC09P077113

Summaries for NIPSNAP3A Gene

Entrez Gene Summary for NIPSNAP3A Gene

  • NIPSNAP3A belongs to a family of proteins with putative roles in vesicular transport (Buechler et al., 2004 [PubMed 15177564]).[supplied by OMIM, Mar 2008]

GeneCards Summary for NIPSNAP3A Gene

NIPSNAP3A (Nipsnap Homolog 3A) is a Protein Coding gene. An important paralog of this gene is NIPSNAP3B.

Additional gene information for NIPSNAP3A Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NIPSNAP3A Gene

Genomics for NIPSNAP3A Gene

GeneHancer (GH) Regulatory Elements for NIPSNAP3A Gene

Promoters and enhancers for NIPSNAP3A 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
GH09I104745 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 570.6 -0.3 -349 3.9 FOXA2 PKNOX1 ATF1 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 E2F8 NIPSNAP3A ABCA1 OR13D3P
GH09I104763 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 20 +16.6 16566 2 HDGF ATF1 ARID4B SIN3A DMAP1 ZNF48 POLR2B ZNF766 GLIS2 ZNF213 NIPSNAP3B NIPSNAP3A RALGAPA1P1 FKTN GC09P104774
GH09I104772 Enhancer 1.4 Ensembl ENCODE dbSUPER 14.5 +27.0 26999 4 HDGF PKNOX1 ATF1 SMAD1 ARNT IRF4 YY1 TCF12 ZNF766 GATA2 GC09P104774 NIPSNAP3A GC09P104783 NIPSNAP3B
GH09I104743 Enhancer 0.8 Ensembl ENCODE 16.5 -4.0 -4038 0.3 SMARCA5 CTCF ZNF654 ZSCAN4 TRIM22 REST RAD21 SMC3 ZNF143 NIPSNAP3A OR13D3P
GH09I104758 Enhancer 0.5 ENCODE 21.3 +11.7 11670 1.1 CREB1 EBF1 ATF2 EZH2 NIPSNAP3A NIPSNAP3B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NIPSNAP3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NIPSNAP3A gene promoter:

Genomic Locations for NIPSNAP3A Gene

Genomic Locations for NIPSNAP3A Gene
12,435 bases
Plus strand

Genomic View for NIPSNAP3A Gene

Genes around NIPSNAP3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NIPSNAP3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NIPSNAP3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NIPSNAP3A Gene

Proteins for NIPSNAP3A Gene

  • Protein details for NIPSNAP3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein NipSnap homolog 3A
    Protein Accession:
    Secondary Accessions:
    • A6NM55
    • Q5VX32
    • Q9BRV7
    • Q9H843
    • Q9P083

    Protein attributes for NIPSNAP3A Gene

    247 amino acids
    Molecular mass:
    28467 Da
    Quaternary structure:
    • Interacts with the Salmonella typhimurium virulence protein spiC.
    • Sequence=AAF28977.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for NIPSNAP3A Gene

Post-translational modifications for NIPSNAP3A Gene

No Post-translational modifications

Other Protein References for NIPSNAP3A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NIPSNAP3A Gene

Domains & Families for NIPSNAP3A Gene

Gene Families for NIPSNAP3A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NIPSNAP3A Gene


Suggested Antigen Peptide Sequences for NIPSNAP3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the NipSnap family.
  • Belongs to the NipSnap family.
genes like me logo Genes that share domains with NIPSNAP3A: view

Function for NIPSNAP3A Gene

Phenotypes From GWAS Catalog for NIPSNAP3A Gene

Gene Ontology (GO) - Molecular Function for NIPSNAP3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21988832
genes like me logo Genes that share ontologies with NIPSNAP3A: view

Phenotypes for NIPSNAP3A Gene

GenomeRNAi human phenotypes for NIPSNAP3A:
genes like me logo Genes that share phenotypes with NIPSNAP3A: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for NIPSNAP3A Gene

Localization for NIPSNAP3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for NIPSNAP3A Gene

Cytoplasm, cytosol. Note=May be part of some vesicular structure distinct from lysosomal vesicles.

