This locus represents naturally occurring read-through transcription between the neighboring C1q and tumor necrosis factor related protein 3 (C1QTNF3) and alpha-methylacyl-CoA racemase (AMACR) genes on chromosome 5. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus not likely to produce a protein product. [provided by RefSeq, Mar 201... See more...

Aliases for C1QTNF3-AMACR Gene

Data sources for C1QTNF3-AMACR Gene:

Subcategory (RNA class) for C1QTNF3-AMACR Gene

lncRNA

Aliases for C1QTNF3-AMACR Gene

External Ids for C1QTNF3-AMACR Gene

Previous GeneCards Identifiers for C1QTNF3-AMACR Gene

  • GC05U901547
  • GC05M033988

Summaries for C1QTNF3-AMACR Gene

Entrez Gene Summary for C1QTNF3-AMACR Gene

  • This locus represents naturally occurring read-through transcription between the neighboring C1q and tumor necrosis factor related protein 3 (C1QTNF3) and alpha-methylacyl-CoA racemase (AMACR) genes on chromosome 5. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus not likely to produce a protein product. [provided by RefSeq, Mar 2011]

GeneCards Summary for C1QTNF3-AMACR Gene

C1QTNF3-AMACR (C1QTNF3-AMACR Readthrough (NMD Candidate)) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with C1QTNF3-AMACR include Alpha-Methylacyl-Coa Racemase Deficiency and Bile Acid Synthesis Defect, Congenital, 4. An important paralog of this gene is C1QTNF3.

Additional gene information for C1QTNF3-AMACR Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for C1QTNF3-AMACR Gene

Genomics for C1QTNF3-AMACR Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for C1QTNF3-AMACR 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
GH05J034122 Enhancer 0.2 Ensembl 250.7 +1.9 1927 1.2 C1QTNF3-AMACR ENSG00000279995 HSALNG0041070 AMACR HSALNG0041069 C1QTNF3
GH05J034124 Enhancer 0.2 ENCODE 250.7 +0.1 87 0.1 C1QTNF3-AMACR ENSG00000279995 HSALNG0041070 AMACR C1QTNF3
GH05J034006 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 0.1 +115.9 115879 4.5 TBP ZBTB10 MXD4 FEZF1 CEBPA MNT DEK SMAD5 HES1 MBD2 AMACR BRIX1 TTC23L ENSG00000215158 C1QTNF3 piR-41405-009 C1QTNF3-AMACR
GH05J034059 Enhancer 0.9 Ensembl ENCODE 0.2 +63.1 63067 3.9 CEBPA SMAD4 RXRA RARA FOXA2 ZBTB33 ZNF585B BCL6 JUND FOXP1 BRIX1 AMACR HSALNG0041066 AF480515 C1QTNF3-AMACR C1QTNF3
GH05J034129 Enhancer 0.3 Ensembl 0.7 -4.7 -4673 0.4 SPI1 C1QTNF3-AMACR HSALNG0041071 C1QTNF3 AMACR
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around C1QTNF3-AMACR on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for C1QTNF3-AMACR Gene

Latest Assembly
chr5:33,986,985-34,124,528
(GRCh38/hg38)
Size:
137,544 bases
Orientation:
Minus strand

Previous Assembly
chr5:33,987,091-34,124,633
(GRCh37/hg19 by Entrez Gene)
Size:
137,543 bases
Orientation:
Minus strand

chr5:33,987,279-34,124,633
(GRCh37/hg19 by Ensembl)
Size:
137,355 bases
Orientation:
Minus strand

Genomic View for C1QTNF3-AMACR Gene

Genes around C1QTNF3-AMACR on UCSC Golden Path with GeneCards custom track
C1QTNF3-AMACR in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
C1QTNF3-AMACR Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C1QTNF3-AMACR Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C1QTNF3-AMACR Gene

Proteins for C1QTNF3-AMACR Gene

  • Protein details for C1QTNF3-AMACR Gene (UniProtKB/TrEMBL)

