Expression of this gene has been shown to be upregulated in some individuals with chronic lymphocytic leukemia (CLL), and has been used for prognostic and diagnostic purposes. This gene was originally identified as a human-specific putative protein-coding gene due to the presence of a peptide (PAp00140670, HIIYSTFLSK) that could have supported translation at this locus. This pe... See more...

Aliases for CLLU1 Gene

Subcategory (RNA class) for CLLU1 Gene

lncRNA

Number of RNA Genes sources:

3 / 17

Aliases for CLLU1 Gene

  • Chronic Lymphocytic Leukemia Up-Regulated 1 2 3 5
  • Chronic Lymphocytic Leukemia Up-Regulated Protein 1 3 4
  • CLLU1 2 5
  • HSALNG0093062 164
  • LINC02397 165

External Ids for CLLU1 Gene

Previous GeneCards Identifiers for CLLU1 Gene

  • GC12U900504
  • GC12P091341
  • GC12P092817
  • GC12P089882

Summaries for CLLU1 Gene

Entrez Gene Summary for CLLU1 Gene

  • Expression of this gene has been shown to be upregulated in some individuals with chronic lymphocytic leukemia (CLL), and has been used for prognostic and diagnostic purposes. This gene was originally identified as a human-specific putative protein-coding gene due to the presence of a peptide (PAp00140670, HIIYSTFLSK) that could have supported translation at this locus. This peptide is not present in more recent builds of PeptideAtlas, and the presence of a protein product at this locus has not been independently verified. For this reason, this gene is being represented as non-coding. Sequence comparisons to other primates indicates that no other primate is predicted to contain an open reading frame. [provided by RefSeq, Feb 2017]

GeneCards Summary for CLLU1 Gene

CLLU1 (Chronic Lymphocytic Leukemia Up-Regulated 1) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with CLLU1 include Leukemia and Chromosome 13Q14 Deletion Syndrome.

Additional gene information for CLLU1 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLLU1 Gene

Genomics for CLLU1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLLU1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLLU1 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the CLLU1 gene promoter:
  • AML1a
  • Nkx2-5
  • POU3F2
  • Sox5
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT2
  • STAT3
  • STAT4

Genomic Locations for CLLU1 Gene

Genomic Locations for CLLU1 Gene
chr12:92,421,531-92,431,002
(GRCh38/hg38)
Size:
9,472 bases
Orientation:
Plus strand
chr12:92,815,307-92,824,778
(GRCh37/hg19)
Size:
9,472 bases
Orientation:
Plus strand

Genomic View for CLLU1 Gene

Genes around CLLU1 on UCSC Golden Path with GeneCards custom track
CLLU1 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Cytogenetic band:
CLLU1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLLU1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLLU1 Gene

Proteins for CLLU1 Gene

  • Protein details for CLLU1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5K131-CLLU1_HUMAN
    Recommended name:
    Chronic lymphocytic leukemia up-regulated protein 1
    Protein Accession:
    Q5K131

    Protein attributes for CLLU1 Gene

    Size:
    121 amino acids
    Molecular mass:
    14228 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Tridimensional modeling predicts that it may interact with the IL-4 receptor.
    • This protein has no orthologs in other species and appears to be the product of a protein-coding gene which has arisen since divergence from chimp.

neXtProt entry for CLLU1 Gene

Post-translational modifications for CLLU1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for CLLU1 Gene

Domains & Families for CLLU1 Gene

Gene Families for CLLU1 Gene

Protein Domains for CLLU1 Gene

ProtoNet:

Suggested Antigen Peptide Sequences for CLLU1 Gene

GenScript: Design optimal peptide antigens:
  • Chronic lymphocytic leukemia up-regulated protein 1 (CLLU1_HUMAN)
genes like me logo Genes that share domains with CLLU1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CLLU1 Gene

Function for CLLU1 Gene

Phenotypes From GWAS Catalog for CLLU1 Gene

Phenotypes for CLLU1 Gene

genes like me logo Genes that share phenotypes with CLLU1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLLU1

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 CLLU1 Gene

Localization for CLLU1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLLU1 Gene

Cytoplasm. Note=Detected in the cytoplasm of chronic lymphocytic leukemia (CLL) cells.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLLU1 gene
Compartment Confidence
plasma membrane 1
nucleus 1

Gene Ontology (GO) - Cellular Components for CLLU1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with CLLU1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CLLU1 Gene

