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Aliases for LIN28B Gene

Aliases for LIN28B Gene

  • Lin-28 Homolog B (C. Elegans) 2 3
  • Lin-28B 3 4
  • CSDD2 3 4
  • Lin-28.2 3

External Ids for LIN28B Gene

Previous GeneCards Identifiers for LIN28B Gene

  • GC06P105512
  • GC06P105404
  • GC06P102848

Summaries for LIN28B Gene

Entrez Gene Summary for LIN28B Gene

  • The protein encoded by this gene belongs to the lin-28 family, which is characterized by the presence of a cold-shock domain and a pair of CCHC zinc finger domains. This gene is highly expressed in testis, fetal liver, placenta, and in primary human tumors and cancer cell lines. It is negatively regulated by microRNAs that target sites in the 3' UTR, and overexpression of this gene in primary tumors is linked to the repression of let-7 family of microRNAs and derepression of let-7 targets, which facilitates cellular transformation. [provided by RefSeq, Jun 2012]

GeneCards Summary for LIN28B Gene

LIN28B (Lin-28 Homolog B (C. Elegans)) is a Protein Coding gene. Diseases associated with LIN28B include idiopathic central precocious puberty and oral cavity cancer. Among its related pathways are Cardiac Progenitor Differentiation and Translational Control. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is LIN28A.

UniProtKB/Swiss-Prot for LIN28B Gene

  • Suppressor of microRNA (miRNA) biogenesis, including that of let-7 and possibly of miR107, miR-143 and miR-200c. Binds primary let-7 transcripts (pri-let-7), including pri-let-7g and pri-let-7a-1, and sequester them in the nucleolus, away from the microprocessor complex, hence preventing their processing into mature miRNA (PubMed:22118463). Does not act on pri-miR21 (PubMed:22118463). The repression of let-7 expression is required for normal development and contributes to maintain the pluripotent state of embryonic stem cells by preventing let-7-mediated differentiation. When overexpressed, recruits ZCCHC11/TUT4 uridylyltransferase to pre-let-7 transcripts, leading to their terminal uridylation and degradation (PubMed:19703396). This activity might not be relevant in vivo, as LIN28B-mediated inhibition of let-7 miRNA maturation appears to be ZCCHC11-independent (PubMed:22118463). Interaction with target pre-miRNAs occurs via an 5-GGAG-3 motif in the pre-miRNA terminal loop. Mediates MYC-induced let-7 repression (By similarity). When overexpressed, isoform 1 stimulates growth of the breast adenocarcinoma cell line MCF-7. Isoform 2 has no effect on cell growth.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LIN28B Gene

Genomics for LIN28B Gene

Regulatory Elements for LIN28B Gene

Genomic Location for LIN28B Gene

Chromosome:
6
Start:
104,936,999 bp from pter
End:
105,083,332 bp from pter
Size:
146,334 bases
Orientation:
Plus strand

Genomic View for LIN28B Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LIN28B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LIN28B Gene

Proteins for LIN28B Gene

  • Protein details for LIN28B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZN17-LN28B_HUMAN
    Recommended name:
    Protein lin-28 homolog B
    Protein Accession:
    Q6ZN17
    Secondary Accessions:
    • A1L165
    • B2RPN6
    • Q5TCM4

    Protein attributes for LIN28B Gene

    Size:
    250 amino acids
    Molecular mass:
    27084 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for LIN28B Gene

    Alternative splice isoforms for LIN28B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LIN28B Gene

Proteomics data for LIN28B Gene at MOPED

Post-translational modifications for LIN28B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LIN28B Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for LIN28B (LIN28B)

No data available for DME Specific Peptides for LIN28B Gene

Domains & Families for LIN28B Gene

Suggested Antigen Peptide Sequences for LIN28B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6ZN17

UniProtKB/Swiss-Prot:

LN28B_HUMAN :
  • The tandem zinc fingers, also referred as zinc knuckle domain (ZKD), mediate specific binding to the GGAG/GGUG motif while the CSD shows only limited pyrimidine-rich sequence specificity. Both domains bind single-stranded nucleic acids
  • Belongs to the lin-28 family.
  • Contains 2 CCHC-type zinc fingers.
Domain:
  • The tandem zinc fingers, also referred as zinc knuckle domain (ZKD), mediate specific binding to the GGAG/GGUG motif while the CSD shows only limited pyrimidine-rich sequence specificity. Both domains bind single-stranded nucleic acids
  • Contains 1 CSD (cold-shock) domain.
Family:
  • Belongs to the lin-28 family.
Similarity:
  • Contains 2 CCHC-type zinc fingers.
genes like me logo Genes that share domains with LIN28B: view