    Protein Symbol:
    E9PGA6-E9PGA6_HUMAN
    Recommended name:
    C1QTNF3-AMACR readthrough (NMD candidate)
    Protein Accession:
    E9PGA6

    Protein attributes for C1QTNF3-AMACR Gene

    Size:
    284 amino acids
    Molecular mass:
    31075 Da
    Quaternary structure:
    No Data Available

neXtProt entry for C1QTNF3-AMACR Gene

Protein Expression for C1QTNF3-AMACR Gene

Post-translational modifications for C1QTNF3-AMACR Gene

No Post-translational modifications

Other Protein References for C1QTNF3-AMACR Gene

ENSEMBL proteins:

No data available for DME Specific Peptides for C1QTNF3-AMACR Gene

Domains & Families for C1QTNF3-AMACR Gene

Protein Domains for C1QTNF3-AMACR Gene

genes like me logo Genes that share domains with C1QTNF3-AMACR: view

No data available for Gene Families , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for C1QTNF3-AMACR Gene

Function for C1QTNF3-AMACR Gene

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for C1QTNF3-AMACR Gene

Localization for C1QTNF3-AMACR Gene

Gene Ontology (GO) - Cellular Components for C1QTNF3-AMACR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
genes like me logo Genes that share ontologies with C1QTNF3-AMACR: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Subcellular locations from the Human Protein Atlas (HPA) for C1QTNF3-AMACR Gene

Pathways & Interactions for C1QTNF3-AMACR Gene

PathCards logo

SuperPathways for C1QTNF3-AMACR Gene

No Data Available

Gene Ontology (GO) - Biological Process for C1QTNF3-AMACR Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for C1QTNF3-AMACR Gene

Drugs & Compounds for C1QTNF3-AMACR Gene

No Compound Related Data Available

Transcripts for C1QTNF3-AMACR Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for C1QTNF3-AMACR Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS000075C2B5_9606 lncRNA 3621 2

RefSeq: NR_037951,

LNCipedia: lnc-C1QTNF3-AMACR-1:1,

C1QTNF3-AMACR in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for C1QTNF3-AMACR Gene

1 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for C1QTNF3-AMACR Gene

No ASD Table

Relevant External Links for C1QTNF3-AMACR Gene

GeneLoc Exon Structure for
C1QTNF3-AMACR

Expression for C1QTNF3-AMACR Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for C1QTNF3-AMACR Gene

Protein differential expression in normal tissues from HIPED for C1QTNF3-AMACR Gene

This gene is overexpressed in Fetal gut (23.3), Bone marrow mesenchymal stem cell (14.7), Breast (11.4), and Vitreous humor (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from MOPED for C1QTNF3-AMACR Gene



Protein tissue co-expression partners for C1QTNF3-AMACR Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for C1QTNF3-AMACR

genes like me logo Genes that share expression patterns with C1QTNF3-AMACR: 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 , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for C1QTNF3-AMACR Gene

Orthologs for C1QTNF3-AMACR Gene

This gene was present in the common ancestor of chordates.

Orthologs for C1QTNF3-AMACR Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia -- 31
  • 99 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia C1QTNF3 31
  • 89 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 85 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 79 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia -- 31
  • 69 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia C1qtnf3 31
  • 68 (a)
OneToMany
Chicken
(Gallus gallus)
Aves -- 31
  • 79 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii cbln12 31
  • 25 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 30 (a)
OneToMany
Species where no ortholog for C1QTNF3-AMACR was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Lizard (Anolis carolinensis)
  • 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)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for C1QTNF3-AMACR Gene

ENSEMBL:
Gene Tree for C1QTNF3-AMACR (if available)
TreeFam:
Gene Tree for C1QTNF3-AMACR (if available)

