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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
Subcategory (RNA class) for C1QTNF3-AMACR Gene
lncRNA
Number of RNA Genes sources:
1 / 17
Aliases for C1QTNF3-AMACR Gene
External Ids for C1QTNF3-AMACR Gene
- HGNC: 49198
- Entrez Gene: 100534612
- Ensembl: ENSG00000273294
- UniProtKB: E9PGA6
Previous GeneCards Identifiers for C1QTNF3-AMACR Gene
- GC05U901547
- GC05M033988
Summaries 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 Congenital Bile Acid Synthesis Defect. An important paralog of this gene is C1QTNF3.
Additional gene information for C1QTNF3-AMACR Gene
- HGNC(49198)
- Entrez Gene(100534612)
- Ensembl(ENSG00000273294)
- UniProtKB(E9PGA6)
- Open Targets Platform(ENSG00000273294)
- Monarch Initiative
- Search for C1QTNF3-AMACR at DataMed
- Search for C1QTNF3-AMACR at HumanCyc
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 |
|---|---|---|---|---|---|---|---|---|---|---|
| GH05J034124 | Enhancer | 0.2 | ENCODE | 600.7 | +0.1 | 87 | 0.1 | C1QTNF3-AMACR ENSG00000279995 AMACR C1QTNF3 | ||
| GH05J034122 | Enhancer | 0.2 | Ensembl | 600.7 | +1.9 | 1927 | 1.2 | C1QTNF3-AMACR ENSG00000279995 AMACR ENSG00000278900 C1QTNF3 | ||
| GH05J034006 | Promoter/Enhancer | 2.6 | EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER | 0.1 | +115.9 | 115879 | 4.5 | HNRNPL GATAD2A TEAD4 PRDM10 ZNF629 REST TFE3 ZNF512 ZNF692 POLR2A | AMACR ENSG00000249572 BRIX1 TTC23L ENSG00000215158 C1QTNF3 piR-41405-009 C1QTNF3-AMACR | |
| GH05J034059 | Enhancer | 0.9 | Ensembl ENCODE | 0.2 | +63.1 | 63067 | 3.9 | GATAD2A REST PRDM1 RXRB SP1 CEBPA FOXA2 ZNF585B ATF3 YY1 | BRIX1 AMACR AF480515 ENSG00000278900 C1QTNF3-AMACR C1QTNF3 | |
| GH05J034129 | Enhancer | 0.3 | Ensembl | 0.7 | -4.8 | -4773 | 0.2 | SPI1 | C1QTNF3-AMACR piR-45012-399 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
Genomic Locations for C1QTNF3-AMACR Gene
- chr5:33,986,986-34,124,528
- (GRCh38/hg38)
- Size:
- 137,543 bases
- Orientation:
- Minus strand
- chr5:33,987,091-34,035,863
- (GRCh37/hg19)
- Size:
- 48,773 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 GeneCards ncRNA compendium hub on the UCSC Golden Path
- Cytogenetic band:
-
- 5p13.2 by HGNC
- 5p13.2 by Entrez Gene
- 5p13.2 by Ensembl
C1QTNF3-AMACR Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene 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
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:
Antibody Products
Protein Products
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for C1QTNF3-AMACR
- Origene Custom Protein Services for C1QTNF3-AMACR
No data available for DME Specific Peptides for C1QTNF3-AMACR Gene
Domains & Families for C1QTNF3-AMACR Gene
Protein Domains for C1QTNF3-AMACR Gene
- InterPro:
- ProtoNet:
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
Phenotypes From GWAS Catalog for C1QTNF3-AMACR Gene
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
CRISPR Products
- Browse CRISPR knockouts for C1QTNF3-AMACR
miRNA Products
Inhibitory RNA Products
Clone Products
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
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005576 | extracellular region | IEA | -- |
| GO:0005581 | collagen trimer | IEA | -- |
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
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 | 3612 | 2 |
RefSeq: NR_037951, LNCipedia: lnc-C1QTNF3-AMACR-1:1, |
C1QTNF3-AMACR in the 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 :
-
- ENST00000382079 3424 nts (view in UCSC)
CRISPR Products
- Browse CRISPR knockouts for C1QTNF3-AMACR
miRNA Products
Inhibitory RNA Products
Clone Products
Relevant External Links for C1QTNF3-AMACR Gene
- GeneLoc Exon Structure for
- C1QTNF3-AMACR
Expression 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).
