Aliases for LOC643542 Gene

Subcategory (RNA class) for LOC643542 Gene

lncRNA

Number of RNA Genes sources:

3 / 17

Aliases for LOC643542 Gene

  • Uncharacterized LOC643542 3
  • Novel Transcript 5
  • NONHSAG024082.2 91
  • Lnc-CCDC102B-7 165
  • HSALNG0122181 164
  • AC114689.3 5

External Ids for LOC643542 Gene

Previous GeneCards Identifiers for LOC643542 Gene

  • GC18U900280
  • GC18P065184

Summaries for LOC643542 Gene

GeneCards Summary for LOC643542 Gene

LOC643542 (Uncharacterized LOC643542) is an RNA Gene, and is affiliated with the lncRNA class.

Additional gene information for LOC643542 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 LOC643542 Gene

Genomics for LOC643542 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LOC643542 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
GH18J067514 Promoter/Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas 600.7 -0.6 -568 4.4 GATAD2A CTCF POLR2A REST SP1 ZNF501 EZH2 CEBPA SCRT2 SP2 DSEL LOC643542 ENSG00000260578 ENSG00000263424 CDH19
GH18J067524 Enhancer 0.8 Ensembl ENCODE 0.4 +9.1 9055 2 SP1 JUND CEBPB FOS JUN ATF3 EP300 FOSL2 RAD21 RFX5 DSEL LOC643542 MN298114-102
GH18J067509 Enhancer 0.5 Ensembl ENCODE 0.4 -6.1 -6067 1.8 JUND POLR2A ENSG00000263424 DSEL LOC643542 CDH19
GH18J067519 Enhancer 0.3 ENCODE 0.7 +4.1 4087 2.1 CEBPB ENSG00000260578 DSEL LOC643542 MN298114-102
GH18J067599 Enhancer 0.8 Ensembl ENCODE 0.2 +83.6 83645 2.8 SP1 JUND CEBPB FOXA2 ATF3 FOS YY1 PRDM1 RCOR1 RAD21 ENSG00000264040 lnc-DSEL-4 LOC105372174 MN298114-102 DSEL LOC643542
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LOC643542 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for LOC643542 Gene

Genomic Locations for LOC643542 Gene
chr18:67,516,546-67,899,619
(GRCh38/hg38)
Size:
383,074 bases
Orientation:
Plus strand
chr18:65,183,783-65,566,856
(GRCh37/hg19)
Size:
383,074 bases
Orientation:
Plus strand

Genomic View for LOC643542 Gene

Genes around LOC643542 on UCSC Golden Path with GeneCards custom track
LOC643542 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Cytogenetic band:
LOC643542 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LOC643542 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LOC643542 Gene

Proteins for LOC643542 Gene

Post-translational modifications for LOC643542 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LOC643542 Gene

Domains & Families for LOC643542 Gene

No data available for Gene Families , Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LOC643542 Gene

Function for LOC643542 Gene

Phenotypes From GWAS Catalog for LOC643542 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 LOC643542 Gene

Localization for LOC643542 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 LOC643542 Gene

Pathways & Interactions for LOC643542 Gene

PathCards logo

SuperPathways for LOC643542 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LOC643542 Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for LOC643542 Gene

Drugs & Compounds for LOC643542 Gene

No Compound Related Data Available

Transcripts for LOC643542 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for LOC643542 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS000033268A_9606 lncRNA 2991 4

Ensembl: ENST00000583687 (view in UCSC) ,

LncBook: HSALNT0252555,

LNCipedia: lnc-CCDC102B-7:1,

NONCODE: NONHSAT059720.2,

URS000075AD6C_9606 lncRNA 2991 1

RefSeq: NR_033921,

URS00009BFD8E_9606 lncRNA 3051 2

LncBook: HSALNT0252556,

NONCODE: NONHSAT177935.1,

URS00008BFDF0_9606 lncRNA 2988 1

LNCipedia: lnc-CCDC102B-7:2,

LOC643542 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for LOC643542 Gene

1 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for LOC643542 Gene

No ASD Table

Relevant External Links for LOC643542 Gene

GeneLoc Exon Structure for
LOC643542

Expression for LOC643542 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LOC643542 Gene

SOURCE GeneReport for Unigene cluster for LOC643542 Gene:

Hs.652901
genes like me logo Genes that share expression patterns with LOC643542: 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 LOC643542 Gene

Orthologs for LOC643542 Gene

Evolution for LOC643542 Gene

ENSEMBL:
Gene Tree for LOC643542 (if available)
TreeFam:
Gene Tree for LOC643542 (if available)