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 NIPSNAP3A gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 3

Gene Ontology (GO) - Cellular Components for NIPSNAP3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus HDA,IDA 21630459
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IBA --
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with NIPSNAP3A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NIPSNAP3A Gene

Pathways & Interactions for NIPSNAP3A Gene

SuperPathways for NIPSNAP3A Gene

No Data Available

Interacting Proteins for NIPSNAP3A Gene

Gene Ontology (GO) - Biological Process for NIPSNAP3A Gene


No data available for Pathways by source and SIGNOR curated interactions for NIPSNAP3A Gene

Drugs & Compounds for NIPSNAP3A Gene

No Compound Related Data Available

Transcripts for NIPSNAP3A Gene


Unigene Clusters for NIPSNAP3A Gene

Nipsnap homolog 3A (C. elegans):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for NIPSNAP3A Gene

No ASD Table

Relevant External Links for NIPSNAP3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NIPSNAP3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NIPSNAP3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NIPSNAP3A Gene

This gene is overexpressed in Fetal testis (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NIPSNAP3A Gene

Protein tissue co-expression partners for NIPSNAP3A Gene

NURSA nuclear receptor signaling pathways regulating expression of NIPSNAP3A Gene:


SOURCE GeneReport for Unigene cluster for NIPSNAP3A Gene:


mRNA Expression by UniProt/SwissProt for NIPSNAP3A Gene:

Tissue specificity: Ubiquitous. Highly expressed in liver, kidney and muscle. Expressed at intermediate level in brain, heart, colon, thymus, kidney, small intestine, placenta, lung, leukocytes and spleen.

Evidence on tissue expression from TISSUES for NIPSNAP3A Gene

  • Nervous system(4.8)
  • Blood(4.2)
  • Bone marrow(4.2)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with NIPSNAP3A: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NIPSNAP3A Gene

Orthologs for NIPSNAP3A Gene

This gene was present in the common ancestor of chordates.

Orthologs for NIPSNAP3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NIPSNAP3A 33 34
  • 99.87 (n)
(Bos Taurus)
Mammalia NIPSNAP3A 33 34
  • 91.5 (n)
(Canis familiaris)
Mammalia LOC474791 33
  • 90.96 (n)
  • 90 (a)
(Mus musculus)
Mammalia Nipsnap3b 33 16
  • 83.94 (n)
Nipsnap3a 34
  • 76 (a)
(Rattus norvegicus)
Mammalia Nipsnap3b 33
  • 83.54 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 76 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 66 (a)
(Gallus gallus)
  • 72.98 (n)
-- 34
  • 66 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 58 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia nipsnap3a 33
  • 65.56 (n)
(Danio rerio)
Actinopterygii nipsnap3 33 34
  • 62.16 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8944 34
  • 36 (a)
Species where no ortholog for NIPSNAP3A 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)
  • 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 NIPSNAP3A Gene

Gene Tree for NIPSNAP3A (if available)
Gene Tree for NIPSNAP3A (if available)

Paralogs for NIPSNAP3A Gene

Paralogs for NIPSNAP3A Gene

(1) SIMAP similar genes for NIPSNAP3A Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with NIPSNAP3A: view

Variants for NIPSNAP3A Gene

Sequence variations from dbSNP and Humsavar for NIPSNAP3A Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000038817 -- 104,756,151(+) G/A intron_variant
rs1000130806 -- 104,756,993(+) A/G intron_variant
rs1000170407 -- 104,752,220(+) AAA/ intron_variant
rs1000226865 -- 104,751,865(+) A/G intron_variant
rs1000638128 -- 104,754,947(+) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NIPSNAP3A Gene

Variant ID Type Subtype PubMed ID
nsv521783 CNV loss 19592680
esv3891706 CNV gain 25118596
esv3891705 CNV loss 25118596

Variation tolerance for NIPSNAP3A Gene

Residual Variation Intolerance Score: 81% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.23; 52.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NIPSNAP3A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NIPSNAP3A Gene

Disorders for NIPSNAP3A Gene

Additional Disease Information for NIPSNAP3A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for NIPSNAP3A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NIPSNAP3A Gene

Publications for NIPSNAP3A Gene

  1. Expression pattern and raft association of NIPSNAP3 and NIPSNAP4, highly homologous proteins encoded by genes in close proximity to the ATP-binding cassette transporter A1. (PMID: 15177564) Buechler C … Schmitz G (Genomics 2004) 2 3 22 58
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. 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
  5. Identification of a NIPSNAP homologue as host cell target for Salmonella virulence protein SpiC. (PMID: 12427096) Lee AH … Daefler S (Cellular microbiology 2002) 3 4 58

Products for NIPSNAP3A Gene

Sources for NIPSNAP3A Gene

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