No data available for Gene Families for LIN28B Gene

Function for LIN28B Gene

Molecular function for LIN28B Gene

UniProtKB/Swiss-Prot Function:
Suppressor of microRNA (miRNA) biogenesis, including that of let-7 and possibly of miR107, miR-143 and miR-200c. Binds primary let-7 transcripts (pri-let-7), including pri-let-7g and pri-let-7a-1, and sequester them in the nucleolus, away from the microprocessor complex, hence preventing their processing into mature miRNA (PubMed:22118463). Does not act on pri-miR21 (PubMed:22118463). The repression of let-7 expression is required for normal development and contributes to maintain the pluripotent state of embryonic stem cells by preventing let-7-mediated differentiation. When overexpressed, recruits ZCCHC11/TUT4 uridylyltransferase to pre-let-7 transcripts, leading to their terminal uridylation and degradation (PubMed:19703396). This activity might not be relevant in vivo, as LIN28B-mediated inhibition of let-7 miRNA maturation appears to be ZCCHC11-independent (PubMed:22118463). Interaction with target pre-miRNAs occurs via an 5-GGAG-3 motif in the pre-miRNA terminal loop. Mediates MYC-induced let-7 repression (By similarity). When overexpressed, isoform 1 stimulates growth of the breast adenocarcinoma cell line MCF-7. Isoform 2 has no effect on cell growth.
UniProtKB/Swiss-Prot Induction:
Might be negatively regulated by the microRNA let-7b.

Gene Ontology (GO) - Molecular Function for LIN28B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IDA 19703396
GO:0005515 protein binding IPI 19703396
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with LIN28B: view
genes like me logo Genes that share phenotypes with LIN28B: view

Animal Models for LIN28B Gene

MGI Knock Outs for LIN28B:

Animal Model Products

miRNA for LIN28B Gene

miRTarBase miRNAs that target LIN28B

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LIN28B

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for LIN28B Gene

Localization for LIN28B Gene

Subcellular locations from UniProtKB/Swiss-Prot for LIN28B Gene

Nucleus. Nucleus, nucleolus. Cytoplasm. Note=Predominantly nucleolar (PubMed:22118463). In Huh7 cells, predominantly cytoplasmic, with only a subset of cells exhibiting strong nuclear staining; however, the specificity of the polyclonal antibody used in these experiments has not been not documented (PubMed:16971064). {ECO:0000269 PubMed:16971064, ECO:0000269 PubMed:22118463}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LIN28B Gene COMPARTMENTS Subcellular localization image for LIN28B gene
Compartment Confidence
mitochondrion 4
nucleus 4
cytosol 2

Gene Ontology (GO) - Cellular Components for LIN28B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IDA --
GO:0005739 mitochondrion IDA --
genes like me logo Genes that share ontologies with LIN28B: view

Pathways & Interactions for LIN28B Gene

genes like me logo Genes that share pathways with LIN28B: view

Pathways by source for LIN28B Gene

2 Cell Signaling Technology pathways for LIN28B Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Stem Cell Transcription Factors in human,mouse,rat

Gene Ontology (GO) - Biological Process for LIN28B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0010587 miRNA catabolic process IMP 19703396
GO:0031054 pre-miRNA processing IMP 19703396
GO:0031123 RNA 3-end processing IMP 19703396
genes like me logo Genes that share ontologies with LIN28B: view

No data available for SIGNOR curated interactions for LIN28B Gene

Drugs & Compounds for LIN28B Gene

No Compound Related Data Available

Transcripts for LIN28B Gene

mRNA/cDNA for LIN28B Gene

Unigene Clusters for LIN28B Gene

Lin-28 homolog B (C. elegans):
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LIN28B

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LIN28B Gene

No ASD Table

Relevant External Links for LIN28B Gene

GeneLoc Exon Structure for
LIN28B
ECgene alternative splicing isoforms for
LIN28B

Expression for LIN28B Gene

mRNA expression in normal human tissues for LIN28B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LIN28B Gene

This gene is overexpressed in Testis (x21.6), Brain - Hypothalamus (x4.2), and Brain - Frontal Cortex (BA9) (x4.0).

Protein differential expression in normal tissues from HIPED for LIN28B Gene

This gene is overexpressed in Placenta (65.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for LIN28B Gene



SOURCE GeneReport for Unigene cluster for LIN28B Gene Hs.23616

mRNA Expression by UniProt/SwissProt for LIN28B Gene

Q6ZN17-LN28B_HUMAN
Tissue specificity: Expressed at high levels in the placenta and, at mucher lower, in testis and fetal liver (PubMed:16971064). Isoform 1 is only detected in placenta and in moderately and poorly differentiated hepatocellular carcinoma cells (at protein level). Isoform 2 is detected in fetal liver, non-tumor liver tissues, as well as well-differentiated tumor tissues (at protein level). Tends to be up-regulated in triple-negative (ER-,PR-,HER2-) breast tumors, as well as in liver, ovarian, and thyroid carcinomas (PubMed:22118463).
genes like me logo Genes that share expression patterns with LIN28B: view

Protein tissue co-expression partners for LIN28B Gene

Primer Products

In Situ Assay Products

Orthologs for LIN28B Gene

This gene was present in the common ancestor of animals.

