Aliases for HLCS-IT1 Gene

Subcategory (RNA class) for HLCS-IT1 Gene


Number of RNA Genes sources:

3 / 17

Aliases for HLCS-IT1 Gene

  • HLCS Intronic Transcript 1 2 3 5
  • HLCS-IT1 2 5 165
  • HLCS Intronic Transcript 1 (Non-Protein Coding) 2 3
  • NONHSAG032789.2 91
  • HSALNG0132961 164
  • Bde1 3

External Ids for HLCS-IT1 Gene

Previous GeneCards Identifiers for HLCS-IT1 Gene

  • GC00U932982
  • GC21M038177

Summaries for HLCS-IT1 Gene

GeneCards Summary for HLCS-IT1 Gene

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

Additional gene information for HLCS-IT1 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 HLCS-IT1 Gene

Genomics for HLCS-IT1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HLCS-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
GH21J036806 Enhancer 0.3 ENCODE 600.7 -1.3 -1284 1.4 CEBPB NR3C1 HLCS-IT1 ENSG00000224269 SIM2 HLCS LOC105369305 RF00017-3703
GH21J036787 Enhancer 0.9 Ensembl ENCODE 0.4 +17.9 17884 1.6 PRDM10 ZNF692 FOXA1 PRDM1 ZIC2 ZNF600 ZNF341 SMARCC2 CEBPB JUN ENSG00000242553 HLCS SIM2 RF00017-3704 HLCS-IT1 RF00017-3703
GH21J036783 Enhancer 0.9 Ensembl ENCODE 0.4 +21.6 21584 2.6 PRDM10 ZNF629 ZNF692 ZSCAN4 ZNF239 ZNF639 JUND ZNF10 CEBPB ZEB1 DYRK1A ENSG00000242553 SETD4 MORC3 SIM2 RF00017-3704 HLCS-IT1 RF00017-3703 HLCS
GH21J036792 Enhancer 0.8 Ensembl ENCODE 0.4 +14.1 14084 2 EZH2 ZNF600 SCRT2 MNT SCRT1 POLR2A USF2 ZSCAN5A ATF3 TOE1 ENSG00000224269 SIM2 CLDN14 HLCS HLCS-IT1 RF00017-3704 RF00017-3703
GH21J036799 Enhancer 0.3 ENCODE 0.4 +6.3 6329 0.7 BHLHE40 CLDN14 HLCS HLCS-IT1 RF00017-3704 RF00017-3703 SIM2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HLCS-IT1 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for HLCS-IT1 Gene

Genomic Locations for HLCS-IT1 Gene
3,696 bases
Minus strand
2,301 bases
Minus strand

Genomic View for HLCS-IT1 Gene

Genes around HLCS-IT1 on UCSC Golden Path with GeneCards custom track
HLCS-IT1 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Cytogenetic band:
HLCS-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 HLCS-IT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

No data available for RefSeq DNA sequence for HLCS-IT1 Gene

Proteins for HLCS-IT1 Gene

Post-translational modifications for HLCS-IT1 Gene

No Post-translational modifications

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

Domains & Families for HLCS-IT1 Gene

Gene Families for HLCS-IT1 Gene

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

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for HLCS-IT1 Gene

Function for HLCS-IT1 Gene

Phenotypes From GWAS Catalog for HLCS-IT1 Gene

Animal Model Products

CRISPR 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 HLCS-IT1 Gene

Localization for HLCS-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 HLCS-IT1 Gene

Pathways & Interactions for HLCS-IT1 Gene

PathCards logo

SuperPathways for HLCS-IT1 Gene

No Data Available

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


No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for HLCS-IT1 Gene

Drugs & Compounds for HLCS-IT1 Gene

No Compound Related Data Available

Transcripts for HLCS-IT1 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for HLCS-IT1 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS00005E7179_9606 lncRNA 531 5

HGNC: 41343,

Ensembl: ENST00000434195 (view in UCSC) ,

LncBook: HSALNT0273331,

LNCipedia: HLCS-IT1:1,


URS00009AD429_9606 lncRNA 651 2

LncBook: HSALNT0273330,


HLCS-IT1 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for HLCS-IT1 Gene

1 NCBI additional mRNA sequence :

CRISPR Products

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

No ASD Table

Relevant External Links for HLCS-IT1 Gene

GeneLoc Exon Structure for

Expression for HLCS-IT1 Gene

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

mRNA differential expression in normal tissues according to GTEx for HLCS-IT1 Gene

This gene is overexpressed in Testis (x9.6).
genes like me logo Genes that share expression patterns with HLCS-IT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , 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 HLCS-IT1 Gene

Orthologs for HLCS-IT1 Gene

Evolution for HLCS-IT1 Gene

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

No data available for Orthologs for HLCS-IT1 Gene

Paralogs for HLCS-IT1 Gene

No data available for Paralogs for HLCS-IT1 Gene

Variants for HLCS-IT1 Gene

Additional Variant Information for HLCS-IT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP , Additional dbSNP identifiers (rs#s) , Structural Variations from Database of Genomic Variants (DGV) and Variation tolerance for HLCS-IT1 Gene

Disorders for HLCS-IT1 Gene

Additional Disease Information for HLCS-IT1

No disorders were found for HLCS-IT1 Gene.

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

Publications for HLCS-IT1 Gene

No publications were found for HLCS-IT1 Gene.

Products for HLCS-IT1 Gene

Sources for HLCS-IT1 Gene