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

Aliases for NPTN-IT1 Gene

Subcategory (RNA class) for NPTN-IT1 Gene


Quality Score for this RNA gene is


Aliases for NPTN-IT1 Gene

  • NPTN Intronic Transcript 1 2 3 5
  • NPTN Intronic Transcript 1 (Non-Protein Coding) 2 3
  • Long Non-Coding RNA, Low Expression In Tumor 2 3
  • LncRNA-LET 3

External Ids for NPTN-IT1 Gene

ORGUL Members for NPTN-IT1 Gene

Previous GeneCards Identifiers for NPTN-IT1 Gene

  • GC15U901473

Summaries for NPTN-IT1 Gene

GeneCards Summary for NPTN-IT1 Gene

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

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPTN-IT1 Gene

Genomics for NPTN-IT1 Gene

Regulatory Elements for NPTN-IT1 Gene

Enhancers for NPTN-IT1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15F073596 1.2 Ensembl ENCODE 0.3 -30.5 -30458 8.0 PKNOX1 ZNF133 INSM2 FEZF1 NFXL1 ZNF2 ZEB1 ZNF335 ZNF366 SCRT2 NPTN BBS4 ISLR ADPGK GC15M073574 NPTN-IT1
GH15F073564 0.8 ENCODE 0.4 +5.0 5049 0.2 SOX13 CTCF ZNF792 TAL1 JUN MAX ZIC2 RAD21 NCOR1 POLR2A NPTN NPTN-IT1 MRPS15P1
GH15F073572 0.7 ENCODE 0.4 -5.1 -5114 4.3 CTCF NR2F1 REST MNT NR2F2 ZNF121 RAD51 POLR2A FOS FOXP2 NPTN-IT1 GC15M073574
GH15F073577 0.5 ENCODE 0.4 -8.3 -8327 1.3 ATF1 ZBTB11 ZNF785 NPTN-IT1 GC15M073574
GH15F073584 0.6 ENCODE 0.3 -16.1 -16069 2.5 ZNF316 MAFG NFE2 EMSY ZBTB40 CD276 NPTN-IT1 GC15M073574
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NPTN-IT1 on UCSC Golden Path with GeneCards custom track

Genomic Location for NPTN-IT1 Gene

73,566,938 bp from pter
73,569,543 bp from pter
2,606 bases
Minus strand

Genomic View for NPTN-IT1 Gene

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

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

RefSeq DNA sequence for NPTN-IT1 Gene

Proteins for NPTN-IT1 Gene

Post-translational modifications for NPTN-IT1 Gene

No Post-translational modifications

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

Domains & Families for NPTN-IT1 Gene

Graphical View of Domain Structure for InterPro Entry

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

Function for NPTN-IT1 Gene

Animal Model 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 NPTN-IT1 Gene

Localization for NPTN-IT1 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for NPTN-IT1 Gene

Pathways & Interactions for NPTN-IT1 Gene

SuperPathways for NPTN-IT1 Gene

No Data Available

Interacting Proteins for NPTN-IT1 Gene

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


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

Transcripts for NPTN-IT1 Gene

mRNA/cDNA for NPTN-IT1 Gene

(2) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NPTN-IT1 Gene

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

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

No ASD Table

Relevant External Links for NPTN-IT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NPTN-IT1 Gene

SOURCE GeneReport for Unigene cluster for NPTN-IT1 Gene:

No Expression Related Data Available

No data available for mRNA expression in normal human tissues , 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 and mRNA Expression by UniProt/SwissProt for NPTN-IT1 Gene

Orthologs for NPTN-IT1 Gene

Evolution for NPTN-IT1 Gene

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

No data available for Orthologs for NPTN-IT1 Gene

Paralogs for NPTN-IT1 Gene

No data available for Paralogs for NPTN-IT1 Gene

Variants for NPTN-IT1 Gene

Sequence variations from dbSNP and Humsavar for NPTN-IT1 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs10539085 -- 73,567,003(+) GGGGC(-/T)TTTTT intron-variant, nc-transcript-variant
rs111525661 -- 73,570,425(+) TGTCC(A/T)GCAAA upstream-variant-2KB, splice-acceptor-variant
rs113646259 -- 73,568,450(+) CCTTT(C/T)CAGGA intron-variant, nc-transcript-variant
rs114249671 -- 73,567,531(+) TAAGT(C/T)TGTCC intron-variant, nc-transcript-variant
rs114705376 -- 73,567,902(+) CAATA(C/T)TCTCC intron-variant, nc-transcript-variant

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

Variant ID Type Subtype PubMed ID
nsv1121512 CNV deletion 24896259

Relevant External Links for NPTN-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 NPTN-IT1 Gene

Disorders for NPTN-IT1 Gene

Relevant External Links for NPTN-IT1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for NPTN-IT1 Gene.

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

Publications for NPTN-IT1 Gene

  1. Repression of the long noncoding RNA-LET by histone deacetylase 3 contributes to hypoxia-mediated metastasis. (PMID: 23395002) Yang F. … Sun S.H. (Mol. Cell 2013) 2 3 64
  2. Long noncoding RNA-LET, which is repressed by EZH2, inhibits cell proliferation and induces apoptosis of nasopharyngeal carcinoma cell. (PMID: 26243049) Sun Q. … Yang C. (Med. Oncol. 2015) 3 64
  3. Long non-coding RNA-LET is a positive prognostic factor and exhibits tumor-suppressive activity in gallbladder cancer. (PMID: 25213660) Ma M.Z. … Quan Z.W. (Mol. Carcinog. 2014) 3 64
  4. Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans. (PMID: 21769904) Yang F. … Sun S.H. (Hepatology 2011) 3 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 64

Products for NPTN-IT1 Gene

Sources for NPTN-IT1 Gene

Loading form....