Orthologs for LIN28B Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LIN28B 35
  • 91.63 (n)
  • 92.64 (a)
LIN28B 36
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LIN28B 35
  • 88.89 (n)
  • 89.16 (a)
LIN28B 36
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lin28b 35
  • 86.64 (n)
  • 86.64 (a)
Lin28b 16
Lin28b 36
  • 77 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LIN28B 35
  • 99.73 (n)
  • 99.6 (a)
LIN28B 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lin28b 35
  • 84.55 (n)
  • 85.77 (a)
oppossum
(Monodelphis domestica)
Mammalia LIN28B 36
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LIN28B 36
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves LIN28B 35
  • 85.54 (n)
  • 83.13 (a)
LIN28B 36
  • 83 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LIN28B 36
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lin28b 35
  • 81.87 (n)
  • 80 (a)
Str.9971 35
African clawed frog
(Xenopus laevis)
Amphibia LOC373796 35
zebrafish
(Danio rerio)
Actinopterygii LOC799825 35
  • 65.37 (n)
  • 71.11 (a)
LIN28B 36
  • 72 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006591 35
  • 50.2 (n)
  • 48.19 (a)
fruit fly
(Drosophila melanogaster)
Insecta lin-28 35
  • 48.57 (n)
  • 50.33 (a)
lin-28 36
  • 37 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea lin-28 36
  • 28 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 41 (a)
OneToMany
Species with no ortholog for LIN28B:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for LIN28B Gene

ENSEMBL:
Gene Tree for LIN28B (if available)
TreeFam:
Gene Tree for LIN28B (if available)

Paralogs for LIN28B Gene

Paralogs for LIN28B Gene

(1) SIMAP similar genes for LIN28B Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for LIN28B Gene

genes like me logo Genes that share paralogs with LIN28B: view

Variants for LIN28B Gene

Sequence variations from dbSNP and Humsavar for LIN28B Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs140791 -- 104,942,907(-) CTATT(-/AATT/ATTA)GAGAA intron-variant
rs149246 -- 105,040,907(-) TAAAA(G/T)AAATA intron-variant
rs160592 -- 105,020,719(-) actca(A/G)aaggg intron-variant
rs160593 -- 105,018,457(-) GCAGT(C/T)GAAAC intron-variant
rs160594 -- 105,041,191(-) CTCAC(A/G)CCTGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LIN28B Gene

Variant ID Type Subtype PubMed ID
dgv2000e1 CNV Complex 17122850
dgv216e55 CNV Gain 17911159
essv19736 CNV CNV 17122850
nsv818450 CNV Gain 17921354
nsv830754 CNV Gain 17160897

Variation tolerance for LIN28B Gene

Residual Variation Intolerance Score: 35.61% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.58; 12.49% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LIN28B Gene

HapMap Linkage Disequilibrium report
LIN28B
Human Gene Mutation Database (HGMD)
LIN28B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LIN28B Gene

Disorders for LIN28B Gene

MalaCards: The human disease database

(6) MalaCards diseases for LIN28B Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
idiopathic central precocious puberty
oral cavity cancer
  • malignant tumor of the floor of the mouth
neuroblastoma
  • neuroblastoma 1
autonomic nervous system neoplasm
  • tumor of autonomic nervous system
peripheral nervous system neoplasm
  • neoplasm of peripheral nerve
- elite association

Relevant External Links for LIN28B

Genetic Association Database (GAD)
LIN28B
Human Genome Epidemiology (HuGE) Navigator
LIN28B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LIN28B
genes like me logo Genes that share disorders with LIN28B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LIN28B Gene

Publications for LIN28B Gene

  1. LIN28B in constitutional delay of growth and puberty. (PMID: 20350940) Tommiska J. … Dunkel L. (J. Clin. Endocrinol. Metab. 2010) 23 67
  2. Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. (PMID: 19211792) Chang T.C. … Mendell J.T. (Proc. Natl. Acad. Sci. U.S.A. 2009) 23 67
  3. Identification and characterization of lin-28 homolog B (LIN28B) in human hepatocellular carcinoma. (PMID: 16971064) Guo Y. … Aburatani H. (Gene 2006) 23 67
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 67
  5. Overexpression of the RNA-binding proteins Lin28B and IGF2BP3 (IMP3) is associated with chemoresistance and poor disease outcome in ovarian cancer. (PMID: 26158423) Hsu K.F. … Ho C.L. (Br. J. Cancer 2015) 67

Products for LIN28B Gene

Sources for LIN28B Gene

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