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What's New GeneCards Guide Getting Started About GeneCards Data Sources Citing This Resource Publications
Weizmann Institute of
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| GeneCards section | Queried fields | Sources |
|---|---|---|
| Gene Symbol |   | HGNC, NCBI, Ensembl |
| GeneCards ID | GeneCards ID | GeneCards, GeneLoc | Category | Category | Entrez Gene, Ensembl, GeneCards | Gene Description |   | HGNC, Entrez Gene | Approval | Approved, Not approved | HGNC | Source |   | HGNC, Entrez Gene, Ensembl |
| Aliases and Descriptions | Aliases, Descriptions | HGNC, UniProt, SwissProt, TrEMBL, NCBI, GDB, OMIM, GeneLoc |
| Genomic Location | Chromosome, strand, cytogenetic band, genomic location start/end, gene size, Mapped to contig (flag if the information is not genomic) | GeneLoc, NCBI, Ensembl, Entrez Gene, HGNC, HORDE, miRBase |
| Proteins | Aliases, UniProt ID, protein name, size, cofactor, subunit, subcellular location, tissue specificity, developmental stage, ptm, miscellaneous, RefSeq ID, Ensembl ID | UniProt, Entrez Gene(NCBI), Ensembl |
| Protein Domains / Families | InterPro domains, UniProt ID, UniProt domains, UniProt similarities | EBI, UniProt |
| Gene Function | UniProt ID, UniProt function, MGI mutant phenotype | UniProt, MGD |
| Ontologies | GO ID, GO term | GO |
| Pathways and Interactions | KEGG ID, KEGG pathway description, Invitrogen ID, Invitrogen pathway description, CST(Cell Signaling Technology) ID, CST pathway description | KEGG, iPath, CST |
| AKS compounds | Compound name | AKS |
| Transcripts | Refseq transcripts, Unigene cluster, Unigene cluster description | RefSeq, Unigene |
| Expression in Human tissues | U95 probe-sets, binary expression patterns in tissues ordered as in the GeneCards display, sensitivity, specificity | GeneNote, GeneAnnot |
| Similar Genes in Other Organisms | Organism, gene, percent protein similarity to the human gene, percent nucleotide similarity to the human gene | HomoloGene, euGenes |
| HomoloGene Paralogs | gene | HomoloGene |
| Ensembl Paralogs | gene | Ensembl |
| SNPs/Variants | number of NCBI snps, NCBI ID, location type, populations studied, validation, position, amino acid change, sequence, number of sources number of additional AB snps, AB ID | NCBI, AB |
| OMIM disorders | OMIM ID, Disorder description | OMIM |
| UniProt disorders | UniProt ID, Disorder description | UniProt |
| AKS disorders | Disorder description | AKS |
| Other Genome Wide Resources | EntrezGene ID, Ensembl ID | NCBI, Ensembl |
Field formats
GeneCards_ID
gc_id
Category
protein-coding,
pseudogene, RNA gene, genetic locus,
gene cluster, or uncategorized
Gene Description
Gene description according to HGNC or Entrez Gene
Approval
Approved, not approved according to HGNC
Source
Gene symbol from HGNC, Entrez Gene or Ensembl
Aliases
alias1|alias2|alias3|...
Descriptions
description1|description2|description3|...
Chromosome
1-22 or X,Y,MT (mitochondria). NA appears where chromosome is unknown.
Strand
Plus, Minus or NA (where strand is unknown)
Cytogenetic band
Cytogenetic band according to Entrez Gene, Ensembl and/or HGNC
Gene start
chromosomal coordinate in bp from pter
Gene end
chromosomal coordinate in bp from pter
Gene size
size of genomic sequence in bp
UniProt Protein details
source:aliases|uniprot protein_id1#protein name#size#cofactor & cofactor#subunit & subunit#subcellular location & subcellular location#tissue specificity & tissue specificity#
developmental stage & developmental stage#ptm & ptm#miscellaneous & miscellaneous|
uniprot protein_id2#protein name#size#cofactor..#subunit..#subcellular location..#tissue specificity..#developmental stage..#ptm..#miscellaneous..|
uniprot protein_id3#protein name#size#cofactor..#subunit..#subcellular location..#tissue specificity..#developmental stage..#ptm..#miscellaneous..|...
RefSeq Protein ID
refseq protein_id1|refseq protein_id2|refseq protein_id3|...
Ensembl Protein ID
ensembl protein_id1|ensembl protein_id2|ensembl protein_id3|...
InterPro domains and families
InterPro_id1#domain_name|InterPro_id2#domain_name...
UniProt Domains and Families
source:uniprot_id1#domain & domain..#similarity & similarity..|uniprot_id2#domain & domain..#similarity & similarity..|uniprot_id3#domain & domain..#similarity & similarity..|...
