Aliases for LOC574538 Gene

Subcategory (RNA class) for LOC574538 Gene

lncRNA

Number of RNA Genes sources:

3 / 14

Aliases for LOC574538 Gene

  • Uncharacterized LOC574538 3
  • Novel Transcript, Antisense To IQSEC3 5
  • Lnc-SLC6A12-3 168
  • HSALNG0088446 167
  • NONHSAG010124 92
  • AC026369.1 5

External Ids for LOC574538 Gene

Additional External Ids for LOC574538 Gene

Previous GeneCards Identifiers for LOC574538 Gene

  • GC12U900512
  • GC12M000248

Summaries for LOC574538 Gene

GeneCards Summary for LOC574538 Gene

LOC574538 (Uncharacterized LOC574538) is an RNA Gene, and is affiliated with the lncRNA class.

Additional gene information for LOC574538 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LOC574538 Gene

Genomics for LOC574538 Gene

GeneHancer (GH) Regulatory Elements for LOC574538 Gene

Promoters and enhancers for LOC574538 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
GH12J000147 Enhancer 0.4 dbSUPER 513.7 +1.8 1771 0.7 JUND ZFP36 FOS LOC574538 piR-41525-097 IQSEC3
GH12J000149 Enhancer 0.3 Ensembl dbSUPER 513.8 -0.1 -131 0.6 LOC574538 IQSEC3 ENSG00000256694
GH12J000180 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 11 -31.4 -31394 0.9 ZIC2 TCF12 USF2 USF1 MAX NR3C1 SPI1 MNT MAZ BHLHE40 ENSG00000256540 LOC574538 SLC6A12 LOC105369592 lnc-CCDC77-4
GH12J000152 Enhancer 1 ENCODE dbSUPER 10.7 -3.6 -3607 1.3 CTCF USF1 ZIC2 REST RAD21 MYC TRIM22 TEAD1 ATF2 ZBTB26 ENSG00000255671 LOC101929384 SLC6A12 SLC6A13 LOC574538 LOC102723544 IQSEC3 ENSG00000256694
GH12J000109 Enhancer 0.9 Ensembl ENCODE 12 +37.8 37817 5.6 ZNF300 ZIC2 CTCF ZNF316 NFIC ZNF592 PBX2 IKZF1 NFIB PRDM6 ENSG00000256948 LOC105369593 ENSG00000256694 LOC574538 ENSG00000255671 LOC101929384 SLC6A12 RAD52 IQSEC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LOC574538 on UCSC Golden Path with GeneCards custom track

Genomic Locations for LOC574538 Gene

Genomic Locations for LOC574538 Gene
chr12:137,411-149,170
(GRCh38/hg38)
Size:
11,760 bases
Orientation:
Minus strand
chr12:246,577-258,335
(GRCh37/hg19)
Size:
11,759 bases
Orientation:
Minus strand

Genomic View for LOC574538 Gene

Genes around LOC574538 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LOC574538 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LOC574538 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LOC574538 Gene

Proteins for LOC574538 Gene

Post-translational modifications for LOC574538 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LOC574538 Gene

Domains & Families for LOC574538 Gene

No data available for Gene Families , Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LOC574538 Gene

Function for LOC574538 Gene

Phenotypes From GWAS Catalog for LOC574538 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 LOC574538 Gene

Localization for LOC574538 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 LOC574538 Gene

Pathways & Interactions for LOC574538 Gene

PathCards logo

SuperPathways for LOC574538 Gene

No Data Available
;

Gene Ontology (GO) - Biological Process for LOC574538 Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for LOC574538 Gene

Drugs & Compounds for LOC574538 Gene

No Compound Related Data Available

Transcripts for LOC574538 Gene

mRNA/cDNA for LOC574538 Gene

7 RNACentral transcripts :
1 REFSEQ mRNAs :
2 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
5 NONCODE transcripts :
4 LncBook transcripts :
6 LNCipedia transcripts :

Alternative Splicing Database (ASD) splice patterns (SP) for LOC574538 Gene

No ASD Table

Relevant External Links for LOC574538 Gene

GeneLoc Exon Structure for
LOC574538

Expression for LOC574538 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LOC574538 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LOC574538

SOURCE GeneReport for Unigene cluster for LOC574538 Gene:

Hs.589138
genes like me logo Genes that share expression patterns with LOC574538: view

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 LOC574538 Gene

Orthologs for LOC574538 Gene

Evolution for LOC574538 Gene

ENSEMBL:
Gene Tree for LOC574538 (if available)
TreeFam:
Gene Tree for LOC574538 (if available)

No data available for Orthologs for LOC574538 Gene

Paralogs for LOC574538 Gene

No data available for Paralogs for LOC574538 Gene

Variants for LOC574538 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LOC574538 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
692309 Uncertain Significance: Fetal akinesia sequence; Arthrogryposis multiplex congenita 138,421(-) T/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
717712 Benign: not provided 138,470(-) G/A SYNONYMOUS_VARIANT
718779 Benign: not provided 138,744(-) C/T MISSENSE_VARIANT
785895 Likely Benign: not provided 138,424(-) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for LOC574538 Gene

Structural Variations from Database of Genomic Variants (DGV) for LOC574538 Gene

Variant ID Type Subtype PubMed ID
dgv1329n100 CNV gain 25217958
dgv1330n100 CNV gain 25217958
dgv1331n100 CNV gain 25217958
dgv430e212 CNV gain 25503493
esv3628221 CNV gain 21293372
esv3628222 CNV loss 21293372
esv3628223 CNV gain 21293372
nsv1035539 CNV gain 25217958
nsv1041720 CNV gain 25217958
nsv428269 CNV gain+loss 18775914
nsv468943 CNV gain 19166990
nsv470252 CNV gain 18288195
nsv556852 CNV gain 21841781
nsv556853 CNV gain 21841781
nsv568 CNV insertion 18451855
nsv826171 CNV gain 20364138
nsv826172 CNV gain 20364138
nsv832301 CNV gain+loss 17160897
nsv832302 CNV gain 17160897

Variation tolerance for LOC574538 Gene

Gene Damage Index Score: 0.74; 15.71% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Additional Variant Information for LOC574538 Gene

Disorders for LOC574538 Gene

No disorders were found for LOC574538 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot , Genatlas and External Links for LOC574538 Gene

Publications for LOC574538 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 54
  2. 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) 3 54

No data available for Mastermind for LOC574538 Gene

Products for LOC574538 Gene

Sources for LOC574538 Gene