Free for academic non-profit institutions. Other users need a Commercial license

Aliases for AGPAT4-IT1 Gene

Subcategory (RNA class) for AGPAT4-IT1 Gene


Quality Score for this RNA gene is


Aliases for AGPAT4-IT1 Gene

  • AGPAT4 Intronic Transcript 1 2 3 4 5
  • AGPAT4 Intronic Transcript 1 (Non-Protein Coding) 2 3
  • NCRNA00241 3 4
  • C6orf59 3 4
  • Chromosome 6 Open Reading Frame 59 2
  • Non-Protein Coding RNA 241 2

External Ids for AGPAT4-IT1 Gene

ORGUL Members for AGPAT4-IT1 Gene

Previous HGNC Symbols for AGPAT4-IT1 Gene

  • C6orf59
  • NCRNA00241

Previous GeneCards Identifiers for AGPAT4-IT1 Gene

  • GC06M161583

Summaries for AGPAT4-IT1 Gene

GeneCards Summary for AGPAT4-IT1 Gene

AGPAT4-IT1 (AGPAT4 Intronic Transcript 1) is an RNA Gene, and is affiliated with the lncRNA class.

Additional gene information for AGPAT4-IT1 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 AGPAT4-IT1 Gene

Genomics for AGPAT4-IT1 Gene

GeneHancer (GH) Regulatory Elements for AGPAT4-IT1 Gene

Promoters and enhancers for AGPAT4-IT1 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
GH06J161163 Enhancer 0.6 ENCODE dbSUPER 650.7 -1.7 -1722 0.2 MAX POU5F1 MNT AGPAT4-IT1 PIR49622 AGPAT4
GH06J161160 Enhancer 0.5 ENCODE dbSUPER 650.7 +1.3 1348 0.9 SETDB1 AGPAT4-IT1 PIR56804 AGPAT4
GH06J161151 Enhancer 0.7 dbSUPER 0.4 +9.2 9222 2.8 HDGF CTCF NFIB ZMYM3 ZIC2 RAD21 HIC1 CC2D1A LCORL ARID2 AGPAT4 AGPAT4-IT1 PIR56804
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around AGPAT4-IT1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for AGPAT4-IT1 Gene

Genomic Locations for AGPAT4-IT1 Gene
1,878 bases
Minus strand
1,869 bases
Minus strand

Genomic View for AGPAT4-IT1 Gene

Genes around AGPAT4-IT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AGPAT4-IT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AGPAT4-IT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AGPAT4-IT1 Gene

Proteins for AGPAT4-IT1 Gene

  • Protein details for AGPAT4-IT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Putative uncharacterized protein encoded by AGPAT4-IT1
    Protein Accession:
    Secondary Accessions:
    • A7E1X1
    • Q2M1M7
    • Q5TEF2
    • Q9H5S5

    Protein attributes for AGPAT4-IT1 Gene

    198 amino acids
    Molecular mass:
    20949 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAB15545.1; Type=Frameshift; Positions=66; Evidence={ECO:0000305};

neXtProt entry for AGPAT4-IT1 Gene

Post-translational modifications for AGPAT4-IT1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for AGPAT4-IT1 Gene

Domains & Families for AGPAT4-IT1 Gene

Protein Domains for AGPAT4-IT1 Gene


Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with AGPAT4-IT1: view

No data available for Gene Families , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for AGPAT4-IT1 Gene

Function for AGPAT4-IT1 Gene

genes like me logo Genes that share phenotypes with AGPAT4-IT1: view

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for AGPAT4-IT1 Gene

Localization for AGPAT4-IT1 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for AGPAT4-IT1 Gene

Pathways & Interactions for AGPAT4-IT1 Gene

SuperPathways for AGPAT4-IT1 Gene

No Data Available

Interacting Proteins for AGPAT4-IT1 Gene

Gene Ontology (GO) - Biological Process for AGPAT4-IT1 Gene


No data available for Pathways by source and SIGNOR curated interactions for AGPAT4-IT1 Gene

Drugs & Compounds for AGPAT4-IT1 Gene

No Compound Related Data Available

Transcripts for AGPAT4-IT1 Gene

mRNA/cDNA for AGPAT4-IT1 Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(153) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :
(1) RNA Central transcripts :

Unigene Clusters for AGPAT4-IT1 Gene

AGPAT4 intronic transcript 1 (non-protein coding):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for AGPAT4-IT1 Gene

No ASD Table

Relevant External Links for AGPAT4-IT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for AGPAT4-IT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AGPAT4-IT1 Gene

mRNA expression in normal human tissues for AGPAT4-IT1 Gene

SOURCE GeneReport for Unigene cluster for AGPAT4-IT1 Gene:

genes like me logo Genes that share expression patterns with AGPAT4-IT1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for AGPAT4-IT1 Gene

Orthologs for AGPAT4-IT1 Gene

Evolution for AGPAT4-IT1 Gene

Gene Tree for AGPAT4-IT1 (if available)
Gene Tree for AGPAT4-IT1 (if available)

No data available for Orthologs for AGPAT4-IT1 Gene

Paralogs for AGPAT4-IT1 Gene

No data available for Paralogs for AGPAT4-IT1 Gene

Variants for AGPAT4-IT1 Gene

Sequence variations from dbSNP and Humsavar for AGPAT4-IT1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000035192 -- 161,162,074(-) A/G upstream_transcript_variant
rs1001646803 -- 161,163,336(-) G/C upstream_transcript_variant
rs1001708742 -- 161,163,015(-) T/C upstream_transcript_variant
rs1002832032 -- 161,160,825(-) G/A non_coding_transcript_variant
rs1003884408 -- 161,161,714(-) G/A/C non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for AGPAT4-IT1 Gene

Variant ID Type Subtype PubMed ID
nsv1026543 CNV gain 25217958
nsv1030852 CNV gain 25217958
nsv528938 CNV loss 19592680

Additional Variant Information for AGPAT4-IT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for AGPAT4-IT1 Gene

Disorders for AGPAT4-IT1 Gene

Additional Disease Information for AGPAT4-IT1

No disorders were found for AGPAT4-IT1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for AGPAT4-IT1 Gene

Publications for AGPAT4-IT1 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 58
  3. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4 58
  4. Mig-6 controls EGFR trafficking and suppresses gliomagenesis. (PMID: 20351267) Ying H … DePinho RA (Proceedings of the National Academy of Sciences of the United States of America 2010) 3 58
  5. 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 58

Products for AGPAT4-IT1 Gene

Sources for AGPAT4-IT1 Gene

Loading form....