Gene Function - UniProt
source:uniprot_id1#function|uniprot_id2#function|uniprot_id3#function...
Gene Function - MGI mutant phenotype
Allele1: MGI_id1#Phenotypes: |Allele2: MGI_id2#Phenotypes: phenotype_id1#phenotype_name||phenotype_id2#phenotype_name...
Gene Ontologies (GO)
go_id1#go_term1|go_id2#go_term2|go_id3#go_term3|...
Pathways (KEGG)
kegg_id1#kegg_pathway1|kegg_id2#kegg_pathway2|kegg_id3#kegg_pathway3|...
Pathways (Invitrogen)
Invitrogen_id1#Invitrogen_pathway1|Invitrogen_id2#Invitrogen_pathway2|Invitrogen_id3#Invitrogen_pathway3|...
Pathways (CST)
cst_id1#cst_pathway1|cst_id2#cst_pathway2|cst_id3#cst_pathway3|...
AKS Compounds
compound1|compound2|compound3|...
Transcripts (Refseq)
transcript1|transcript2|transcript3|...
Transcripts (Unigene)
ug_cluster1#description|ug_cluster2#description|ug_cluster3#description...
Expression in Human tissues
probe-set_id1#binary_pattern1#sensitivity1#specificity1|probe-set_id2#binary_pattern2#sensitivity2#specificity2|probe-set_id3#binary_pattern3#sensitivity3#specificity3...
Similar Genes in Other Organisms
organism1#gene1#percent protein similarity#percent nucleotide similarity|organism2#gene2#percent protein similarity#percent nucleotide similarity|organism3#gene3#percent protein similarity#percent nucleotide similarity|...
The organisms are depicted by their two or three letter acronyms as follows:
| Acronym | Scientific name | Common name |
|---|---|---|
| Aga | Anopheles gambiae | African malaria mosquito |
| At | Arabidopsis thaliana | Thale cress |
| Bt | Bos taurus | Cow |
| Cel | Caenorhabditis elegans | Worm |
| Cfa | Canis familiaris | Dog |
| Cin | Ciona intestinalis | Sea squirt |
| Cre | Chlamydomonas reinhardtii | Green algae |
| Ddi | Dictyostelium discoideum | Amoeba |
| Dm | Drosophila melanogaster | Fruit fly |
| Dr | Danio rerio | Zebrafish |
| Eg | Ashbya gossypii | A. gosspyii yeast |
| Gga | Gallus gallus | Chicken |
| Gma | Glycine max | Soybean |
| Hv | Hordeum vulgare | Barley |
| Kl | Kluyveromyces lactis | K. lactis yeast |
| Les | Lycopersicon esculentum | Tomato |
| Mgr | Magnaporthe grisea | Rice blast fungus |
| Mm | Mus musculus | Mouse |
| Mtr | Medicago truncatula | Medicago trunc |
| Ncr | Neurospora crassa | Bread mold |
| Omy | Oncorhynchus mykiss | Rainbow trout |
| Os | Oryza sativa | Rice |
| Pf | Plasmodium falciparum | Malaria parasite |
| Pt | Pan troglodytes | Chimpanzee |
| Pta | Pinus taeda | Loblolly pine |
| Rn | Rattus norvegicus | Rat |
| Sbi | Sorghum bicolor | Sorghum |
| Sc | Saccharomyces cerevisiae | Baker's yeast |
| Sma | Schistosoma mansoni | Schistosome parasite |
| Sof | Saccharum officinarum | Sugarcane |
| Sp | Schizosaccharomyces pombe | Fission yeast |
| Ssc | Sus scrofa | Pig |
| Str | Silurana tropicalis | Tropical clawed frog |
| Ta | Triticum aestivum | Wheat |
| Tgo | Toxoplasma gondii | Toxoplasmosis |
| Vva | Vitis vinifera | Alicante grape |
| Xl | Xenopus laevis | African clawed frog |
| Zm | Zea mays | Corn |
gene1|gene2|gene3|...
Ensembl Paralogs
gene1|gene2|gene3|...
Snps (NCBI)
number of snps: ncbi_id1#location type#populations studied#validation#position#amino acid change#sequence#number of sources|ncbi_id2#location type#populations studied#validation#position#amino acid change#sequence#number of sources...
Snps (AB)
additional number of snps: ab_id1, ab_id2, ab_id3...
Disorders - Omim_ID & disorder description
omim_id#disorder1|disorder2|disorder3|...
UniProt Disorders
source:uniprot_id1#disorder & disorder..|uniprot_id2#disorder & disorder..|uniprot_id3#disorder & disorder..|...
AKS Disorders
disorder1|disorder2|disorder3|...
EntrezGene_ID
entrezgene_id
Ensembl_ID
ensembl_id