No data available for Orthologs for LOC643542 Gene

Paralogs for LOC643542 Gene

No data available for Paralogs for LOC643542 Gene

Variants for LOC643542 Gene

Additional dbSNP identifiers (rs#s) for LOC643542 Gene

Structural Variations from Database of Genomic Variants (DGV) for LOC643542 Gene

Variant ID Type Subtype PubMed ID
dgv192n21 CNV loss 19592680
dgv26n64 CNV loss 17921354
dgv3383n100 CNV gain 25217958
dgv3386n100 CNV gain 25217958
dgv3387n100 CNV loss 25217958
dgv3388n100 CNV gain 25217958
dgv6010n54 CNV loss 21841781
dgv6011n54 CNV loss 21841781
dgv67e203 CNV loss 21179565
dgv998e212 CNV loss 25503493
esv1685376 CNV deletion 17803354
esv2422116 CNV deletion 20811451
esv2658141 CNV deletion 23128226
esv2676626 CNV deletion 23128226
esv26877 CNV loss 19812545
esv27124 CNV gain 19812545
esv2717253 CNV deletion 23290073
esv2717254 CNV deletion 23290073
esv2717255 CNV deletion 23290073
esv2717256 CNV deletion 23290073
esv2717257 CNV deletion 23290073
esv3307876 CNV mobile element insertion 20981092
esv3377112 CNV insertion 20981092
esv3555562 CNV deletion 23714750
esv3583127 CNV loss 25503493
esv3642903 CNV gain 21293372
esv3642905 CNV loss 21293372
esv3642906 CNV gain 21293372
esv3642907 CNV gain 21293372
esv3642908 CNV loss 21293372
esv3642910 CNV gain 21293372
esv3642911 CNV gain 21293372
esv3642912 CNV loss 21293372
esv3642913 CNV gain 21293372
esv3642914 CNV gain 21293372
esv3642915 CNV loss 21293372
esv3642916 CNV loss 21293372
esv3642917 CNV loss 21293372
esv3642919 CNV loss 21293372
esv3893123 CNV loss 25118596
nsv1055555 CNV loss 25217958
nsv1057236 CNV loss 25217958
nsv1057874 CNV loss 25217958
nsv1063279 CNV gain 25217958
nsv1138637 CNV deletion 24896259
nsv1146970 CNV deletion 26484159
nsv1151630 CNV insertion 26484159
nsv2344 CNV insertion 18451855
nsv2345 CNV deletion 18451855
nsv442756 CNV loss 18776908
nsv458102 CNV loss 19166990
nsv470424 CNV loss 18288195
nsv470425 CNV loss 18288195
nsv470426 CNV loss 18288195
nsv498886 CNV loss 21111241
nsv507879 OTHER sequence alteration 20534489
nsv514883 CNV loss 21397061
nsv517766 CNV gain+loss 19592680
nsv521537 CNV gain 19592680
nsv524650 CNV loss 19592680
nsv528890 CNV loss 19592680
nsv577157 CNV loss 21841781
nsv577302 CNV loss 21841781
nsv577312 CNV loss 21841781
nsv577313 CNV loss 21841781
nsv577314 CNV gain 21841781
nsv577315 CNV loss 21841781
nsv577316 CNV loss 21841781
nsv577317 CNV loss 21841781
nsv577318 CNV loss 21841781
nsv577319 CNV loss 21841781
nsv577321 CNV gain 21841781
nsv817799 CNV gain+loss 17921354
nsv828287 CNV gain 20364138
nsv833680 CNV loss 17160897
nsv954108 CNV deletion 24416366
nsv978639 CNV duplication 23825009

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP , Variation tolerance and Additional Variant Information for LOC643542 Gene

Disorders for LOC643542 Gene

No disorders were found for LOC643542 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot , Genatlas and External Links for LOC643542 Gene

Publications for LOC643542 Gene

  1. Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2. (PMID: 24322204) Winham SJ … Biernacka JM (Molecular psychiatry 2014) 3
  2. Genome-wide association study of recurrent early-onset major depressive disorder. (PMID: 20125088) Shi J … Levinson DF (Molecular psychiatry 2011) 3
  3. Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations. (PMID: 18821565) Lasky-Su J … Faraone SV (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2008) 3
  4. 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

No data available for Mastermind for LOC643542 Gene

Products for LOC643542 Gene

Sources for LOC643542 Gene