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Aliases for C12orf49 Gene

Aliases for C12orf49 Gene

  • Chromosome 12 Open Reading Frame 49 2 3 5
  • UPF0454 Protein C12orf49 3

External Ids for C12orf49 Gene

Previous GeneCards Identifiers for C12orf49 Gene

  • GC12M115617
  • GC12M117153
  • GC12M114163

Summaries for C12orf49 Gene

GeneCards Summary for C12orf49 Gene

C12orf49 (Chromosome 12 Open Reading Frame 49) is a Protein Coding gene.

Additional gene information for C12orf49 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for C12orf49 Gene

Genomics for C12orf49 Gene

GeneHancer (GH) Regulatory Elements for C12orf49 Gene

Promoters and enhancers for C12orf49 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
GH12J116735 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 650.7 +0.8 756 3 CLOCK MLX DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D GLIS1 C12orf49 RNFT2 FBXW8 MED13L ENSG00000258034 RPL36P15 MAP1LC3B2 PIR60746
GH12J116716 Enhancer 1 Ensembl ENCODE 12.1 +20.6 20557 1.3 INSM2 FEZF1 ZNF335 GLIS2 ZNF366 ZSCAN5C SCRT2 ZNF680 OVOL3 TSHZ1 C12orf49 RNFT2 GC12M116721 PIR42431 ENSG00000257654
GH12J116713 Enhancer 0.4 ENCODE 12.1 +24.7 24686 0.1 CTCF SCRT2 ZIC2 C12orf49 RNFT2 PIR42431 GC12M116721 ENSG00000257654
GH12J116802 Enhancer 0.8 FANTOM5 ENCODE dbSUPER 1.5 -66.0 -65967 3 ZNF121 POLR2A RPL21P105 HRK C12orf49 ENSG00000275467 GC12M116856 RNFT2
GH12J116718 Enhancer 0.9 ENCODE 0.4 +19.2 19180 1.1 PKNOX1 INSM2 KLF17 MZF1 FEZF1 ZNF2 ZNF335 ZNF213 ZNF366 ZSCAN5C GC12M116721 PIR42431 PIR60746 C12orf49 ENSG00000257654
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around C12orf49 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the C12orf49 gene promoter:
  • SEF-1 (1)
  • Msx-1
  • Egr-4
  • p53
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c
  • CBF-A
  • CBF-B
  • CBF-C

Genomic Locations for C12orf49 Gene

Genomic Locations for C12orf49 Gene
27,886 bases
Minus strand
22,283 bases
Minus strand

Genomic View for C12orf49 Gene

Genes around C12orf49 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C12orf49 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C12orf49 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C12orf49 Gene

Proteins for C12orf49 Gene

  • Protein details for C12orf49 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    UPF0454 protein C12orf49
    Protein Accession:
    Secondary Accessions:
    • Q53GE8

    Protein attributes for C12orf49 Gene

    205 amino acids
    Molecular mass:
    23594 Da
    Quaternary structure:
    No Data Available

neXtProt entry for C12orf49 Gene

Post-translational modifications for C12orf49 Gene

  • Glycosylation at Thr185 and posLast=6767
  • Modification sites at PhosphoSitePlus

Other Protein References for C12orf49 Gene

No data available for DME Specific Peptides for C12orf49 Gene

Domains & Families for C12orf49 Gene

Gene Families for C12orf49 Gene

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

Protein Domains for C12orf49 Gene


Suggested Antigen Peptide Sequences for C12orf49 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the UPF0454 family.
  • Belongs to the UPF0454 family.
genes like me logo Genes that share domains with C12orf49: view

Function for C12orf49 Gene

Phenotypes From GWAS Catalog for C12orf49 Gene

Gene Ontology (GO) - Molecular Function for C12orf49 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with C12orf49: view
genes like me logo Genes that share phenotypes with C12orf49: view

Animal Model Products

miRNA for C12orf49 Gene

miRTarBase miRNAs that target C12orf49

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for C12orf49 Gene

Localization for C12orf49 Gene

Subcellular locations from UniProtKB/Swiss-Prot for C12orf49 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 C12orf49 gene
Compartment Confidence
extracellular 4
cytoskeleton 2
mitochondrion 2
nucleus 2
cytosol 2
plasma membrane 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for C12orf49 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
genes like me logo Genes that share ontologies with C12orf49: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for C12orf49 Gene