Pathways & Interactions for CLLU1 Gene

PathCards logo

SuperPathways for CLLU1 Gene

No Data Available

Interacting Proteins for CLLU1 Gene

Selected Interacting proteins: Q5K131-CLLU1_HUMAN for CLLU1 Gene via IID

Symbol External ID(s) Details
CD38
ZAP70

Gene Ontology (GO) - Biological Process for CLLU1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for CLLU1 Gene

Drugs & Compounds for CLLU1 Gene

No Compound Related Data Available

Transcripts for CLLU1 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for CLLU1 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS00002B2394_9606 lncRNA 2274 4

RefSeq: NR_027933,

Ensembl: ENST00000512817 (view in UCSC) ,

LNCipedia: LINC02397:22,

ENA: AJ845162.1:1..2274:misc_RNA,

URS00008B6E4E_9606 lncRNA 2831 3

HGNC: 29841,

RefSeq: NR_027932,

LNCipedia: LINC02397:21,

URS00003802C5_9606 lncRNA 2817 3

Ensembl: ENST00000472839 (view in UCSC) ,

LNCipedia: LINC02397:6,

ENA: AJ845163.1:1..2817:misc_RNA,

URS0000D61B90_9606 lncRNA 3897 2

Ensembl: ENST00000378485 (view in UCSC) ,

LNCipedia: LINC02397:8,

URS0000EA3C9A_9606 lncRNA 2834 1

LncBook: HSALNT0289467,

CLLU1 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for CLLU1 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLLU1

Alternative Splicing Database (ASD) splice patterns (SP) for CLLU1 Gene

No ASD Table

Relevant External Links for CLLU1 Gene

GeneLoc Exon Structure for
CLLU1

Expression for CLLU1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLLU1 Gene

mRNA differential expression in normal tissues according to GTEx for CLLU1 Gene

This gene is overexpressed in Muscle - Skeletal (x5.4).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLLU1

SOURCE GeneReport for Unigene cluster for CLLU1 Gene:

Hs.730377

mRNA Expression by UniProt/SwissProt for CLLU1 Gene:

Q5K131-CLLU1_HUMAN
Tissue specificity: Specifically expressed in chronic lymphocytic leukemia (CLL) cells from patients without immunoglobulin heavy-chain hypermutations. Expression is detected in all CLL cells and levels are similar in patients before and after treatment.

Evidence on tissue expression from TISSUES for CLLU1 Gene

  • Blood(4.2)
genes like me logo Genes that share expression patterns with CLLU1: 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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLLU1 Gene

Orthologs for CLLU1 Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for CLLU1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CLLU1 30
  • 98.07 (n)
Species where no ortholog for CLLU1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Cow (Bos Taurus)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for CLLU1 Gene

ENSEMBL:
Gene Tree for CLLU1 (if available)
TreeFam:
Gene Tree for CLLU1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLLU1: view image

Paralogs for CLLU1 Gene

No data available for Paralogs for CLLU1 Gene

Variants for CLLU1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLLU1 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs12580153 - p.Ser9Phe

Additional dbSNP identifiers (rs#s) for CLLU1 Gene

Structural Variations from Database of Genomic Variants (DGV) for CLLU1 Gene

Variant ID Type Subtype PubMed ID
nsv7234 OTHER inversion 18451855

Variation tolerance for CLLU1 Gene

Gene Damage Index Score: 3.85; 58.83% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLLU1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLLU1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLLU1 Gene

Disorders for CLLU1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CLLU1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
leukemia
  • leukemias
chromosome 13q14 deletion syndrome
  • chromosome 13q deletion syndrome
leukemia, chronic lymphocytic
  • cll
- elite association - COSMIC cancer census association via MalaCards
Search CLLU1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLLU1

genes like me logo Genes that share disorders with CLLU1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLLU1 Gene

Publications for CLLU1 Gene

  1. Recent de novo origin of human protein-coding genes. (PMID: 19726446) Knowles DG … McLysaght A (Genome research 2009) 2 3 4
  2. De novo origin of human protein-coding genes. (PMID: 22102831) Wu DD … Zhang YP (PLoS genetics 2011) 2 3
  3. The CLLU1 expression level is a stable and inherent feature of the chronic lymphocytic leukemia clone. (PMID: 19212335) Buhl AM … Leffers H (Leukemia 2009) 3 4
  4. CLLU1 expression analysis adds prognostic information to risk prediction in chronic lymphocytic leukemia. (PMID: 17284524) Josefsson P … Buhl AM (Blood 2007) 3 4
  5. Identification of a gene on chromosome 12q22 uniquely overexpressed in chronic lymphocytic leukemia. (PMID: 16339396) Buhl AM … Leffers H (Blood 2006) 3 4

Products for CLLU1 Gene

Sources for CLLU1 Gene