Aliases for LINC00643 Gene

Subcategory (RNA class) for LINC00643 Gene

lncRNA

Number of RNA Genes sources:

3 / 17

Aliases for LINC00643 Gene

  • Long Intergenic Non-Protein Coding RNA 643 2 3 4 5
  • LINC00643 2 5
  • Putative UPF0730 Protein Encoded By LINC00643 4
  • NONHSAG015189.2 91
  • HSALNG0101793 164
  • Lnc-SYT16-67 165

External Ids for LINC00643 Gene

Previous GeneCards Identifiers for LINC00643 Gene

  • GC14P062586

Summaries for LINC00643 Gene

GeneCards Summary for LINC00643 Gene

LINC00643 (Long Intergenic Non-Protein Coding RNA 643) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with LINC00643 include Retinitis Pigmentosa 13.

Additional gene information for LINC00643 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 LINC00643 Gene

Genomics for LINC00643 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LINC00643 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
GH14J062113 Enhancer 0.2 Ensembl 600.7 -1.1 -1052 0.6 LINC00643 ENSG00000258903 lnc-SYT16-1 SYT16 KCNH5
GH14J062116 Promoter/Enhancer 1.3 Ensembl ENCODE CraniofacialAtlas 5.4 +2.9 2889 1.1 CTCF RFX1 ZIC2 POLR2A PKNOX1 SCRT2 RFX3 SP2 RAD21 RNF2 ENSG00000258903 LINC00643 LINC00644 SYT16 KCNH5
GH14J062080 Enhancer 0.9 Ensembl ENCODE 7 -33.3 -33252 3 SP1 ZNF143 TCF12 IKZF2 RCOR1 TRIM22 POLR2A PKNOX1 EED DPF2 ENSG00000258842 LINC00643 piR-48553-111 SYT16
GH14J062076 Enhancer 0.8 Ensembl ENCODE 6.3 -36.4 -36369 3.2 SP1 EED RUNX3 ASH2L BCLAF1 CBFB TCF12 BCL11A TARDBP JUNB LINC00643 ENSG00000258842 piR-48553-111 SYT16
GH14J062097 Enhancer 0.6 Ensembl ENCODE 6.7 -16.4 -16393 1.8 POLR2A TBX21 MTA2 SPI1 MAFK LINC00643 lnc-SYT16-1 ENSG00000258842 SYT16
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LINC00643 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for LINC00643 Gene

Genomic Locations for LINC00643 Gene
chr14:62,114,353-62,134,243
(GRCh38/hg38)
Size:
19,891 bases
Orientation:
Plus strand
chr14:62,584,075-62,600,904
(GRCh37/hg19)
Size:
16,830 bases
Orientation:
Plus strand

Genomic View for LINC00643 Gene

Genes around LINC00643 on UCSC Golden Path with GeneCards custom track
LINC00643 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Cytogenetic band:
LINC00643 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LINC00643 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LINC00643 Gene

Proteins for LINC00643 Gene

  • Protein details for LINC00643 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86TS7-U730_HUMAN
    Recommended name:
    Putative UPF0730 protein encoded by LINC00643
    Protein Accession:
    Q86TS7

    Protein attributes for LINC00643 Gene

    Size:
    51 amino acids
    Molecular mass:
    6040 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LINC00643 Gene

Post-translational modifications for LINC00643 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LINC00643 Gene

Domains & Families for LINC00643 Gene

Gene Families for LINC00643 Gene

Protein Domains for LINC00643 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q86TS7

UniProtKB/Swiss-Prot:

U730_HUMAN :
  • Belongs to the UPF0730 family.
Family:
  • Belongs to the UPF0730 family.
genes like me logo Genes that share domains with LINC00643: view

No data available for Suggested Antigen Peptide Sequences for LINC00643 Gene

Function for LINC00643 Gene

Phenotypes From GWAS Catalog for LINC00643 Gene

Phenotypes for LINC00643 Gene

genes like me logo Genes that share phenotypes with LINC00643: view

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LINC00643 Gene

Localization for LINC00643 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 LINC00643 Gene

Pathways & Interactions for LINC00643 Gene

PathCards logo

SuperPathways for LINC00643 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LINC00643 Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for LINC00643 Gene

Drugs & Compounds for LINC00643 Gene

No Compound Related Data Available

Transcripts for LINC00643 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for LINC00643 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS000075D248_9606 lncRNA 6636 3

HGNC: 44296,

RefSeq: NR_015358,

LNCipedia: lnc-SYT16-67:6,

URS00007E13A5_9606 lncRNA 962 3

LncBook: HSALNT0212016,

LNCipedia: lnc-SYT16-67:4,

NONCODE: NONHSAT168547.1,

URS000020510C_9606 lncRNA 552 3

LncBook: HSALNT0212021,

LNCipedia: lnc-SYT16-67:13,

NONCODE: NONHSAT037289.2,

URS000015D3CE_9606 lncRNA 526 3

LncBook: HSALNT0212015,

LNCipedia: lnc-SYT16-67:1,

NONCODE: NONHSAT037287.2,

URS00008C147B_9606 lncRNA 6635 2

LNCipedia: lnc-SYT16-67:3,

NONCODE: NONHSAT037288.2,

LINC00643 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for LINC00643 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LINC00643

Alternative Splicing Database (ASD) splice patterns (SP) for LINC00643 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c
SP1: - -
SP2: - - -
SP3: -
SP4:

Relevant External Links for LINC00643 Gene

GeneLoc Exon Structure for
LINC00643

Expression for LINC00643 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LINC00643 Gene

mRNA differential expression in normal tissues according to GTEx for LINC00643 Gene

This gene is overexpressed in Pituitary (x13.2), Brain - Nucleus accumbens (basal ganglia) (x6.4), and Testis (x5.0).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LINC00643

SOURCE GeneReport for Unigene cluster for LINC00643 Gene:

Hs.445241
genes like me logo Genes that share expression patterns with LINC00643: view

Primer Products

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 LINC00643 Gene

Orthologs for LINC00643 Gene

Evolution for LINC00643 Gene

ENSEMBL:
Gene Tree for LINC00643 (if available)
TreeFam:
Gene Tree for LINC00643 (if available)

No data available for Orthologs for LINC00643 Gene

Paralogs for LINC00643 Gene

No data available for Paralogs for LINC00643 Gene

Variants for LINC00643 Gene

Additional dbSNP identifiers (rs#s) for LINC00643 Gene

Structural Variations from Database of Genomic Variants (DGV) for LINC00643 Gene

Variant ID Type Subtype PubMed ID
esv2422467 CNV deletion 17116639
esv2761839 CNV gain 21179565
nsv456321 CNV loss 19166990
nsv564887 CNV loss 21841781

Additional Variant Information for LINC00643 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LINC00643

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for LINC00643 Gene

Disorders for LINC00643 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LINC00643 Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 13
  • rp13
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for LINC00643

genes like me logo Genes that share disorders with LINC00643: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LINC00643 Gene

Publications for LINC00643 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  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

Products for LINC00643 Gene

Sources for LINC00643 Gene