Paralogs for C1QTNF3-AMACR Gene

genes like me logo Genes that share paralogs with C1QTNF3-AMACR: view

Variants for C1QTNF3-AMACR Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for C1QTNF3-AMACR Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
845848 Uncertain Significance: Alpha-methylacyl-CoA racemase deficiency 33,998,777(-) CA/TG
NM_014324.6(AMACR):c.602_603inv (p.Leu201Ser)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT
903704 Uncertain Significance: Alpha-methylacyl-CoA racemase deficiency 34,005,858(-) G/T
NM_014324.6(AMACR):c.289C>A (p.Arg97=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
903705 Uncertain Significance: Alpha-methylacyl-CoA racemase deficiency 34,007,920(-) C/G
NM_014324.6(AMACR):c.100G>C (p.Val34Leu)
MISSENSE
903706 Uncertain Significance: Alpha-methylacyl-CoA racemase deficiency 34,007,993(-) C/T
NM_014324.6(AMACR):c.27G>A (p.Val9=)
SYNONYMOUS
904696 Uncertain Significance: Alpha-methylacyl-CoA racemase deficiency 33,987,108(-) C/T
NM_014324.6(AMACR):c.*1985G>A
NON_CODING_TRANSCRIPT_VARIANT,THREE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for C1QTNF3-AMACR Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for C1QTNF3-AMACR Gene

Variant ID Type Subtype PubMed ID
dgv5626n100 CNV loss 25217958
esv1163132 CNV insertion 17803354
esv26035 CNV loss 19812545
esv2759340 CNV gain+loss 17122850
esv32686 CNV loss 17666407
esv33890 CNV gain+loss 17666407
esv3604666 CNV gain 21293372
esv3604667 CNV loss 21293372
esv3604668 CNV loss 21293372
esv3604669 CNV loss 21293372
nsv1019937 CNV loss 25217958
nsv428116 CNV gain+loss 18775914
nsv469604 CNV gain 16826518
nsv507243 OTHER sequence alteration 20534489
nsv519240 CNV gain 19592680
nsv522715 CNV gain 19592680
nsv830255 CNV loss 17160897
nsv830256 CNV gain 17160897
nsv964836 CNV duplication 23825009
nsv964837 CNV duplication 23825009
nsv964838 CNV duplication 23825009
nsv968161 CNV duplication 23825009
nsv980631 CNV duplication 23825009

Additional Variant Information for C1QTNF3-AMACR Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
C1QTNF3-AMACR

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for C1QTNF3-AMACR Gene

Disorders for C1QTNF3-AMACR Gene

MalaCards: The human disease database

(3) MalaCards diseases for C1QTNF3-AMACR Gene - From: CVR and GCD

Disorder Aliases PubMed IDs
alpha-methylacyl-coa racemase deficiency
  • amacrd
bile acid synthesis defect, congenital, 4
  • cbas4
congenital bile acid synthesis defect
  • 3-beta-hydroxy-delta-5-c27-steroid oxidoreductase deficiency
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for C1QTNF3-AMACR

genes like me logo Genes that share disorders with C1QTNF3-AMACR: view

No data available for UniProtKB/Swiss-Prot and Genatlas for C1QTNF3-AMACR Gene

Publications for C1QTNF3-AMACR Gene

  1. AMACR mutations cause late-onset autosomal recessive cerebellar ataxia. (PMID: 21576695) Dick D … Chinnery PF (Neurology 2011) 74
  2. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PMID: 20967262) Prakash T … Taylor TD (PloS one 2010) 3
  3. An adult onset case of alpha-methyl-acyl-CoA racemase deficiency. (PMID: 20821052) Smith EH … Tortorelli S (Journal of inherited metabolic disease 2010) 74
  4. Relapsing encephalopathy in a patient with alpha-methylacyl-CoA racemase deficiency. (PMID: 18032455) Thompson SA … Barker RA (Journal of neurology, neurosurgery, and psychiatry 2008) 74
  5. The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J … Rubin EM (Nature 2004) 13

Products for C1QTNF3-AMACR Gene

Sources for C1QTNF3-AMACR Gene