Pathways & Interactions for C12orf49 Gene

SuperPathways for C12orf49 Gene

No Data Available

Interacting Proteins for C12orf49 Gene

Gene Ontology (GO) - Biological Process for C12orf49 Gene


No data available for Pathways by source and SIGNOR curated interactions for C12orf49 Gene

Drugs & Compounds for C12orf49 Gene

No Compound Related Data Available

Transcripts for C12orf49 Gene

Unigene Clusters for C12orf49 Gene

Chromosome 12 open reading frame 49:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for C12orf49 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c
SP2: - -
SP3: - -

Relevant External Links for C12orf49 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for C12orf49 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for C12orf49 Gene

Protein differential expression in normal tissues from HIPED for C12orf49 Gene

This gene is overexpressed in Vitreous humor (67.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for C12orf49 Gene

Protein tissue co-expression partners for C12orf49 Gene

NURSA nuclear receptor signaling pathways regulating expression of C12orf49 Gene:


SOURCE GeneReport for Unigene cluster for C12orf49 Gene:


Evidence on tissue expression from TISSUES for C12orf49 Gene

  • Intestine(4.3)
genes like me logo Genes that share expression patterns with C12orf49: 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 C12orf49 Gene

Orthologs for C12orf49 Gene

This gene was present in the common ancestor of animals.

Orthologs for C12orf49 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia C12orf49 34
  • 100 (a)
C12H12orf49 33
  • 99.67 (n)
(Bos Taurus)
Mammalia C12orf49 34
  • 96 (a)
C9H12orf49 33
  • 90.41 (n)
(Canis familiaris)
Mammalia -- 34
  • 95 (a)
LOC102153143 33
  • 91.54 (n)
-- 34
  • 55 (a)
-- 34
  • 32 (a)
(Mus musculus)
Mammalia 2410131K14Rik 16 34 33
  • 85.53 (n)
(Rattus norvegicus)
Mammalia RGD1562310 33
  • 85.37 (n)
(Monodelphis domestica)
Mammalia C12orf49 34
  • 69 (a)
(Gallus gallus)
Aves C15H12ORF49 34 33
  • 80.81 (n)
(Anolis carolinensis)
Reptilia C12orf49 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia c12orf49 33
  • 72.41 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.4670 33
(Danio rerio)
Actinopterygii C5H12orf49 34
  • 79 (a)
zgc:110063 33
  • 74.24 (n)
Dr.15241 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.554 33
fruit fly
(Drosophila melanogaster)
Insecta CG15643 34 33
  • 56.52 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000855 33
  • 52.18 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
Species where no ortholog for C12orf49 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 C12orf49 Gene

Gene Tree for C12orf49 (if available)
Gene Tree for C12orf49 (if available)

Paralogs for C12orf49 Gene

genes like me logo Genes that share paralogs with C12orf49: view

No data available for Paralogs for C12orf49 Gene

Variants for C12orf49 Gene

Sequence variations from dbSNP and Humsavar for C12orf49 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000244233 -- 116,738,242(-) C/G upstream_transcript_variant
rs1000319004 -- 116,738,454(-) C/A upstream_transcript_variant
rs1000580260 -- 116,739,522(-) C/G upstream_transcript_variant
rs1000653651 -- 116,739,745(-) A/C/T upstream_transcript_variant
rs1000653913 -- 116,732,402(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for C12orf49 Gene

Variant ID Type Subtype PubMed ID
esv3630848 CNV gain 21293372
nsv1039046 CNV gain 25217958
nsv832523 CNV gain+loss 17160897

Variation tolerance for C12orf49 Gene

Residual Variation Intolerance Score: 65.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.48; 55.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for C12orf49 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C12orf49 Gene

Disorders for C12orf49 Gene

Additional Disease Information for C12orf49

No disorders were found for C12orf49 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for C12orf49 Gene

Publications for C12orf49 Gene

  1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  3. RNA sequencing of esophageal adenocarcinomas identifies novel fusion transcripts, including NPC1-MELK, arising from a complex chromosomal rearrangement. (PMID: 28640357) Wang Z … Meltzer SJ (Cancer 2017) 3 58
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 58
  5. A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells. (PMID: 23284306) Xie L … Green MR (PLoS genetics 2012) 3 58

Products for C12orf49 Gene

Sources for C12orf49 Gene

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