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for C1QTNF3-AMACR
Primer Products
Gene Expression Assay Products
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.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| Chimpanzee (Pan troglodytes) |
Mammalia | -- 31 |
|
OneToMany | |
| Cow (Bos Taurus) |
Mammalia | C1QTNF3 31 |
|
OneToMany | |
| Oppossum (Monodelphis domestica) |
Mammalia | -- 31 |
|
OneToMany | |
| Platypus (Ornithorhynchus anatinus) |
Mammalia | -- 31 |
|
OneToMany | |
| Dog (Canis familiaris) |
Mammalia | -- 31 |
|
OneToMany | |
| Mouse (Mus musculus) |
Mammalia | C1qtnf3 31 |
|
OneToMany | |
| Chicken (Gallus gallus) |
Aves | -- 31 |
|
OneToMany | |
| Zebrafish (Danio rerio) |
Actinopterygii | cbln12 31 |
|
ManyToMany | |
| Sea Squirt (Ciona savignyi) |
Ascidiacea | -- 31 |
|
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)
Paralogs for C1QTNF3-AMACR Gene
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 |
|---|---|---|---|---|---|
| 725410 | Likely Benign: not provided | 33,998,699(-) | A/G | MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT | |
| 752016 | Likely Benign: not provided | 34,005,877(-) | C/T | NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT | |
| 802109 | Uncertain Significance: Alpha-methylacyl-CoA racemase deficiency | 33,989,384(-) | GA/G | FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,THREE_PRIME_UTR_VARIANT | |
| 802110 | Uncertain Significance: Alpha-methylacyl-CoA racemase deficiency | 34,007,814(-) | A/G | MISSENSE_VARIANT | |
| 809742 | Uncertain Significance: not provided | 33,998,777(-) | C/T | MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT |
| 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
SNP Genotyping and Copy Number Assay Products
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for C1QTNF3-AMACR Gene
Disorders for C1QTNF3-AMACR Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| alpha-methylacyl-coa racemase deficiency |
|
|
| congenital bile acid synthesis defect |
|
|
Search C1QTNF3-AMACR in MalaCards
View complete list of genes associated with diseases
Additional Disease Information for C1QTNF3-AMACR
No data available for UniProtKB/Swiss-Prot and Genatlas for C1QTNF3-AMACR Gene
Publications for C1QTNF3-AMACR Gene
- Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PMID: 20967262) Prakash T … Taylor TD (PloS one 2010) 3
- The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J … Rubin EM (Nature 2004) 13
Products for C1QTNF3-AMACR Gene
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- High-throughput Antibody Production Service
- Protein Production Service
- Epitope Tag Antibodies & Reporter Protein Antibodies
- Lentiviral ORF Clones
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for knockout CRISPR/Cas9 clones, lentivirus, and/or AAV products for C1QTNF3-AMACR
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Sources for C1QTNF3-AMACR Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) ProtoNet
- (16) Blocks
- (17) MGI
- (18) IUBMB
- (19) KEGG
- (20) MINT
- (21) STRING
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) ASD
- (28) SAGE
- (29) SOURCE
- (30) HomoloGene
- (31) PanEnsembl
- (32) euGenes
- (33) SGD
- (34) FlyBase
- (35) WormBase
- (36) Pseudogene
- (37) DGV
- (38) dbSNP
- (39) GenAtlas
- (40) HGMD
- (41) GAD
- (42) BGMUT
- (43) HuGE
- (44) Atlas
- (45) GenBank
- (46) HORDE
- (47) HUGE
- (48) IMGT
- (49) Leiden
- (50) miRBase
- (51) DME
- (52) OriGene
- (53) PubMed
- (54) R&D Systems
- (55) TGDB
- (56) Tocris
- (57) Abcam
- (58) Novus Biologicals
- (59) ProSpec
- (60) Sino Biological
- (61) GenScript
- (62) Qiagen
- (63) OCA
- (64) Proteopedia
- (65) MOPED
- (66) neXtProt
- (67) Reactome
- (68) GeneGo (Thomson Reuters)
- (69) DISEASES
- (70) SIMAP
- (71) GenomeRNAi
- (72) LifeMap
- (73) miRTarBase
- (74) MalaCards
- (75) Invitrogen
- (76) BitterDB
- (77) ESI-BIO
- (78) RefSeq
- (79) BioSystems
- (80) MaxQB
- (81) IUPHAR
- (82) BioGPS
- (83) Illumina
- (84) COMPARTMENTS
- (85) HOMER
- (86) PaxDb
- (87) ApexBio
- (88) Addgene
- (89) antibodies-online
- (90) CYP
- (91) NONCODE
- (92) TreeFam
- (93) PathCards
- (94) GeneReviews
- (95) GeneTex
- (96) Taconic Biosciences
- (97) GTEx
- (98) ProteomicsDB
- (99) SCBT
- (100) DGIdb
- (101) ClinicalTrials
- (102) RVIS
- (103) SIGNOR
- (104) diseasecard
- (105) NIH Rare Diseases
- (106) Orphanet
- (107) UMLS
- (108) GTR
- (109) Disease Ontology
- (110) Genetics Home Reference
- (111) MeSH
- (112) MedlinePlus
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- (115) NCBI Bookshelf
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- (124) Horizon
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- (130) CIViC
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- (132) dbSUPER
- (133) TISSUES
- (134) Gene ORGANizer
- (135) abm
- (136) Human Protein Atlas
- (137) GWAS Catalog
- (138) Monarch Initiative
- (139) DataMed
- (140) HumanCyc
- (141) UCNEbase
- (142) EPDnew
- (143) Applied Biosystems
- (144) GlyConnect
- (145) Aminode
- (146) GeneCopoeia
- (147) GPS-Prot
- (148) RNACentral
- (149) LncRNADisease
- (150) LOVD
- (151) miR2Disease
- (152) DiseaseEnhancer
- (153) Boster Bio
- (154) Biorbyt
- (155) Biocompare
- (156) Mastermind
- (157) CTD^2 Dashboard
- (158) CraniofacialAtlas
- (159) GeneImprint
- (160) Synthego
- (161) ENA
- (162) GtRNAdb
- (163) LncBase
- (164) LncBook
- (165) LNCipedia
- (166) Modomics
- (167) PDBe
- (168) Rfam
- (169) SILVA
- (170) snOPY
- (171) SRPDB
- (172) GENCODE
- (173) TarBase
- (174) Signalway Antibody
- (175) Open Targets Platform
- (176) 5SRRNADB
- (177) snoDB
- (178) MirGeneDB